Conserved syntenic clusters of protein coding genes are missing in birds

Abstract

BackgroundBirds 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.ResultsUsing 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.ConclusionsTogether 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-014-0565-1) contains supplementary material, which is available to authorized users.

Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling

“…1C) and found that the twophase model, which includes multiple gene loss, provided a better fit than did the single gene loss model. This suggests that a major cause of the rapid gene loss may have been multiple gene loss events, such as deletions of chromosomal segments containing multiple genes as suggested by studies of yeast (3), bird (21), and teleost (15) genomes. Furthermore, inactivation of coregulated gene groups (cis-regulated gene sets [e.g., in plant (16)] and trans-regulated gene networks) might also be regarded as the simultaneous loss of multiple genes.…”

Corticotropin-releasing hormone family evolution: five ancestral genes remain in some lineages

“…This possibility appears especially likely for chicken because putative CRH2 genes were identified in other bird genomes such as duck (Anas platyrhynchos, KB744325_0.354 Mb), flycatcher (Ficedula albicollis, JH603360_1.093 Mb), and zebra finch (Taeniopygia guttata, chr_20_8.814 Mb). The microchromosomes of chicken are known to be underrepresented in the genome assemblies (Lovell et al 2014. This might apply also to the lizard as it has microchromosomes too.…”

Dynamics of genome size evolution in birds and mammals

“…In fact, there are strong hints that large deletions caused a substantial level of gene loss in birds (274 protein-coding genes) with potentially profound phenotypic consequences (46,81,82). The foreseeable improvement of genome assembly via third-generation sequencing (e.g., long-read sequencing and gap filling; see ref.…”