The bowfin genome illuminates the developmental evolution of ray-finned fishes.
Andrew W. Thompson,M. Brent Hawkins,Elise Parey,Dustin J. Wcisel,Tatsuya Ota,Kazuhiko Kawasaki,Emily Funk,Emily Funk,Mauricio Losilla,Olivia E Fitch,Qiaowei Pan,Romain Feron,Romain Feron,Alexandra Louis,Jérôme Montfort,Marine Milhes,Brett Racicot,Kevin L. Childs,Quenton C. Fontenot,Allyse M. Ferrara,Solomon R. David,Amy R. McCune,Alex Dornburg,Jeffrey A. Yoder,Yann Guiguen,Hugues Roest Crollius,Camille Berthelot,Matthew P. Harris,Matthew P. Harris,Ingo Braasch +29 more
TLDR
In this article, a chromosome-level genome assembly for the bowfin (Amia calva) is presented, which enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships.Abstract:
The bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin's importance for illuminating vertebrate biology and diversity in the genomic era.read more
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On the relationship between extant innate immune receptors and the evolutionary origins of jawed vertebrate adaptive immunity
Alex Dornburg,Jeffrey A. Yoder +1 more
TL;DR: A conceptual model of the evolutionary origins and phylogenetic distribution of known VJ-containing innate immune receptors is provided, highlighting opportunities for future comparative research that are empowered by this emerging evolutionary perspective.
Journal ArticleDOI
On the relationship between extant innate immune receptors and the evolutionary origins of jawed vertebrate adaptive immunity
Alex Dornburg,Jeffrey A. Yoder +1 more
Journal ArticleDOI
Holosteans contextualize the role of the teleost genome duplication in promoting the rise of evolutionary novelties in the ray-finned fish innate immune system.
Alex Dornburg,Dustin J. Wcisel,Katerina L. Zapfe,Emma Ferraro,Lindsay Roupe-Abrams,Andrew W. Thompson,Ingo Braasch,Tatsuya Ota,Jeffrey A. Yoder +8 more
TL;DR: In this paper, a detailed investigation of the phylogenetic history and conserved synteny of gene clusters encoding diverse immunoglobulin domain-containing proteins (DICPs) and novel immune-type receptors (NITRs) is presented.
Journal ArticleDOI
Genome structures resolve the early diversification of teleost fishes
Elise Parey,Alexandra Louis,Jérôme Montfort,Olivier Bouchez,Céline Roques,Carole Iampietro,Jérôme Lluch,Adrien Castinel,Cécile Donnadieu,Thomas Desvignes,Christabel Floi Bucao,Elodie Jouanno,Ming Wen,Sahar Mejri,Ron P. Dirks,Hans Jansen,Christiaan V. Henkel,Wei-Jen Chen,Margot Zahm,Cédric Cabau,Christophe Klopp,Andrew W. Thompson,Marc Robinson-Rechavi,Ingo Braasch,Guillaume Lecointre,Julien Bobe,John H. Postlethwait,Camille Berthelot,Hugues Roest Crollius,Yann Guiguen +29 more
TL;DR: W Whole-genome analyses place Elopomorpha and Osteoglossom orpha (bony-tongues) as sister groups at the deepest branching of crown teleosts and resolves over 50 years of controversy on the evolutionary relationships of these lineages.
Journal ArticleDOI
FishmiRNA: An Evolutionarily Supported MicroRNA Annotation and Expression Database for Ray-Finned Fishes
Thomas Desvignes,Philippe Bardou,Jérôme Montfort,Jason Sydes,Cervin Guyomar,Simon George,John H. Postlethwait,Julien Bobe +7 more
TL;DR: FishmiRNA is an evolutionarily supported miRNA annotation and expression database for ray-finned fishes, specifically designed for ease of use to reach a wide audience.
References
More filters
Journal ArticleDOI
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Journal ArticleDOI
Trimmomatic: a flexible trimmer for Illumina sequence data
TL;DR: Timmomatic is developed as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data and is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested.
Journal ArticleDOI
Fast gapped-read alignment with Bowtie 2
TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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