About: A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species

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An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species
Creator	Drosten, Christian Müller, Marcel Hawkins, John Holder, Joshua Kaczmarek, Maria Plotkin, Tony Press, William Sawyer, Sara Schountz,
Source	Medline; PMC
abstract	Historically, the evolution of bats has been analyzed using a small number of genetic loci for many species or many genetic loci for a few species. Here we present a phylogeny of 18 bat species, each of which is represented in 1,107 orthologous gene alignments used to build the tree. We generated a transcriptome sequence of Hypsignathus monstrosus, the African hammer-headed bat, and additional transcriptome sequence for Rousettus aegyptiacus, the Egyptian fruit bat. We then combined these data with existing genomic and transcriptomic data from 16 other bat species. In the analysis of such datasets, there is no clear consensus on the most reliable computational methods for the curation of quality multiple sequence alignments since these public datasets represent multiple investigators and methods, including different source materials (chromosomal DNA or expressed RNA). Here we lay out a systematic analysis of parameters and produce an advanced pipeline for curating orthologous gene alignments from combined transcriptomic and genomic data, including a software package: the Mismatching Isoform eXon Remover (MIXR). Using this method, we created alignments of 11,677 bat genes, 1,107 of which contain orthologs from all 18 species. Using the orthologous gene alignments created, we assessed bat phylogeny and also performed a holistic analysis of positive selection acting in bat genomes. We found that 181 genes have been subject to positive natural selection. This list is dominated by genes involved in immune responses and genes involved in the production of collagens.
has issue date	2019-06-04(xsd:dateTime)
bibo:doi	10.1073/pnas.1814995116
bibo:pmid	31113885
has license	cc-by-nc-nd
sha1sum (hex)	5335dd626c2c607a3a6f7abefb0d341f0fd63164
schema:url	https://doi.org/10.1073/pnas.1814995116
resource representing a document's title	A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species
has PubMed Central identifier	PMC6561249
has PubMed identifier	31113885
schema:publication	Proc Natl Acad Sci U S A
resource representing a document's body	covid:5335dd626c2c607a3a6f7abefb0d341f0fd63164#body_text
is schema:about of	named entity 'POSITIVE SELECTION' named entity 'BASED' named entity 'GENOMES' named entity 'BAT' named entity 'PHYLOGENETICS' named entity 'SPECIES' named entity 'METAANALYSIS' named entity 'based' named entity 'transcriptomes' named entity 'paralogy' named entity 'posterior probability' named entity 'clade' named entity 'gene' named entity 'transcriptome' named entity 'Phyllostominae' named entity 'maximum parsimony' named entity 'syntenic' named entity 'phylogeny' named entity 'HMMER' named entity 'bat species' named entity 'synteny' named entity 'posterior probability' named entity 'sequence alignments' named entity '10,650' named entity 'Sequence Alignments' named entity 'sequence alignments' named entity 'genetic loci' named entity 'evolutionary origins' named entity 'locomotion' named entity 'exons' named entity 'Yangochiroptera' named entity 'exons' named entity 'genetic data' named entity 'bat' named entity 'NCBI' named entity 'collagen formation' named entity 'positive selection' named entity 'protein-coding genes' named entity 'posterior probability' named entity 'exons' named entity 'energy metabolism' named entity 'protein' named entity 'bioinformatic' named entity 'transcriptomic' named entity 'algorithm' named entity 'exons' named entity 'Chiroptera' named entity 'orthology' named entity 'Positive Selection' named entity 'natural selection' named entity 'alternative history' named entity 'transcriptome' named entity 'Chiroptera' named entity 'gene' named entity 'phylogeny' named entity 'adaptive evolution' named entity 'data type' named entity 'algorithm' named entity 'gene families' named entity 'transcriptomic' named entity 'transcriptome' named entity 'coding sequence' named entity 'bat' named entity 'genome-wide' named entity 'protein sequences' named entity 'phylogeny' named entity 'nested models' named entity 'codon' named entity 'HMMER' named entity 'Chiroptera' named entity 'codon' named entity 'contigs' named entity 'transcriptome'

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