Conserved syntenic clusters of protein coding genes are missing in birds.
Peter V. Lovell,Morgan Wirthlin,Larry J. Wilhelm,Larry J. Wilhelm,Patrick Minx,Nathan H. Lazar,Nathan H. Lazar,Lucia Carbone,Lucia Carbone,Wesley C. Warren,Claudio V. Mello +10 more
TLDR
A clearer definition of the genetic background of extant birds is provided, the findings of previous studies on missing avian genes are extended, and clues about molecular events that shaped avian evolution are provided.Abstract:
Background: Birds are one of the most highly successful and diverse groups of vertebrates, having evolved a number of distinct characteristics, including feathers and wings, a sturdy lightweight skeleton and unique respiratory and urinary/excretion systems. However, the genetic basis of these traits is poorly understood. Results: Using comparative genomics based on extensive searches of 60 avian genomes, we have found that birds lack approximately 274 protein coding genes that are present in the genomes of most vertebrate lineages and are for the most part organized in conserved syntenic clusters in non-avian sauropsids and in humans. These genes are located in regions associated with chromosomal rearrangements, and are largely present in crocodiles, suggesting that their loss occurred subsequent to the split of dinosaurs/birds from crocodilians. Many of these genes are associated with lethality in rodents, human genetic disorders, or biological functions targeting various tissues. Functional enrichment analysis combined with orthogroup analysis and paralog searches revealed enrichments that were shared by non-avian species, present only in birds, or shared between all species. Conclusions: Together these results provide a clearer definition of the genetic background of extant birds, extend the findings of previous studies on missing avian genes, and provide clues about molecular events that shaped avian evolution. They also have implications for fields that largely benefit from avian studies, including development, immune system, oncogenesis, and brain function and cognition. With regards to the missing genes, birds can be considered ‘natural knockouts’ that may become invaluable model organisms for several human diseases.read more
Citations
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Dynamics of genome size evolution in birds and mammals
TL;DR: The data provide evidence for an “accordion” model of genome size evolution in birds and mammals, whereby the amount of DNA gained by transposable element expansion was counteracted by DNA loss through large segmental deletions, and proposed that extensive DNA loss has been the primary force maintaining the greater genomic compaction of flying birds and bats relative to their flightless relatives.
Journal ArticleDOI
Contraction of the type I IFN locus and unusual constitutive expression of IFN-α in bats.
Peng Zhou,Peng Zhou,Mary Tachedjian,James W. Wynne,Victoria Boyd,Jie Cui,Ina Smith,Christopher Cowled,Justin H. J. Ng,Justin H. J. Ng,Lawrence Mok,Wojtek P. Michalski,Ian H. Mendenhall,Gilda Tachedjian,Lin-Fa Wang,Lin-Fa Wang,Michelle L. Baker +16 more
TL;DR: It is demonstrated that bat IFN-α genes are constitutively expressed in unstimulated bat tissues and cells and their expression is unaffected by viral infection, providing evidence for a unique IFN system that may be linked to the ability of bats to coexist with viruses.
Journal ArticleDOI
A New Chicken Genome Assembly Provides Insight into Avian Genome Structure
Wesley C. Warren,LaDeana W. Hillier,Chad Tomlinson,Patrick Minx,Milinn Kremitzki,Tina Graves,Chris Markovic,Nathan Bouk,Kim D. Pruitt,Françoise Thibaud-Nissen,Valerie A. Schneider,Tamer A. Mansour,C. Titus Brown,Aleksey V. Zimin,Rachel Hawken,Mitch Abrahamsen,Alexis B. Pyrkosz,Mireille Morisson,Valerie Fillon,Alain Vignal,William Chow,Kerstin Howe,Janet E. Fulton,Marcia M. Miller,Peter V. Lovell,Claudio V. Mello,Morgan Wirthlin,Andrew S. Mason,Richard Kuo,David W. Burt,Jerry B. Dodgson,Hans H. Cheng +31 more
TL;DR: A new version of the chicken genome assembly is presented, built from combined long single molecule sequencing technology, finished BACs, and improved physical maps, and revisited the question of what genes are missing in the avian lineage, and found that a large fraction of the original set of missing genes are still absent in sequenced bird species.
Journal ArticleDOI
Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats
Se Jin Song,Jon G. Sanders,Frédéric Delsuc,Jessica L. Metcalf,Katherine R. Amato,Michael W. Taylor,Florent Mazel,Holly L. Lutz,Holly L. Lutz,Kevin Winker,Gary R. Graves,Gary R. Graves,Gregory Humphrey,Jack A. Gilbert,Shannon J. Hackett,Kevin P. White,Heather R. Skeen,Heather R. Skeen,Sarah M. Kurtis,Jack J. Withrow,Thomas M. Braile,Matthew J. Miller,Matthew J. Miller,Kevin G. McCracken,James M. Maley,Vanessa O. Ezenwa,Allison E. Williams,Jessica M. Blanton,Valerie J. McKenzie,Rob Knight +29 more
TL;DR: Assessment of gut microbiomes from ∼900 vertebrate species, including 315 mammals and 491 birds, concludes that host-gut microbiome phylosymbiosis depends on factors convergently absent in birds and bats, potentially associated with physiological adaptations to flight.
Journal ArticleDOI
Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling.
Jun G. Inoue,Jun G. Inoue,Yukuto Sato,Yukuto Sato,Robert Sinclair,Katsumi Tsukamoto,Katsumi Tsukamoto,Mutsumi Nishida,Mutsumi Nishida +8 more
TL;DR: The comparative genome analysis suggests that rapid gene loss just after the WGD reshaped teleost genomes before the major divergence is suggested, and provides a useful set of marker genes for future phylogenetic analysis.
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