The homology of the tridactyl hand of birds is a still debated subject, with both paleontological and developmental evidence used in support of alternative identity patterns in the avian fingers. With its simplified phalangeal morphology, the Late Jurassic ceratosaurian Limusaurus<\/i> has been argued to support a II\u2013III\u2013IV digital identity in birds and a complex pattern of homeotic transformations in three-fingered (tetanuran) theropods. We report a new large-bodied theropod, Saltriovenator zanellai<\/i> gen. et sp. nov., based on a partial skeleton from the marine Saltrio Formation (Sinemurian, lowermost Jurassic) of Lombardy (Northern Italy). Taphonomical analyses show bone bioerosion by marine invertebrates (first record for dinosaurian remains) and suggest a complex history for the carcass before being deposited on a well-oxygenated and well-illuminated sea bottom. Saltriovenator<\/i> shows a mosaic of features seen in four-fingered theropods and in basal tetanurans. Phylogenetic analysis supports sister taxon relationships between the new Italian theropod and the younger Early Jurassic Berberosaurus<\/i> from Morocco, in a lineage which is the basalmost of Ceratosauria. Compared to the atrophied hand of later members of Ceratosauria, Saltriovenator<\/i> demonstrates that a fully functional hand, well-adapted for struggling and grasping, was primitively present in ceratosaurians. Ancestral state reconstruction along the avian stem supports 2-3-4-1-X and 2-3-4-0-X as the manual phalangeal formulae at the roots of Ceratosauria and Tetanurae, confirming the I\u2013II\u2013III pattern in the homology of the avian fingers. Accordingly, the peculiar hand of Limusaurus<\/i> represents a derived condition restricted to late-diverging ceratosaurians and cannot help in elucidating the origin of the three-fingered condition of tetanurans. The evolution of the tridactyl hand of birds is explained by step-wise lateral simplification among non-tetanuran theropod dinosaurs, followed by a single primary axis shift from digit position 4 to 3 at the root of Tetanurae once the fourth finger was completely lost, which allowed independent losses of the vestigial fourth metacarpal among allosaurians, tyrannosauroids, and maniraptoromorphs. With an estimated body length of 7.5 m, Saltriovenator<\/i> is the largest and most robust theropod from the Early Jurassic, pre-dating the occurrence in theropods of a body mass approaching 1,000 Kg by over 25 My. The radiation of larger and relatively stockier averostran theropods earlier than previously known may represent one of the factors that ignited the trend toward gigantism in Early Jurassic sauropods.<\/p>\n","title-html":"The oldest ceratosaurian (Dinosauria: Theropoda), from the Lower Jurassic of Italy, sheds light on the evolution of the three-fingered hand of birds","subjects":["Evolutionary Studies","Paleontology"],"identifiers":{"peerj":"5976","pubmed":null,"pmc":null},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/articles\/5976","_links":{"self":{"href":"https:\/\/peerj.com\/articles\/5976.json"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/articles\/5976.html"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/articles\/5976.xml"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/articles\/5976.pdf"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/articles\/5976.rdf"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/articles\/5976.ris"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/articles\/5976.bib"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/articles\/5976.citeproc"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/articles\/5976.bibjson"},"unixref":{"type":"application\/unixref+xml","href":"https:\/\/peerj.com\/articles\/5976.unixref"}}}},{"title":"Feeding response of the tropical copepod Acartia erythraea to short-term thermal stress: more animal-derived food was consumed","date":"2018-12-19","doi":"10.7717\/peerj.6129","language":"en","pdf_url":"https:\/\/peerj.com\/articles\/6129.pdf","fulltext_html_url":"https:\/\/peerj.com\/articles\/6129","volume":"6","firstpage":"e6129","author":["Simin Hu","Sheng Liu","Lingli Wang","Tao Li","Hui Huang"],"author_institution":["Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China","Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China","Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China","University of Chinese Academy of Sciences, Beijing, China","Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China","Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, Hainan, China","Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China","Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, Hainan, China"],"author_email":"shliu@scsio.ac.cn","authors":"Hu, Simin; Liu, Sheng; Wang, Lingli; Li, Tao; Huang, Hui","author_institutions":"Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China; University of Chinese Academy of Sciences, Beijing, China; Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, Hainan, China","keywords":["Feeding response","Thermal pollution","Tropical coastal ecosystem","Copepod"],"journal_title":"PeerJ","journal_abbrev":"PeerJ","publisher":"PeerJ Inc.","issn":"2167-8359","description":"The objective of this study was to explore the feeding response of tropical copepods to short-term thermal shock and provide insight into the potential impact of coastal power plants on the trophic dynamics of tropical coastal ecosystems. Feeding experiments were conducted at three different temperatures (29\u00a0\u00b0C, 33\u00a0\u00b0C, and 35\u00a0\u00b0C) using the copepod Acartia erythraea, collected from Sanya Bay, China. The grazing rate of A. erythraea decreased dramatically in the high temperature treatment. Analysis of 18S rDNA clone libraries revealed that the diet of copepods from different treatments was mainly comprised of diatoms, metazoans, and protozoans; A. erythraea exhibited an obvious feeding preference shift with temperature, with a change from a diatom-dominated diet at 29\u00a0\u00b0C to a metazoan-dominated diet at 35\u00a0\u00b0C, and the omnivory index shifted from 0.1 to 2.84 correspondingly. Furthermore, A. erythraea showed a positive feeding response to plant food (i.e., phytoplankton and land plants) in the control treatment (29\u00a0\u00b0C), but a positive response to animal prey (i.e., metazoans and protozoans) at temperatures exceeding 33\u00a0\u00b0C, as evaluated by the Ivlev\u2019s selectivity index. Our results suggest that copepods could regulate their food intake by considering their energy demands when exposed to short-term thermal stress, which might influence the pathway of materials moving up the trophic system. However, further studies are required to elucidate the effects of elevated temperature on feeding of different organisms in order to predict the influence of thermal pollution on the food web of tropical coastal ecosystems.","description-html":"\n
The objective of this study was to explore the feeding response of tropical copepods to short-term thermal shock and provide insight into the potential impact of coastal power plants on the trophic dynamics of tropical coastal ecosystems. Feeding experiments were conducted at three different temperatures (29\u00a0\u00b0C, 33\u00a0\u00b0C, and 35\u00a0\u00b0C) using the copepod Acartia erythraea<\/i>, collected from Sanya Bay, China. The grazing rate of A. erythraea<\/i> decreased dramatically in the high temperature treatment. Analysis of 18S rDNA clone libraries revealed that the diet of copepods from different treatments was mainly comprised of diatoms, metazoans, and protozoans; A. erythraea<\/i> exhibited an obvious feeding preference shift with temperature, with a change from a diatom-dominated diet at 29\u00a0\u00b0C to a metazoan-dominated diet at 35\u00a0\u00b0C, and the omnivory index shifted from 0.1 to 2.84 correspondingly. Furthermore, A. erythraea<\/i> showed a positive feeding response to plant food (i.e., phytoplankton and land plants) in the control treatment (29\u00a0\u00b0C), but a positive response to animal prey (i.e., metazoans and protozoans) at temperatures exceeding 33\u00a0\u00b0C, as evaluated by the Ivlev\u2019s selectivity index. Our results suggest that copepods could regulate their food intake by considering their energy demands when exposed to short-term thermal stress, which might influence the pathway of materials moving up the trophic system. However, further studies are required to elucidate the effects of elevated temperature on feeding of different organisms in order to predict the influence of thermal pollution on the food web of tropical coastal ecosystems.<\/p>\n ","title-html":"Feeding response of the tropical copepod Acartia erythraea<\/i> to short-term thermal stress: more animal-derived food was consumed","subjects":["Ecosystem Science","Marine Biology","Environmental Contamination and Remediation","Biological Oceanography"],"identifiers":{"peerj":"6129","pubmed":null,"pmc":null},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/articles\/6129","_links":{"self":{"href":"https:\/\/peerj.com\/articles\/6129.json"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/articles\/6129.html"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/articles\/6129.xml"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/articles\/6129.pdf"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/articles\/6129.rdf"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/articles\/6129.ris"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/articles\/6129.bib"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/articles\/6129.citeproc"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/articles\/6129.bibjson"},"unixref":{"type":"application\/unixref+xml","href":"https:\/\/peerj.com\/articles\/6129.unixref"}}}},{"title":"Transposons and pathogenicity in Xanthomonas: acquisition of murein lytic transglycosylases by TnXax1 enhances Xanthomonas citri subsp. citri 306 virulence and fitness","date":"2018-12-19","doi":"10.7717\/peerj.6111","language":"en","pdf_url":"https:\/\/peerj.com\/articles\/6111.pdf","fulltext_html_url":"https:\/\/peerj.com\/articles\/6111","volume":"6","firstpage":"e6111","author":["Amanda C.P. Oliveira","Rafael M. Ferreira","Maria In\u00eas T. Ferro","Jesus A. Ferro","Mick Chandler","Alessandro M. Varani"],"author_institution":["School of Agricultural and Veterinarian Sciences\u2014Agricultural and Livestock Microbiology Graduation Program, Universidade Estadual Paulista, Jaboticabal, Sao Paulo, Brazil","School of Agricultural and Veterinarian Sciences, Universidade Estadual Paulista, Jaboticabal, Sao Paulo, Brazil","School of Agricultural and Veterinarian Sciences, Universidade Estadual Paulista, Jaboticabal, Sao Paulo, Brazil","School of Agricultural and Veterinarian Sciences, Universidade Estadual Paulista, Jaboticabal, Sao Paulo, Brazil","Department of Biochemistry, Georgetown University, WA, USA","School of Agricultural and Veterinarian Sciences, Universidade Estadual Paulista, Jaboticabal, Sao Paulo, Brazil"],"author_email":"alessandro.varani@unesp.br","authors":"Oliveira, Amanda C.P.; Ferreira, Rafael M.; Ferro, Maria In\u00eas T.; Ferro, Jesus A.; Chandler, Mick; Varani, Alessandro M.","author_institutions":"School of Agricultural and Veterinarian Sciences\u2014Agricultural and Livestock Microbiology Graduation Program, Universidade Estadual Paulista, Jaboticabal, Sao Paulo, Brazil; School of Agricultural and Veterinarian Sciences, Universidade Estadual Paulista, Jaboticabal, Sao Paulo, Brazil; Department of Biochemistry, Georgetown University, WA, USA","keywords":["Lateral gene transfer","Comparative genomics","Biofilm","Xanthan gum","Tn3"],"journal_title":"PeerJ","journal_abbrev":"PeerJ","publisher":"PeerJ Inc.","issn":"2167-8359","description":"Xanthomonas citri subsp. citri 306 (XccA) is the causal agent of type A citrus canker (CC), one of the most significant citriculture diseases. Murein lytic transglycosylases (LT), potentially involved in XccA pathogenicity, are enzymes responsible for peptidoglycan structure assembly, remodeling and degradation. They directly impact cell wall expansion during bacterial growth, septum division allowing cell separation, cell wall remodeling allowing flagellar assembly, bacterial conjugation, muropeptide recycling, and secretion system assembly, in particular the Type 3 Secretion System involved in bacterial virulence, which play a fundamental role in XccA pathogenicity. Information about the XccA LT arsenal is patchy: little is known about family diversity, their exact role or their connection to virulence in this bacterium. Among the LTs with possible involvement in virulence, two paralogue open reading frames (ORFs) (one on the chromosome and one in plasmid pXAC64) are passenger genes of the Tn3 family transposon TnXax1, known to play a significant role in the evolution and emergence of pathogenicity in Xanthomonadales and to carry a variety of virulence determinants. This study addresses LT diversity in the XccA genome and examines the role of plasmid and chromosomal TnXax1 LT passenger genes using site-directed deletion mutagenesis and functional characterization. We identified 13 XccA LTs: 12 belong to families 1A, 1B, 1C, 1D (two copies), 1F, 1G, 3A, 3B (two copies), 5A, 6A and one which is non-categorized. The non-categorized LT is exclusive to the Xanthomonas genus and related to the 3B family but contains an additional domain linked to carbohydrate metabolism. The categorized LTs are probably involved in cell wall remodeling to allow insertion of type 3, 4 and 6 secretion systems, flagellum assembly, division and recycling of cell wall and degradation and control of peptidoglycan production. The TnXax1 passenger LT genes (3B family) are not essential to XccA or for CC development but are implicated in peptidoglycan metabolism, directly impacting bacterial fitness and CC symptom enhancement in susceptible hosts (e.g., Citrus sinensis). This underlines the role of TnXax1 as a virulence and pathogenicity-propagating agent in XccA and suggests that LT acquisition by horizontal gene transfer mediated by TnXax1 may improve bacterial fitness, conferring adaptive advantages to the plant-pathogen interaction process.","description-html":"\n
Xanthomonas citri<\/i> subsp. citri<\/i> 306 (XccA) is the causal agent of type A citrus canker (CC), one of the most significant citriculture diseases. Murein lytic transglycosylases (LT), potentially involved in XccA pathogenicity, are enzymes responsible for peptidoglycan structure assembly, remodeling and degradation. They directly impact cell wall expansion during bacterial growth, septum division allowing cell separation, cell wall remodeling allowing flagellar assembly, bacterial conjugation, muropeptide recycling, and secretion system assembly, in particular the Type 3 Secretion System involved in bacterial virulence, which play a fundamental role in XccA pathogenicity. Information about the XccA LT arsenal is patchy: little is known about family diversity, their exact role or their connection to virulence in this bacterium. Among the LTs with possible involvement in virulence, two paralogue open reading frames (ORFs) (one on the chromosome and one in plasmid pXAC64) are passenger genes of the Tn3<\/i> family transposon TnXax1<\/i>, known to play a significant role in the evolution and emergence of pathogenicity in Xanthomonadales<\/i> and to carry a variety of virulence determinants. This study addresses LT diversity in the XccA genome and examines the role of plasmid and chromosomal TnXax1<\/i> LT passenger genes using site-directed deletion mutagenesis and functional characterization. We identified 13 XccA LTs: 12 belong to families 1A, 1B, 1C, 1D (two copies), 1F, 1G, 3A, 3B (two copies), 5A, 6A and one which is non-categorized. The non-categorized LT is exclusive to the Xanthomonas<\/i> genus and related to the 3B family but contains an additional domain linked to carbohydrate metabolism. The categorized LTs are probably involved in cell wall remodeling to allow insertion of type 3, 4 and 6 secretion systems, flagellum assembly, division and recycling of cell wall and degradation and control of peptidoglycan production. The TnXax1<\/i> passenger LT genes (3B family) are not essential to XccA or for CC development but are implicated in peptidoglycan metabolism, directly impacting bacterial fitness and CC symptom enhancement in susceptible hosts (e.g., Citrus sinensis<\/i>). This underlines the role of TnXax1<\/i> as a virulence and pathogenicity-propagating agent in XccA and suggests that LT acquisition by horizontal gene transfer mediated by TnXax1<\/i> may improve bacterial fitness, conferring adaptive advantages to the plant-pathogen interaction process.<\/p>\n","title-html":"Transposons and pathogenicity in Xanthomonas<\/i>: acquisition of murein lytic transglycosylases by TnXax1<\/i> enhances Xanthomonas citri<\/i> subsp. citri<\/i> 306 virulence and fitness","subjects":["Biochemistry","Bioinformatics","Genetics","Genomics","Microbiology"],"identifiers":{"peerj":"6111","pubmed":null,"pmc":null},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/articles\/6111","_links":{"self":{"href":"https:\/\/peerj.com\/articles\/6111.json"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/articles\/6111.html"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/articles\/6111.xml"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/articles\/6111.pdf"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/articles\/6111.rdf"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/articles\/6111.ris"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/articles\/6111.bib"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/articles\/6111.citeproc"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/articles\/6111.bibjson"},"unixref":{"type":"application\/unixref+xml","href":"https:\/\/peerj.com\/articles\/6111.unixref"}}}},{"title":"First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes","date":"2018-12-19","doi":"10.7717\/peerj.5963","language":"en","pdf_url":"https:\/\/peerj.com\/articles\/5963.pdf","fulltext_html_url":"https:\/\/peerj.com\/articles\/5963","volume":"6","firstpage":"e5963","author":["Bal\u00e1zs Brankovics","Tomasz Kulik","Jakub Sawicki","Katarzyna Bilska","Hao Zhang","G Sybren de Hoog","Theo AJ van der Lee","Cees Waalwijk","Anne D. van Diepeningen"],"author_institution":["Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands","Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands","Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands","Department of Botany and Nature Protection, University of Warmia and Mazury, Olsztyn, Poland","Department of Botany and Nature Protection, University of Warmia and Mazury, Olsztyn, Poland","Department of Botany and Nature Protection, University of Warmia and Mazury, Olsztyn, Poland","State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, P.R. China","Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands","Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands","Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands","Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands","Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands","Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands"],"author_email":"balazs.brankovics@wur.nl","authors":"Brankovics, Bal\u00e1zs; Kulik, Tomasz; Sawicki, Jakub; Bilska, Katarzyna; Zhang, Hao; de Hoog, G Sybren; van der Lee, Theo AJ; Waalwijk, Cees; van Diepeningen, Anne D.","author_institutions":"Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands; Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands; Department of Botany and Nature Protection, University of Warmia and Mazury, Olsztyn, Poland; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, P.R. China","keywords":["Mitogenome","Comparative genomics","Mitogenomics","Pan-genome","Pool sequencing"],"journal_title":"PeerJ","journal_abbrev":"PeerJ","publisher":"PeerJ Inc.","issn":"2167-8359","description":"There is a gradual shift from representing a species\u2019 genome by a single reference genome sequence to a pan-genome representation. Pan-genomes are the abstract representations of the genomes of all the strains that are present in the population or species. In this study, we employed a pan-genomic approach to analyze the intraspecific mitochondrial genome diversity of Fusarium graminearum. We present an improved reference mitochondrial genome for F. graminearum with an intron-exon annotation that was verified using RNA-seq data. Each of the 24 studied isolates had a distinct mitochondrial sequence. Length variation in the F. graminearum mitogenome was found to be largely due to variation of intron regions (99.98%). The \u201cintronless\u201d mitogenome length was found to be quite stable and could be informative when comparing species. The coding regions showed high conservation, while the variability of intergenic regions was highest. However, the most important variable parts are the intron regions, because they contain approximately half of the variable sites, make up more than half of the mitogenome, and show presence\/absence variation. Furthermore, our analyses show that the mitogenome of F. graminearum is recombining, as was previously shown in F. oxysporum, indicating that mitogenome recombination is a common phenomenon in Fusarium. The majority of mitochondrial introns in F. graminearum belongs to group I introns, which are associated with homing endonuclease genes (HEGs). Mitochondrial introns containing HE genes may spread within populations through homing, where the endonuclease recognizes and cleaves the recognition site in the target gene. After cleavage of the \u201chost\u201d gene, it is replaced by the gene copy containing the intron with HEG. We propose to use introns unique to a population for tracking the spread of the given population, because introns can spread through vertical inheritance, recombination as well as via horizontal transfer. We demonstrate how pooled sequencing of strains can be used for mining mitogenome data. The usage of pooled sequencing offers a scalable solution for population analysis and for species level comparisons studies. This study may serve as a basis for future mitochondrial genome variability studies and representations.","description-html":"\n
There is a gradual shift from representing a species\u2019 genome by a single reference genome sequence to a pan-genome representation. Pan-genomes are the abstract representations of the genomes of all the strains that are present in the population or species. In this study, we employed a pan-genomic approach to analyze the intraspecific mitochondrial genome diversity of Fusarium graminearum<\/i>. We present an improved reference mitochondrial genome for F. graminearum<\/i> with an intron-exon annotation that was verified using RNA-seq data. Each of the 24 studied isolates had a distinct mitochondrial sequence. Length variation in the F. graminearum<\/i> mitogenome was found to be largely due to variation of intron regions (99.98%). The \u201cintronless\u201d mitogenome length was found to be quite stable and could be informative when comparing species. The coding regions showed high conservation, while the variability of intergenic regions was highest. However, the most important variable parts are the intron regions, because they contain approximately half of the variable sites, make up more than half of the mitogenome, and show presence\/absence variation. Furthermore, our analyses show that the mitogenome of F. graminearum<\/i> is recombining, as was previously shown in F. oxysporum<\/i>, indicating that mitogenome recombination is a common phenomenon in Fusarium<\/i>. The majority of mitochondrial introns in F. graminearum<\/i> belongs to group I introns, which are associated with homing endonuclease genes (HEGs). Mitochondrial introns containing HE genes may spread within populations through homing, where the endonuclease recognizes and cleaves the recognition site in the target gene. After cleavage of the \u201chost\u201d gene, it is replaced by the gene copy containing the intron with HEG. We propose to use introns unique to a population for tracking the spread of the given population, because introns can spread through vertical inheritance, recombination as well as via horizontal transfer. We demonstrate how pooled sequencing of strains can be used for mining mitogenome data. The usage of pooled sequencing offers a scalable solution for population analysis and for species level comparisons studies. This study may serve as a basis for future mitochondrial genome variability studies and representations.<\/p>\n ","title-html":"First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum<\/i> mitogenomes","subjects":["Bioinformatics","Genomics","Population Biology"],"identifiers":{"peerj":"5963","pubmed":null,"pmc":null},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/articles\/5963","_links":{"self":{"href":"https:\/\/peerj.com\/articles\/5963.json"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/articles\/5963.html"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/articles\/5963.xml"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/articles\/5963.pdf"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/articles\/5963.rdf"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/articles\/5963.ris"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/articles\/5963.bib"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/articles\/5963.citeproc"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/articles\/5963.bibjson"},"unixref":{"type":"application\/unixref+xml","href":"https:\/\/peerj.com\/articles\/5963.unixref"}}}},{"title":"Iberian pig adaptation to acorn consumption: II. Net portal appearance of amino acids","date":"2018-12-18","doi":"10.7717\/peerj.6137","language":"en","pdf_url":"https:\/\/peerj.com\/articles\/6137.pdf","fulltext_html_url":"https:\/\/peerj.com\/articles\/6137","volume":"6","firstpage":"e6137","author":["Manuel Lachica","Jose Miguel Rodr\u00edguez-L\u00f3pez","Lucrecia Gonz\u00e1lez-Valero","Ignacio Fern\u00e1ndez-F\u00edgares"],"author_institution":["Department of Physiology and Biochemistry of Animal Nutrition, Estaci\u00f3n Experimental del Zaid\u00edn, Consejo Superior de Investigaciones Cient\u00edficas, Granada, Spain","D\u00e9partment Sciences Agronomiques et Animales, Institut Polytechnique LaSalle Beauvais, Beauvais, France","Department of Physiology and Biochemistry of Animal Nutrition, Estaci\u00f3n Experimental del Zaid\u00edn, Consejo Superior de Investigaciones Cient\u00edficas, Granada, Spain","Department of Physiology and Biochemistry of Animal Nutrition, Estaci\u00f3n Experimental del Zaid\u00edn, Consejo Superior de Investigaciones Cient\u00edficas, Granada, Spain"],"author_email":"ifigares@eez.csic.es","authors":"Lachica, Manuel; Rodr\u00edguez-L\u00f3pez, Jose Miguel; Gonz\u00e1lez-Valero, Lucrecia; Fern\u00e1ndez-F\u00edgares, Ignacio","author_institutions":"Department of Physiology and Biochemistry of Animal Nutrition, Estaci\u00f3n Experimental del Zaid\u00edn, Consejo Superior de Investigaciones Cient\u00edficas, Granada, Spain; D\u00e9partment Sciences Agronomiques et Animales, Institut Polytechnique LaSalle Beauvais, Beauvais, France","keywords":["Pig","Net portal appearance","Portal-drained viscera","Acorn","Amino acid"],"journal_title":"PeerJ","journal_abbrev":"PeerJ","publisher":"PeerJ Inc.","issn":"2167-8359","description":"In Iberian pig outdoor production, pigs are fed equilibrated diets until the final fattening period when grazing pigs consume mainly acorns from oak trees. Acorns are rich in energy but poor in crude protein where lysine is the first limiting amino acid (AA). Net portal appearance (NPA) is very useful to ascertain AA available for liver and peripheral tissues. The aim of this study was to determine NPA of AA in Iberian gilts fed with acorns and to ascertain if there was an effect of acorn feeding over time. Two sampling periods were carried out (after one day and after one week of acorn feeding) with six gilts (34 kg average BW) set up with three catheters: in carotid artery and portal vein for blood sampling, and ileal vein for a marker infusion to measure portal plasma flow (PPF). Pigs were fed at 2.5 \u00d7\u00a0ME for maintenance a standard diet in two meals, at 09:00 (0.25) and 15:00 h (the remaining 0.75). The day previous to first sampling, pig diet was replaced by 2.4 kg of acorn. A serial blood collection was done at \u22125 min, 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 5 and 6 h after feeding 0.25 of total daily acorn ration. Following identical protocol, one week later the second sampling was done. NPA of sum of essential AA (EAA) was poor. Although increased NPA of histidine (P\u00a0<\u00a00.001), leucine, phenylalanine and valine (0.05\u00a0<\u00a0P\u00a0<\u00a00.08) was found after one week of acorn consumption, the sum of EAA did not change. Furthermore, fractional absorption (NPA\/AA intake) of EAA, non-essential AA (NEAA) and total AA was 97, 44 and 49% lower, respectively, at the beginning of eating acorn than a week later. Supplementation, with some of the EAA and NEAA to Iberian pigs during the grazing period would be beneficial to overcome the increased portal-drained viscera (PDV) utilization of AA observed in the present\u00a0study.","description-html":"\n
In Iberian pig outdoor production, pigs are fed equilibrated diets until the final fattening period when grazing pigs consume mainly acorns from oak trees. Acorns are rich in energy but poor in crude protein where lysine is the first limiting amino acid (AA). Net portal appearance (NPA) is very useful to ascertain AA available for liver and peripheral tissues. The aim of this study was to determine NPA of AA in Iberian gilts fed with acorns and to ascertain if there was an effect of acorn feeding over time. Two sampling periods were carried out (after one day and after one week of acorn feeding) with six gilts (34 kg average BW) set up with three catheters: in carotid artery and portal vein for blood sampling, and ileal vein for a marker infusion to measure portal plasma flow (PPF). Pigs were fed at 2.5 \u00d7\u00a0ME for maintenance a standard diet in two meals, at 09:00 (0.25) and 15:00 h (the remaining 0.75). The day previous to first sampling, pig diet was replaced by 2.4 kg of acorn. A serial blood collection was done at \u22125 min, 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 5 and 6 h after feeding 0.25 of total daily acorn ration. Following identical protocol, one week later the second sampling was done. NPA of sum of essential AA (EAA) was poor. Although increased NPA of histidine (P<\/i>\u00a0<\u00a00.001), leucine, phenylalanine and valine (0.05\u00a0<\u00a0P<\/i>\u00a0<\u00a00.08) was found after one week of acorn consumption, the sum of EAA did not change. Furthermore, fractional absorption (NPA\/AA intake) of EAA, non-essential AA (NEAA) and total AA was 97, 44 and 49% lower, respectively, at the beginning of eating acorn than a week later. Supplementation, with some of the EAA and NEAA to Iberian pigs during the grazing period would be beneficial to overcome the increased portal-drained viscera (PDV) utilization of AA observed in the present\u00a0study.<\/p>\n ","title-html":"Iberian pig adaptation to acorn consumption: II. Net portal appearance of amino acids","subjects":["Agricultural Science","Nutrition","Natural Resource Management"],"identifiers":{"peerj":"6137","pubmed":null,"pmc":null},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/articles\/6137","_links":{"self":{"href":"https:\/\/peerj.com\/articles\/6137.json"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/articles\/6137.html"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/articles\/6137.xml"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/articles\/6137.pdf"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/articles\/6137.rdf"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/articles\/6137.ris"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/articles\/6137.bib"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/articles\/6137.citeproc"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/articles\/6137.bibjson"},"unixref":{"type":"application\/unixref+xml","href":"https:\/\/peerj.com\/articles\/6137.unixref"}}}},{"title":"ScanFold: an approach for genome-wide discovery of local RNA structural elements\u2014applications to Zika virus and HIV","date":"2018-12-18","doi":"10.7717\/peerj.6136","language":"en","pdf_url":"https:\/\/peerj.com\/articles\/6136.pdf","fulltext_html_url":"https:\/\/peerj.com\/articles\/6136","volume":"6","firstpage":"e6136","author":["Ryan J. Andrews","Julien Roche","Walter N. Moss"],"author_email":"wmoss@iastate.edu","authors":"Andrews, Ryan J.; Roche, Julien; Moss, Walter N.","author_institutions":"Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, USA","keywords":["RNA","RNA structure","Zika virus","Motif discovery","Bioinformatics","Sequence analysis","ncRNA","HIV"],"journal_title":"PeerJ","journal_abbrev":"PeerJ","publisher":"PeerJ Inc.","issn":"2167-8359","description":"In addition to encoding RNA primary structures, genomes also encode RNA secondary and tertiary structures that play roles in gene regulation and, in the case of RNA viruses, genome replication. Methods for the identification of functional RNA structures in genomes typically rely on scanning analysis windows, where multiple partially-overlapping windows are used to predict RNA structures and folding metrics to deduce regions likely to form functional structure. Separate structural models are produced for each window, where the step size can greatly affect the returned model. This makes deducing unique local structures challenging, as the same nucleotides in each window can be alternatively base paired. We are presenting here a new approach where all base pairs from analysis windows are considered and weighted by favorable folding. This results in unique base pairing throughout the genome and the generation of local regions\/structures that can be ranked by their propensity to form unusually thermodynamically stable folds. We applied this approach to the Zika virus (ZIKV) and HIV-1 genomes. ZIKV is linked to a variety of neurological ailments including microcephaly and Guillain\u2013Barr\u00e9 syndrome and its (+)-sense RNA genome encodes two, previously described, functionally essential structured RNA regions. HIV, the cause of AIDS, contains multiple functional RNA motifs in its genome, which have been extensively studied. Our approach is able to successfully identify and model the structures of known functional motifs in both viruses, while also finding additional regions likely to form functional structures. All data have been archived at the RNAStructuromeDB (www.structurome.bb.iastate.edu), a repository of RNA folding data for humans and their pathogens.","description-html":"\n