Hepatocellular carcinoma (HCC) is a kind of cancer with high incidence and often accompanied by intestinal flora imbalance. Many studies have shown that probiotics such as anthocyanins can regulate gut microbiome and improve disease. This study was designed to evaluate the influence of blueberry malvidin-3-galactoside (M3G), a blueberry ingredient with several beneficial properties, on gut microorganisms of liver cancer (LC) mice. LC mice were fed M3G diets (LM, 40 mg\/kg; HM, 80 mg\/kg) or 5-fluorouracil (PC, 20 mg\/kg) for three weeks. High-throughput sequencing using the MiSeq platform coupled with freely-available computational tools adopt 16SrRNA and metagenome analyses. There was a greater abundance of Verrucomicrobiaceae<\/i> (p < 0.05) and Ruminococcus <\/i>(p < 0.05) in mice in the HM group than in those in the LM group. Anti-inflammatory bacteria such as Akkermansia<\/i>, Sutterella<\/i> increase in abundance after fed with M3G for three weeks. A significantly smaller abundance of Proinflammatory bacteria such as Dorea<\/i>, Coprobacillus<\/i>, Clostridium<\/i>, Streptococcus<\/i>, Oscillospira<\/i> in HM mice(p<0.01). Both M3G and chemotherapeutic drugs can increase signal transduction, Membrane transport, and Cell Motility. In addition, the ability of cell growth and death increased in HM and PC groups but decreased in LC and LM groups. This study indicates that M3G supplementation for three weeks may not be enough to cure liver cancer. However, M3G-supplementation was associated with significant differences in the structure and metabolic function of gut microbiome compared to liver cancer controls that merit further research.<\/p>\n ","title-html":"Illumina MiSeq reveals the influence of blueberry malvidin-3-galactoside on fecal microbial community structure and metabolizes of liver cancer mice","subjects":["Agricultural Science","Food Science and Technology","Microbiology"],"identifiers":{"peerj":"27429"},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/preprints\/27429","_links":{"self":{"href":"https:\/\/peerj.com\/preprints\/27429.json"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/preprints\/27429.html"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/preprints\/27429.xml"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/preprints\/27429.pdf"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/preprints\/27429.rdf"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/preprints\/27429.ris"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/preprints\/27429.bib"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/preprints\/27429.citeproc"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/preprints\/27429.bibjson"},"datacite":{"type":"application\/datacite+xml","href":"https:\/\/peerj.com\/preprints\/27429.datacite"}}}},{"title":"What do we mean by the directions \u201ccranial\u201d and \u201ccaudal\u201d on a vertebra?","date":"2018-12-19","doi":"10.7287\/peerj.preprints.27437v1","language":"en","pdf_url":"https:\/\/peerj.com\/preprints\/27437.pdf","fulltext_html_url":"https:\/\/peerj.com\/preprints\/27437","technical_report_number":"e27437v1","author":["Michael P Taylor","Matthew J Wedel"],"author_institution":["Department of Earth Sciences, University of Bristol, Bristol, United Kingdom","College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, California, United States"],"author_email":"dino@miketaylor.org.uk","authors":"Taylor, Michael P; Wedel, Matthew J","author_institutions":"Department of Earth Sciences, University of Bristol, Bristol, United Kingdom; College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, California, United States","keywords":["vertebra","orientation","horizontal","cranial","caudal","anterior","posterior","sauropod","giraffe"],"technical_report_institution":"PeerJ Preprints","publisher":"PeerJ Inc.","issn":"2167-9843","description":"In illustrating vertebrae, it is important to consistently depict their orientation, so we can objectively assess and compare the slope of the neural arch, neural canal, or articular surfaces. However, differing vertebral shapes across taxa and across regions of the spinal column make it difficult to maintain consistency, or even define what we mean by the directions \u201ccranial\u201d and \u201ccaudal\u201d. Consequently, characters such as \u201cNeural arch slopes cranially 30\u00b0 relative to the vertical\u201d are disputable rather than objective measurements. Cranial and caudal are defined as directed along the horizontal, but several different notions of \u201chorizontal\u201d are possible: 1. Long axis of centrum is horizontal. This is appealing for elongate vertebrae such as sauropod cervicals, but is difficult to determine for craniocaudally short vertebrae such as most caudals. 2. Articular facets of centrum are vertical. Difficult to determine when dealing with facets that are concave or (worse) convex; and ambiguous for \u201ckeystoned\u201d vertebrae in which the facets are not parallel. 3. Neural canal is horizontal. Anatomically informative, but difficult to determine in vertebrae that have not been fully prepared or CT-scanned, and impossible to see in lateral view. Ambiguous for vertebrae where the dorsal and ventral margins of the canal are not parallel. 4. When two instances of the vertebra are optimally articulated, the same points are at the same height on both. This is less intuitive than definitions 1\u20133, but more precise and can be determined for any vertebra. We advocate explicitly stating a definition and using it consistently.","description-html":"\n
In illustrating vertebrae, it is important to consistently depict their orientation, so we can objectively assess and compare the slope of the neural arch, neural canal, or articular surfaces. However, differing vertebral shapes across taxa and across regions of the spinal column make it difficult to maintain consistency, or even define what we mean by the directions \u201ccranial\u201d and \u201ccaudal\u201d. Consequently, characters such as \u201cNeural arch slopes cranially 30\u00b0 relative to the vertical\u201d are disputable rather than objective measurements.<\/p>\n
Cranial and caudal are defined as directed along the horizontal, but several different notions of \u201chorizontal\u201d are possible:<\/p>\n
1. Long axis of centrum is horizontal.<\/b> This is appealing for elongate vertebrae such as sauropod cervicals, but is difficult to determine for craniocaudally short vertebrae such as most caudals.<\/p>\n
2. Articular facets of centrum are vertical.<\/b> Difficult to determine when dealing with facets that are concave or (worse) convex; and ambiguous for \u201ckeystoned\u201d vertebrae in which the facets are not parallel.<\/p>\n
3. Neural canal is horizontal.<\/b> Anatomically informative, but difficult to determine in vertebrae that have not been fully prepared or CT-scanned, and impossible to see in lateral view. Ambiguous for vertebrae where the dorsal and ventral margins of the canal are not parallel.<\/p>\n
4. When two instances of the vertebra are optimally articulated, the same points are at the same height on both.<\/b> This is less intuitive than definitions 1\u20133, but more precise and can be determined for any<\/i> vertebra.<\/p>\n
We advocate explicitly stating a definition and using it consistently.<\/p>\n ","title-html":"What do we mean by the directions \u201ccranial\u201d and \u201ccaudal\u201d on a vertebra?","subjects":["Evolutionary Studies","Paleontology","Zoology","Anatomy and Physiology"],"identifiers":{"peerj":"27437"},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/preprints\/27437","_links":{"self":{"href":"https:\/\/peerj.com\/preprints\/27437.json"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/preprints\/27437.html"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/preprints\/27437.xml"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/preprints\/27437.pdf"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/preprints\/27437.rdf"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/preprints\/27437.ris"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/preprints\/27437.bib"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/preprints\/27437.citeproc"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/preprints\/27437.bibjson"},"datacite":{"type":"application\/datacite+xml","href":"https:\/\/peerj.com\/preprints\/27437.datacite"}}}},{"title":"A comparison of acute toxicity methodologies for Bombus spp.","date":"2018-12-18","doi":"10.7287\/peerj.preprints.27436v1","language":"en","pdf_url":"https:\/\/peerj.com\/preprints\/27436.pdf","fulltext_html_url":"https:\/\/peerj.com\/preprints\/27436","technical_report_number":"e27436v1","author":["Kayla Mundy","Nigel E. Raine"],"author_institution":["School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada","School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada"],"author_email":"kmundy03@uoguelph.ca","authors":"Mundy, Kayla; Raine, Nigel E.","author_institutions":"School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada","keywords":["Apis mellifera","Bombus spp.","LC50","LD50","risk assessment","acute test","review"],"technical_report_institution":"PeerJ Preprints","publisher":"PeerJ Inc.","issn":"2167-9843","description":"Acute toxicity testing (lethal dose and lethal concentration for 50% of the population; LD50 and LC50) is a required component of the first level of pesticide risk assessment. A review of peer-reviewed and ECOTOX database toxicity values was conducted to assess methodology and toxicity value consistency. Bumble bee LD50 and LC50 tests varied in five key areas: test subject, active ingredient specifications, test solution specifications, test conditions, test procedure. Only recently has a consistent methodology for bumble bee LD50 tests been released, but differs substantially from previous methods. Study methodologies have varied in at least one component and comparison of acute toxicity values can differ substantially between studies. Although a current standard, the appropriateness of the contact LD50 method of anaesthetisation and test location should be revisited. This work demonstrates inconsistency in current peer-reviewed analysis of acute toxicity to bumble bees and that current standard methods may not be perfected.","description-html":"\n
Acute toxicity testing (lethal dose and lethal concentration for 50% of the population; LD50<\/sub> and LC50<\/sub>) is a required component of the first level of pesticide risk assessment. A review of peer-reviewed and ECOTOX database toxicity values was conducted to assess methodology and toxicity value consistency. Bumble bee LD50<\/sub> and LC50<\/sub> tests varied in five key areas: test subject, active ingredient specifications, test solution specifications, test conditions, test procedure. Only recently has a consistent methodology for bumble bee LD50<\/sub> tests been released, but differs substantially from previous methods. Study methodologies have varied in at least one component and comparison of acute toxicity values can differ substantially between studies. Although a current standard, the appropriateness of the contact LD50<\/sub> method of anaesthetisation and test location should be revisited. This work demonstrates inconsistency in current peer-reviewed analysis of acute toxicity to bumble bees and that current standard methods may not be perfected.<\/p>\n ","title-html":"A comparison of acute toxicity methodologies for Bombus <\/i>spp.","subjects":["Biodiversity","Entomology","Toxicology","Science Policy","Ecotoxicology"],"identifiers":{"peerj":"27436"},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/preprints\/27436","_links":{"self":{"href":"https:\/\/peerj.com\/preprints\/27436.json"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/preprints\/27436.html"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/preprints\/27436.xml"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/preprints\/27436.pdf"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/preprints\/27436.rdf"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/preprints\/27436.ris"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/preprints\/27436.bib"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/preprints\/27436.citeproc"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/preprints\/27436.bibjson"},"datacite":{"type":"application\/datacite+xml","href":"https:\/\/peerj.com\/preprints\/27436.datacite"}}}},{"title":"Environmental variability and phenology evolution: impacts of climate change and spring onset on reproductive timing in a small mammal","date":"2018-12-18","doi":"10.7287\/peerj.preprints.27435v1","language":"en","pdf_url":"https:\/\/peerj.com\/preprints\/27435.pdf","fulltext_html_url":"https:\/\/peerj.com\/preprints\/27435","technical_report_number":"e27435v1","author":["Easton R White","Kalle Parvinen","Ulf Dieckmann"],"author_institution":["Center for Population Biology, University of California, Davis, Davis, CA, United States","Ecology and Evolution Program, International Institute for Applied Systems Analysis, Laxenburg, Austria","Ecology and Evolution Program, International Institute for Applied Systems Analysis, Laxenburg, Austria","Department of Mathematics and Statistics, University of Turku, Turku, Finland","Ecology and Evolution Program, International Institute for Applied Systems Analysis, Laxenburg, Austria"],"author_email":"eastonrwhite@gmail.com","authors":"White, Easton R; Parvinen, Kalle; Dieckmann, Ulf","author_institutions":"Center for Population Biology, University of California, Davis, Davis, CA, United States; Ecology and Evolution Program, International Institute for Applied Systems Analysis, Laxenburg, Austria; Department of Mathematics and Statistics, University of Turku, Turku, Finland","keywords":["adaptive dynamics","climate change","game theory","Ochotona","phenology","pika"],"technical_report_institution":"PeerJ Preprints","publisher":"PeerJ Inc.","issn":"2167-9843","description":"The phenology, or timing of life history events, of organisms affects both ecological and evolutionary dynamics. Recent work has illustrated the effects of climate change on the phenology for many species. Changing selective pressures on phenology can have consequences for species if the reliability of phenological cues decreases or if climate change affects interacting species differentially. There are now numerous examples, in which earlier mean timing of spring has selected for earlier phenology of organisms. However, much less is known about how changes in the variability of spring \u2014 and consequently the reliability of cues \u2014 might affect species. We built a general model of animal population dynamics to study both the ecology and evolution of phenological events under climate change. We parameterized this model for a population of the collared pika (Ochotona collaris) found in the Yukon, Canada. In line with past work, we show that an earlier timing of spring snowmelt will select for an earlier timing of reproduction. In addition, we show that variability in the onset of spring also selects for earlier reproduction. However, evolution or plasticity in juvenile mortality, due to late snowmelt, can lead to later reproduction. These results highlight the importance of looking at the variability, and not only the mean, in spring onset. The specific relationship between the mean and variability of spring onset coupled with the ability of a population to be plastic or adaptable will determine the long-term effects of climate change on the phenology of species.","description-html":"\n The phenology, or timing of life history events, of organisms affects both ecological and evolutionary dynamics. Recent work has illustrated the effects of climate change on the phenology for many species. Changing selective pressures on phenology can have consequences for species if the reliability of phenological cues decreases or if climate change affects interacting species differentially. There are now numerous examples, in which earlier mean timing of spring has selected for earlier phenology of organisms. However, much less is known about how changes in the variability of spring \u2014 and consequently the reliability of cues \u2014 might affect species. We built a general model of animal population dynamics to study both the ecology and evolution of phenological events under climate change. We parameterized this model for a population of the collared pika (Ochotona collaris<\/i>) found in the Yukon, Canada. In line with past work, we show that an earlier timing of spring snowmelt will select for an earlier timing of reproduction. In addition, we show that variability in the onset of spring also selects for earlier reproduction. However, evolution or plasticity in juvenile mortality, due to late snowmelt, can lead to later reproduction. These results highlight the importance of looking at the variability, and not only the mean, in spring onset. The specific relationship between the mean and variability of spring onset coupled with the ability of a population to be plastic or adaptable will determine the long-term effects of climate change on the phenology of species.<\/p>\n ","title-html":"Environmental variability and phenology evolution: impacts of climate change and spring onset on reproductive timing in a small mammal","subjects":["Conservation Biology","Ecology","Evolutionary Studies","Mathematical Biology","Population Biology"],"identifiers":{"peerj":"27435"},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/preprints\/27435","_links":{"self":{"href":"https:\/\/peerj.com\/preprints\/27435.json"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/preprints\/27435.html"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/preprints\/27435.xml"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/preprints\/27435.pdf"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/preprints\/27435.rdf"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/preprints\/27435.ris"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/preprints\/27435.bib"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/preprints\/27435.citeproc"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/preprints\/27435.bibjson"},"datacite":{"type":"application\/datacite+xml","href":"https:\/\/peerj.com\/preprints\/27435.datacite"}}}},{"title":"The transcription factors and its implications in adaptive evolution","date":"2018-12-17","doi":"10.7287\/peerj.preprints.26862v8","language":"en","pdf_url":"https:\/\/peerj.com\/preprints\/26862.pdf","fulltext_html_url":"https:\/\/peerj.com\/preprints\/26862","technical_report_number":"e26862v8","author":"V\u00edctor A Zapata Trejo","author_institution":"Department of Marine Biology, Autonomous University of Yucatan, Campus of Biological and Agricultural Sciences, Merida, Yucatan, Mexico","author_email":"A16018093@alumnos.uady.mx","authors":"Zapata Trejo, V\u00edctor A","author_institutions":"Department of Marine Biology, Autonomous University of Yucatan, Campus of Biological and Agricultural Sciences, Merida, Yucatan, Mexico","keywords":["adaptive system","gametogenesis","stimuli","stochastic","robustness"],"technical_report_institution":"PeerJ Preprints","publisher":"PeerJ Inc.","issn":"2167-9843","description":"The random to explain the emergence of variations in sequence of the alleles is the current scientific paradigm of evolutionary biology. Here is argued that interactions between instincts and transcription factors (TFs) are the main cause of emergence of such variations. Advances in epigenomics show that this molecular function plays an important role in the regulation of gene expression of all cells, both prokaryotes and eukaryotes, and indicates which specific genes should be transcribed and which should be translated. Under this context, the present work pretends evaluate the current evidence on the increase in mutation rate caused by transcription-associated mutational pressure in primordial germ cells due to presence of TFs also present in somatic cells involved in an instinct. In conclusion is established that adaptive evolution can understood as biological superposition of 4 functional states. This work that is added to the evolutionary theoretical framework contributes with an alternative causal understanding of adaptive evolution.","description-html":"\n The random to explain the emergence of variations in sequence of the alleles is the current scientific paradigm of evolutionary biology. Here is argued that interactions between instincts and transcription factors (TFs) are the main cause of emergence of such variations. Advances in epigenomics show that this molecular function plays an important role in the regulation of gene expression of all cells, both prokaryotes and eukaryotes, and indicates which specific genes should be transcribed and which should be translated. Under this context, the present work pretends evaluate the current evidence on the increase in mutation rate caused by transcription-associated mutational pressure in primordial germ cells due to presence of TFs also present in somatic cells involved in an instinct. In conclusion is established that adaptive evolution can understood as biological superposition of 4 functional states. This work that is added to the evolutionary theoretical framework contributes with an alternative causal understanding of adaptive evolution.<\/p>\n ","title-html":"The transcription factors and its implications in adaptive evolution","subjects":["Animal Behavior","Cell Biology","Ecology","Molecular Biology"],"identifiers":{"peerj":"26862"},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/preprints\/26862","_links":{"self":{"href":"https:\/\/peerj.com\/preprints\/26862.json"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/preprints\/26862.html"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/preprints\/26862.xml"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/preprints\/26862.pdf"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/preprints\/26862.rdf"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/preprints\/26862.ris"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/preprints\/26862.bib"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/preprints\/26862.citeproc"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/preprints\/26862.bibjson"},"datacite":{"type":"application\/datacite+xml","href":"https:\/\/peerj.com\/preprints\/26862.datacite"}}}},{"title":"Novel mating behaviours in the squaretail grouper: Response to \u201cFake spawns and floating particles\"","date":"2018-12-17","doi":"10.7287\/peerj.preprints.27433v1","language":"en","pdf_url":"https:\/\/peerj.com\/preprints\/27433.pdf","fulltext_html_url":"https:\/\/peerj.com\/preprints\/27433","technical_report_number":"e27433v1","author":["Rucha P Karkarey","Amod Zambre","Kavita Isvaran","Rohan Arthur"],"author_institution":["Oceans and Coasts Programme, Nature Conservation Foundation, Mysore, India","Manipal Academy of Higher Education, Manipal, India","Post-graduate programme in Wildlife Biology and Conservation, National Centre for Biological Sciences, Bangalore, India","Centre for Ecological Science, Indian Institute of Science, Bangalore, India","Oceans and Coasts Programme, Nature Conservation Foundation, Mysore, India"],"author_email":"rohan@ncf-india.org","authors":"Karkarey, Rucha P; Zambre, Amod; Isvaran, Kavita; Arthur, Rohan","author_institutions":"Oceans and Coasts Programme, Nature Conservation Foundation, Mysore, India; Manipal Academy of Higher Education, Manipal, India; Post-graduate programme in Wildlife Biology and Conservation, National Centre for Biological Sciences, Bangalore, India; Centre for Ecological Science, Indian Institute of Science, Bangalore, India","keywords":["Alternative mating tactics","spawning aggregations","coral reefs","Plectropomus areolatus","Indian Ocean"],"technical_report_institution":"PeerJ Preprints","publisher":"PeerJ Inc.","issn":"2167-9843","description":"Based on two years of in-water observations of a high-density spawning aggregation of the squaretail grouper in the Lakshadweep Archipelago, we described a previously unreported inverse size assortment with large males courting several small females that shoaled mid-water (DOI 10.1186\/s12898-017-0120-5). Critiquing our manuscript, Erisman and colleagues (DOI 10.1186\/s12898-018-0206-8) suggest that our observations and interpretation are flawed, and do not fit within currently accepted theory. Here we offer a detailed counter of their main methodological and theoretical criticisms. Their criticism that this reproductive tactic has never been observed before is hardly a criticism since its novelty is precisely what we wished to highlight. The supplementary video that Erisman et al use to base much of their criticisms was not the basis of our conclusions, which relied on direct in-water observations. These observations were conducted over two spawning years, taking care to ensure that we sampled aggregations at peak densities. Like other researchers working on this species, we did not directly observe mating, but have used courtship as a proxy for mating success \u2013 a well-established proxy across mating systems studies. Apart from these methodological concerns, the authors suggest that there is no theoretical support for our observations. However, sexual selection theory provides a well-established framework showing that, at very high mating densities, a variety of tactics can emerge, that often vary considerably between populations and locations. We agree with the authors that novel observations should be scrutinised carefully. They challenge our current understanding of the range of behaviours populations display and serve as a springboard for theoretical advancement. We stand by our observations and hope they serve as a useful addition to the fascinating and complex natural history of species like the squaretail grouper.","description-html":"\n Based on two years of in-water observations of a high-density spawning aggregation of the squaretail grouper in the Lakshadweep Archipelago, we described a previously unreported inverse size assortment with large males courting several small females that shoaled mid-water (DOI 10.1186\/s12898-017-0120-5). Critiquing our manuscript, Erisman and colleagues (DOI 10.1186\/s12898-018-0206-8) suggest that our observations and interpretation are flawed, and do not fit within currently accepted theory. Here we offer a detailed counter of their main methodological and theoretical criticisms. Their criticism that this reproductive tactic has never been observed before is hardly a criticism since its novelty is precisely what we wished to highlight. The supplementary video that Erisman et al use to base much of their criticisms was not the basis of our conclusions, which relied on direct in-water observations. These observations were conducted over two spawning years, taking care to ensure that we sampled aggregations at peak densities. Like other researchers working on this species, we did not directly observe mating, but have used courtship as a proxy for mating success \u2013 a well-established proxy across mating systems studies. Apart from these methodological concerns, the authors suggest that there is no theoretical support for our observations. However, sexual selection theory provides a well-established framework showing that, at very high mating densities, a variety of tactics can emerge, that often vary considerably between populations and locations. We agree with the authors that novel observations should be scrutinised carefully. They challenge our current understanding of the range of behaviours populations display and serve as a springboard for theoretical advancement. We stand by our observations and hope they serve as a useful addition to the fascinating and complex natural history of species like the squaretail grouper.<\/p>\n ","title-html":"Novel mating behaviours in the squaretail grouper: Response to \u201cFake spawns and floating particles\"<\/i>","subjects":["Animal Behavior","Ecology","Marine Biology"],"identifiers":{"peerj":"27433"},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/preprints\/27433","_links":{"self":{"href":"https:\/\/peerj.com\/preprints\/27433.json"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/preprints\/27433.html"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/preprints\/27433.xml"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/preprints\/27433.pdf"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/preprints\/27433.rdf"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/preprints\/27433.ris"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/preprints\/27433.bib"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/preprints\/27433.citeproc"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/preprints\/27433.bibjson"},"datacite":{"type":"application\/datacite+xml","href":"https:\/\/peerj.com\/preprints\/27433.datacite"}}}},{"title":"Adult zebrafish euthanasia: efficacy of anaesthesia overdose versus rapid cooling","date":"2018-12-17","doi":"10.7287\/peerj.preprints.27432v1","language":"en","pdf_url":"https:\/\/peerj.com\/preprints\/27432.pdf","fulltext_html_url":"https:\/\/peerj.com\/preprints\/27432","technical_report_number":"e27432v1","author":["Jorge M Ferreira","I Anna S Olsson","Ana M Valentim"],"author_institution":["Laboratory Animal Science, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal","Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto, Porto, Portugal","CITAB, Universidade de Tras-os-Montes e Alto Douro, Vila Real, Portugal","Laboratory Animal Science, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal","Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto, Porto, Portugal","Laboratory Animal Science, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal","Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto, Porto, Portugal","CITAB, Universidade de Tras-os-Montes e Alto Douro, Vila Real, Portugal"],"author_email":"amaria@ibmc.up.pt","authors":"Ferreira, Jorge M; Olsson, I Anna S; Valentim, Ana M","author_institutions":"Laboratory Animal Science, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal; Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto, Porto, Portugal; CITAB, Universidade de Tras-os-Montes e Alto Douro, Vila Real, Portugal","keywords":["euthanasia","anaesthesia overdose","rapid cooling","adult zebrafish"],"technical_report_institution":"PeerJ Preprints","publisher":"PeerJ Inc.","issn":"2167-9843","description":"The rapid increase in zebrafish use needs to be accompanied by research into refinement of procedures, such as euthanasia. The EU directive lists three possible euthanasia methods for fish: anaesthetic overdose, electrical stunning and concussion. However, for a small fish like zebrafish, concussion and electrical stunning are difficult to perform, leaving anaesthetic overdose as the only realistic option. Thus, more tailored solutions need to be found for this small tropical water species. Our aim was to test the efficacy of different anaesthetics overdose and of the rapid cooling method to kill adult zebrafish. Adult mixed-sex AB zebrafish (n= 12) were randomly assigned to: 250mg\/L MS222; 20 mg\/L propofol + 100 mg\/L lidocaine; 6 mg\/L etomidate; 50 mg\/L clove oil; rapid cooling (water at 2-4\u00ba C). Two minutes after opercular movement ceased, the animals were transferred to clean water to assess if they could recover. Zebrafish euthanized with rapid cooling ceased the opercular movements significantly quicker compared with the other groups, and etomidate-treated animals took longer to die. No zebrafish recovered after being placed in clean water. All protocols used were efficacious to achieve euthanasia, but rapid cooling was consistently the fastest and so more efficient. Further studies evaluating animal welfare and the quality of the biological samples are needed to refine the rapid cooling protocol before recommendations can be made to change legislation to include this as a method for euthanasia for small tropical fish.","description-html":"\n The rapid increase in zebrafish use needs to be accompanied by research into refinement of procedures, such as euthanasia. The EU directive lists three possible euthanasia methods for fish: anaesthetic overdose, electrical stunning and concussion. However, for a small fish like zebrafish, concussion and electrical stunning are difficult to perform, leaving anaesthetic overdose as the only realistic option. Thus, more tailored solutions need to be found for this small tropical water species. Our aim was to test the efficacy of different anaesthetics overdose and of the rapid cooling method to kill adult zebrafish. Adult mixed-sex AB zebrafish (n= 12) were randomly assigned to: 250mg\/L MS222; 20 mg\/L propofol + 100 mg\/L lidocaine; 6 mg\/L etomidate; 50 mg\/L clove oil; rapid cooling (water at 2-4\u00ba C). Two minutes after opercular movement ceased, the animals were transferred to clean water to assess if they could recover. Zebrafish euthanized with rapid cooling ceased the opercular movements significantly quicker compared with the other groups, and etomidate-treated animals took longer to die. No zebrafish recovered after being placed in clean water. All protocols used were efficacious to achieve euthanasia, but rapid cooling was consistently the fastest and so more efficient. Further studies evaluating animal welfare and the quality of the biological samples are needed to refine the rapid cooling protocol before recommendations can be made to change legislation to include this as a method for euthanasia for small tropical fish.<\/p>\n ","title-html":"Adult zebrafish euthanasia: efficacy of anaesthesia overdose versus rapid cooling","subjects":["Aquaculture, Fisheries and Fish Science","Veterinary Medicine"],"identifiers":{"peerj":"27432"},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/preprints\/27432","_links":{"self":{"href":"https:\/\/peerj.com\/preprints\/27432.json"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/preprints\/27432.html"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/preprints\/27432.xml"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/preprints\/27432.pdf"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/preprints\/27432.rdf"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/preprints\/27432.ris"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/preprints\/27432.bib"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/preprints\/27432.citeproc"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/preprints\/27432.bibjson"},"datacite":{"type":"application\/datacite+xml","href":"https:\/\/peerj.com\/preprints\/27432.datacite"}}}},{"title":"Reconstructing an unusual specimen of Haplocanthosaurus using a blend of physical and digital techniques","date":"2018-12-17","doi":"10.7287\/peerj.preprints.27431v1","language":"en","pdf_url":"https:\/\/peerj.com\/preprints\/27431.pdf","fulltext_html_url":"https:\/\/peerj.com\/preprints\/27431","technical_report_number":"e27431v1","author":["Mathew J Wedel","Jessie Atterholt","Jeff Macalino","Thierra Nalley","Gary Wisser","John Yasmer"],"author_institution":["College of Osteopathic Medicine of the Pacific and College of Podiatric Medicine, Western University of Health Sciences, Pomona, California, United States of America","College of Biomedical Sciences, Western University of Health Sciences, Pomona, California, United States of America","Department of Information Technology, Western University of Health Sciences, Pomona, California, United States of America","College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, California, United States of America","Department of Information Technology, Western University of Health Sciences, Pomona, California, United States of America","College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, California, United States of America"],"author_email":"mathew.wedel@gmail.com","authors":"Wedel, Mathew J; Atterholt, Jessie; Macalino, Jeff; Nalley, Thierra; Wisser, Gary; Yasmer, John","author_institutions":"College of Osteopathic Medicine of the Pacific and College of Podiatric Medicine, Western University of Health Sciences, Pomona, California, United States of America; College of Biomedical Sciences, Western University of Health Sciences, Pomona, California, United States of America; Department of Information Technology, Western University of Health Sciences, Pomona, California, United States of America; College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, California, United States of America","keywords":["dinosaur","sauropod","vertebra","spinal cord","intervertebral disc","Morrison Formation","Haplocanthosaurus","neural canal","intervertebral joint"],"technical_report_institution":"PeerJ Preprints","publisher":"PeerJ Inc.","issn":"2167-9843","description":"A partial skeleton of a sauropod dinosaur, Museum of Western Colorado 8028, was recovered from the Upper Jurassic Morrison Formation near Snowmass, Colorado, USA, and in 2014 it was referred to Haplocanthosaurus sp. The material includes four proximal caudal vertebrae, which are unique in having strongly amphicoelous vertebral bodies, in which the centrum is reduced to a thin vertical plate of bone between the concave articular surfaces, and neural canals that are laterally and ventrally expanded and strongly sloped relative to the centrum. To reconstruct the soft tissues that left these traces on the skeleton, we rebuilt these vertebrae using both physical and digital techniques. We CT scanned the specimens, generated digital models, 3D-printed the vertebrae, physically sculpted missing material onto the printed models, optically scanned the sculpted vertebrae to create second-generation digital models, and finally, retro-deformed and articulated those digital versions of the vertebrae. The spaces between the deeply amphicoelous caudal centra were likely filled by large, ellipsoidal intervertebral discs, as in the amphicoelous vertebrae of Sphenodon and gekkotan lizards. The expanded neural canals remain enigmatic. In ostriches, the lumbosacral spinal cord is expanded laterally and ventrally in each vertebra, lending the spinal cord a shape that roughly resembles beads on a string. Similar spinal cord morphology might explain the expanded neural canals in the Snowmass Haplocanthosaurus, but it is not clear why a relatively small-bodied, small-tailed sauropod would need such a spinal expansion, given that similar expansions have not been reported in larger-bodied and larger-tailed taxa.","description-html":"\n A partial skeleton of a sauropod dinosaur, Museum of Western Colorado 8028, was recovered from the Upper Jurassic Morrison Formation near Snowmass, Colorado, USA, and in 2014 it was referred to Haplocanthosaurus<\/i> sp. The material includes four proximal caudal vertebrae, which are unique in having strongly amphicoelous vertebral bodies, in which the centrum is reduced to a thin vertical plate of bone between the concave articular surfaces, and neural canals that are laterally and ventrally expanded and strongly sloped relative to the centrum. To reconstruct the soft tissues that left these traces on the skeleton, we rebuilt these vertebrae using both physical and digital techniques. We CT scanned the specimens, generated digital models, 3D-printed the vertebrae, physically sculpted missing material onto the printed models, optically scanned the sculpted vertebrae to create second-generation digital models, and finally, retro-deformed and articulated those digital versions of the vertebrae. The spaces between the deeply amphicoelous caudal centra were likely filled by large, ellipsoidal intervertebral discs, as in the amphicoelous vertebrae of Sphenodon<\/i> and gekkotan lizards. The expanded neural canals remain enigmatic. In ostriches, the lumbosacral spinal cord is expanded laterally and ventrally in each vertebra, lending the spinal cord a shape that roughly resembles beads on a string. Similar spinal cord morphology might explain the expanded neural canals in the Snowmass Haplocanthosaurus<\/i>, but it is not clear why a relatively small-bodied, small-tailed sauropod would need such a spinal expansion, given that similar expansions have not been reported in larger-bodied and larger-tailed taxa.<\/p>\n ","title-html":"Reconstructing an unusual specimen of Haplocanthosaurus <\/i>using a blend of physical and digital techniques","subjects":["Evolutionary Studies","Paleontology","Zoology","Anatomy and Physiology"],"identifiers":{"peerj":"27431"},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/preprints\/27431","_links":{"self":{"href":"https:\/\/peerj.com\/preprints\/27431.json"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/preprints\/27431.html"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/preprints\/27431.xml"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/preprints\/27431.pdf"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/preprints\/27431.rdf"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/preprints\/27431.ris"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/preprints\/27431.bib"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/preprints\/27431.citeproc"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/preprints\/27431.bibjson"},"datacite":{"type":"application\/datacite+xml","href":"https:\/\/peerj.com\/preprints\/27431.datacite"}}}},{"title":"Hypothesis: Avian flight originated in arboreal archosaurs gliding on membranous wings","date":"2018-12-17","doi":"10.7287\/peerj.preprints.27213v2","language":"en","pdf_url":"https:\/\/peerj.com\/preprints\/27213.pdf","fulltext_html_url":"https:\/\/peerj.com\/preprints\/27213","technical_report_number":"e27213v2","author":["Piotr Bajdek","Tomasz Sulej"],"author_institution":["Institute of Paleobiology, Polish Academy of Sciences, Warsaw, Poland","Institute of Paleobiology, Polish Academy of Sciences, Warsaw, Poland"],"author_email":"p.bajdek@twarda.pan.pl","authors":"Bajdek, Piotr; Sulej, Tomasz","author_institutions":"Institute of Paleobiology, Polish Academy of Sciences, Warsaw, Poland","keywords":["origins of avian flight","function of feathers","Scansoriopterygidae"],"technical_report_institution":"PeerJ Preprints","publisher":"PeerJ Inc.","issn":"2167-9843","description":"The oldest feathers known to date have been found in archosaurs capable of flight. However, some of them (scansoriopterygids) flew by the use of a membrane rather than feathers. We therefore propose a new mechanism for the origin of avian flight by the use of membranous wings on both the forelimbs and the hindlimbs. It complements Beebe\u2019s (1915) prediction of the tetrapteryx stage. Paleontological and embryological evidence suggest that feathers are a modification of reptilian scales. Scansoriopterygids were covered mostly by down-like feathers which seemingly acted as thermal isolation rather than being adapted for flight. Certain early birds, including scansoriopterygids, possessed elongate shafted tail feathers, which were probably used principally for display and resembled elongate scales. We suppose that display is the primary function of early feathers, which were preadapted for thermal isolation and also flight. The body of theropods was covered mostly by typical reptilian scales, yet some ornithischian dinosaurs possessed filamentous integumentary structures which might have had a comparable display function. However, it is doubtful that these structures in dinosaurs were homologous with avian feathers. Early birds probably shared with theropod dinosaurs an incipient endothermy, which was inherited from their common ancestor in the Triassic Period.","description-html":"\n The oldest feathers known to date have been found in archosaurs capable of flight. However, some of them (scansoriopterygids) flew by the use of a membrane rather than feathers. We therefore propose a new mechanism for the origin of avian flight by the use of membranous wings on both the forelimbs and the hindlimbs. It complements Beebe\u2019s (1915) prediction of the tetrapteryx stage. Paleontological and embryological evidence suggest that feathers are a modification of reptilian scales. Scansoriopterygids were covered mostly by down-like feathers which seemingly acted as thermal isolation rather than being adapted for flight. Certain early birds, including scansoriopterygids, possessed elongate shafted tail feathers, which were probably used principally for display and resembled elongate scales. We suppose that display is the primary function of early feathers, which were preadapted for thermal isolation and also flight. The body of theropods was covered mostly by typical reptilian scales, yet some ornithischian dinosaurs possessed filamentous integumentary structures which might have had a comparable display function. However, it is doubtful that these structures in dinosaurs were homologous with avian feathers. Early birds probably shared with theropod dinosaurs an incipient endothermy, which was inherited from their common ancestor in the Triassic Period.<\/p>\n ","title-html":"Hypothesis: Avian flight originated in arboreal archosaurs gliding on membranous wings","subjects":["Evolutionary Studies","Paleontology","Zoology"],"identifiers":{"peerj":"27213"},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/preprints\/27213","_links":{"self":{"href":"https:\/\/peerj.com\/preprints\/27213.json"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/preprints\/27213.html"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/preprints\/27213.xml"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/preprints\/27213.pdf"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/preprints\/27213.rdf"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/preprints\/27213.ris"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/preprints\/27213.bib"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/preprints\/27213.citeproc"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/preprints\/27213.bibjson"},"datacite":{"type":"application\/datacite+xml","href":"https:\/\/peerj.com\/preprints\/27213.datacite"}}}},{"title":"Whole-genome comparisons of Penicillium spp. reveals secondary metabolic gene clusters and candidate genes associated with fungal aggressiveness during apple fruit decay","date":"2018-12-17","doi":"10.7287\/peerj.preprints.27430v1","language":"en","pdf_url":"https:\/\/peerj.com\/preprints\/27430.pdf","fulltext_html_url":"https:\/\/peerj.com\/preprints\/27430","technical_report_number":"e27430v1","author":["Guangxi Wu","Wayne M Jurick II","Franz J Lichtner","Hui Peng","Guohua Yin","Verneta L Gaskins","Yanbin Yin","Sui-Sheng Hua","Kari A. Peter","Joan W Bennett"],"author_institution":["Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA","Food Quality Laboratory, USDA-ARS, Beltsville, Maryland, United States of America","Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA","Food Quality Laboratory, USDA-ARS, Beltsville, Maryland, United States of America","Department of Plant Biology, Rutgers, The State University of New Jersey - Camden, New Brunswick, New Jersey, United States","Food Quality Laboratory, USDA-ARS, Beltsville, Maryland, United States of America","Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States","Western Regional Research Center, USDA-ARS, Albany, California, United States of America","Plant pathology and environmental microbiology, Penn State University, Biglerville, Pennsylvania, USA","Department of Plant Biology, Rutgers, The State University of New Jersey - Camden, New Brunswick, New Jersey, United States"],"author_email":"wayne.jurick@ars.usda.gov","authors":"Wu, Guangxi; Jurick II, Wayne M; Lichtner, Franz J; Peng, Hui; Yin, Guohua; Gaskins, Verneta L; Yin, Yanbin; Hua, Sui-Sheng; Peter, Kari A.; Bennett, Joan W","author_institutions":"Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA; Food Quality Laboratory, USDA-ARS, Beltsville, Maryland, United States of America; Department of Plant Biology, Rutgers, The State University of New Jersey - Camden, New Brunswick, New Jersey, United States; Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States; Western Regional Research Center, USDA-ARS, Albany, California, United States of America; Plant pathology and environmental microbiology, Penn State University, Biglerville, Pennsylvania, USA","keywords":["Penicillium spp","Blue mold","pome fruit","comparative genomics","gene profiling"],"technical_report_institution":"PeerJ Preprints","publisher":"PeerJ Inc.","issn":"2167-9843","description":"Blue mold is a postharvest rot of pomaceous fruits caused by Penicillium expansum and a number of other Penicillium species. The genome of the highly aggressive P. expansum strain R19 was re-sequenced and analyzed together with the genome of the less aggressive P. solitum strain RS1. Whole genome scale similarities and differences were examined. A phylogenetic analysis of P. expansum, P. solitum, and several closely related Penicillium species revealed that the two pathogens isolated from decayed apple with blue mold symptoms are not each other\u2019s closest relatives. Among a total of 10,560 and 10,672 protein coding sequences respectively, a comparative genomics analysis revealed 41 genes in P. expansum R19 and 43 genes in P. solitum RS1 that are unique to these two species. These genes may be associated with pome fruit\u2013fungal interactions, subsequent decay processes, and mycotoxin accumulation. An intact patulin gene cluster consisting of 15 biosynthetic genes was identified in the patulin producing P. expansum strain R19, while only a remnant, seven-gene cluster was identified in the patulin-deficient P. solitum strain. However, P. solitum contained a large number of additional secondary metabolite gene clusters indicating that this species has the potential capacity to produce an array of known, as well as not-yet-identified products, of possible toxicological or biotechnological interest.","description-html":"\n Blue mold is a postharvest rot of pomaceous fruits caused by Penicillium expansum <\/i>and a number of other Penicillium <\/i>species. <\/i>The genome of the highly aggressive P. expansum <\/i>strain R19 was re-sequenced and analyzed together with the genome of the less aggressive P. solitum <\/i>strain RS1. Whole genome scale similarities and differences were examined. A phylogenetic analysis of P. expansum, P. solitum, <\/i>and several closely related Penicillium<\/i> species revealed that the two pathogens isolated from decayed apple with blue mold symptoms are not each other\u2019s closest relatives. Among a total of 10,560 and 10,672 protein coding sequences respectively, a comparative genomics analysis revealed 41 genes in P. expansum<\/i> R19 and 43 genes in P. solitum<\/i> RS1 that are unique to these two species. These genes may be associated with pome fruit\u2013fungal interactions, subsequent decay processes, and mycotoxin accumulation. An intact patulin gene cluster consisting of 15 biosynthetic genes was identified in the patulin producing P. expansum <\/i>strain R19, while only a remnant, seven-gene cluster was identified in the patulin-deficient P. solitum <\/i>strain. <\/i>However, P. solitum<\/i> contained a large number of additional secondary metabolite gene clusters indicating that this species has the potential capacity to produce an array of known, as well as not-yet-identified products, of possible toxicological or biotechnological interest.<\/p>\n ","title-html":"Whole-genome comparisons of Penicillium <\/i>spp. reveals secondary metabolic gene clusters and candidate genes associated with fungal aggressiveness during apple fruit decay","subjects":["Agricultural Science","Genomics","Mycology","Plant Science"],"identifiers":{"peerj":"27430"},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/preprints\/27430","_links":{"self":{"href":"https:\/\/peerj.com\/preprints\/27430.json"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/preprints\/27430.html"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/preprints\/27430.xml"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/preprints\/27430.pdf"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/preprints\/27430.rdf"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/preprints\/27430.ris"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/preprints\/27430.bib"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/preprints\/27430.citeproc"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/preprints\/27430.bibjson"},"datacite":{"type":"application\/datacite+xml","href":"https:\/\/peerj.com\/preprints\/27430.datacite"}}}}]}