scholarly journals Avian Genomes Revisited: Hidden Genes Uncovered and the Rates versus Traits Paradox in Birds

2017 ◽  
Vol 34 (12) ◽  
pp. 3123-3131 ◽  
Author(s):  
Fidel Botero-Castro ◽  
Emeric Figuet ◽  
Marie-Ka Tilak ◽  
Benoit Nabholz ◽  
Nicolas Galtier
Keyword(s):  
Avian Genomes

scholarly journals De-novo emergence and template switching of SINE retroposons during the early evolution of passerine birds

2016 ◽  
Author(s):  
Alexander Suh ◽  
Sandra Bachg ◽  
Stephen Donnellan ◽  
Leo Joseph ◽  
Jürgen Brosius ◽  
...  
Keyword(s):  
De Novo ◽  
Bird Species ◽  
Early Evolution ◽  
Template Switching ◽  
Passerine Birds ◽  
Short Interspersed Elements ◽  
Mammalian Genomes ◽  
Rapid Diversification ◽  
The Common ◽  
Avian Genomes

AbstractPasseriformes (“perching birds” or passerines) make up more than half of all extant bird species. Here, we resolve their deep phylogenetic relationships using presence/absence patterns of short interspersed elements (SINEs), a group of retroposons which is abundant in mammalian genomes but considered largely inactive in avian genomes. The resultant retroposon-based phylogeny provides a powerful and independent corroboration of previous indications derived from sequence-based analyses. Notably, SINE activity began in the common ancestor of Eupasseres (passerines excl. the New Zealand wrens Acanthisittidae) and ceased before the rapid diversification of oscine passerines (songbirds). Furthermore, we find evidence for very recent SINE activity within suboscine passerines, following the emergence of a SINE via acquisition of a different tRNA head as we suggest through template switching. We propose that the early evolution of passerines was unusual among birds in that it was accompanied by activity of SINEs. Their genomic and transcriptomic impact warrants further study in the light of the massive diversification of passerines.

scholarly journals A whole genome analysis of the red-crowned crane provides insight into avian longevity

2017 ◽  
Author(s):  
HyeJin Lee ◽  
Oksung Chung ◽  
Yun Sung Cho ◽  
Sungwoong Jho ◽  
JeHoon Jun ◽  
...  
Keyword(s):  
Metabolic Rate ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Grus Japonensis ◽  
Low Genetic Diversity ◽  
In Captivity ◽  
In The Wild ◽  
Genetic Mechanisms ◽  
Avian Genomes ◽  
Insight Into

AbstractThe red-crowned crane (Grus japonensis) is an endangered and large-bodied crane native to East Asia. It is a traditional symbol of longevity and its long lifespan has been confirmed both in captivity and in the wild. Lifespan in birds is positively correlated with body size and negatively correlated with metabolic rate; although the genetic mechanisms for the red-crowned crane’s long lifespan have not previously been investigated. Using whole genome sequencing and comparative evolutionary analyses against the grey-crowned crane and other avian genomes, we identified candidate genes that are correlated with longevity. Included among these are positively selected genes with known associations with longevity in metabolism and immunity pathways (NDUFA5, NDUFA8, NUDT12 IL9R, SOD3, NUDT12, PNLIP, CTH, and RPA1). Our analyses provide genetic evidence for low metabolic rate and longevity, accompanied by possible convergent adaptation signatures among distantly related large and long-lived birds. Finally, we identified low genetic diversity in the red-crowned crane, consistent with its listing as an endangered species, and we hope this genome will provide a useful genetic resource for future conservation studies of this rare and iconic species.

Avian genomes: different karyotypes but a similar distribution of the GC-richest chromosome regions at interphase

2005 ◽  
Vol 13 (8) ◽  
pp. 785-793 ◽  
Author(s):  
Concetta Federico ◽  
Catia Daniela Cantarella ◽  
Cinzia Scavo ◽  
Salvatore Saccone ◽  
Bertrand Bed'Hom ◽  
...  
Keyword(s):  
Similar Distribution ◽  
Avian Genomes ◽  
Chromosome Regions

scholarly journals Evolutionary history of the mariner element galluhop in avian genomes

Mobile DNA ◽  
2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Natasha Avila Bertocchi ◽  
Fabiano Pimentel Torres ◽  
Analía del Valle Garnero ◽  
Ricardo José Gunski ◽  
Gabriel Luz Wallau
Keyword(s):  
Evolutionary History ◽  
History Of ◽  
Avian Genomes

scholarly journals A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae)

Diversity ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 144 ◽  
Author(s):  
Laís Coelho ◽  
Lukas Musher ◽  
Joel Cracraft
Keyword(s):  
Genome Assembly ◽  
High Throughput Sequencing ◽  
Population Genomics ◽  
De Novo ◽  
Structural Difference ◽  
Whole Genome ◽  
Sequencing Technology ◽  
A Genome ◽  
Avian Genomes ◽  
Chromosome Level

Current generation high-throughput sequencing technology has facilitated the generation of more genomic-scale data than ever before, thus greatly improving our understanding of avian biology across a range of disciplines. Recent developments in linked-read sequencing (Chromium 10×) and reference-based whole-genome assembly offer an exciting prospect of more accessible chromosome-level genome sequencing in the near future. We sequenced and assembled a genome of the Hairy-crested Antbird (Rhegmatorhina melanosticta), which represents the first publicly available genome for any antbird (Thamnophilidae). Our objectives were to (1) assemble scaffolds to chromosome level based on multiple reference genomes, and report on differences relative to other genomes, (2) assess genome completeness and compare content to other related genomes, and (3) assess the suitability of linked-read sequencing technology for future studies in comparative phylogenomics and population genomics studies. Our R. melanosticta assembly was both highly contiguous (de novo scaffold N50 = 3.3 Mb, reference based N50 = 53.3 Mb) and relatively complete (contained close to 90% of evolutionarily conserved single-copy avian genes and known tetrapod ultraconserved elements). The high contiguity and completeness of this assembly enabled the genome to be successfully mapped to the chromosome level, which uncovered a consistent structural difference between R. melanosticta and other avian genomes. Our results are consistent with the observation that avian genomes are structurally conserved. Additionally, our results demonstrate the utility of linked-read sequencing for non-model genomics. Finally, we demonstrate the value of our R. melanosticta genome for future researchers by mapping reduced representation sequencing data, and by accurately reconstructing the phylogenetic relationships among a sample of thamnophilid species.

Adaptation to nocturnality - learning from avian genomes

BioEssays ◽  
2016 ◽  
Vol 38 (7) ◽  
pp. 694-703 ◽  
Author(s):  
Diana Le Duc ◽  
Torsten Schöneberg
Keyword(s):  
Avian Genomes

DNA sequence organisation in avian genomes

Chromosoma ◽  
1978 ◽  
Vol 69 (3) ◽  
pp. 307-321 ◽  
Author(s):  
J�rg Thomas Epplen ◽  
Michael Leipoldt ◽  
Wolfgang Engel ◽  
J�rg Schmidtke
Keyword(s):  
Dna Sequence ◽  
Avian Genomes

scholarly journals Sequence properties of certain GC rich avian genes, their origins and absence from genome assemblies: case studies

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Linda Beauclair ◽  
Christelle Ramé ◽  
Peter Arensburger ◽  
Benoît Piégu ◽  
Florian Guillou ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Gc Content ◽  
Lower Efficiency ◽  
Genomic Libraries ◽  
Coding Regions ◽  
Red Jungle Fowl ◽  
Genome Model ◽  
Genome Assemblies ◽  
Avian Genomes ◽  
Eukaryotic Genomes

Abstract Background More and more eukaryotic genomes are sequenced and assembled, most of them presented as a complete model in which missing chromosomal regions are filled by Ns and where a few chromosomes may be lacking. Avian genomes often contain sequences with high GC content, which has been hypothesized to be at the origin of many missing sequences in these genomes. We investigated features of these missing sequences to discover why some may not have been integrated into genomic libraries and/or sequenced. Results The sequences of five red jungle fowl cDNA models with high GC content were used as queries to search publicly available datasets of Illumina and Pacbio sequencing reads. These were used to reconstruct the leptin, TNFα, MRPL52, PCP2 and PET100 genes, all of which are absent from the red jungle fowl genome model. These gene sequences displayed elevated GC contents, had intron sizes that were sometimes larger than non-avian orthologues, and had non-coding regions that contained numerous tandem and inverted repeat sequences with motifs able to assemble into stable G-quadruplexes and intrastrand dyadic structures. Our results suggest that Illumina technology was unable to sequence the non-coding regions of these genes. On the other hand, PacBio technology was able to sequence these regions, but with dramatically lower efficiency than would typically be expected. Conclusions High GC content was not the principal reason why numerous GC-rich regions of avian genomes are missing from genome assembly models. Instead, it is the presence of tandem repeats containing motifs capable of assembling into very stable secondary structures that is likely responsible.

scholarly journals Conservation and Losses of Non-Coding RNAs in Avian Genomes

PLoS ONE ◽  
2015 ◽  
Vol 10 (3) ◽  
pp. e0121797 ◽  
Author(s):  
Paul P. Gardner ◽  
Mario Fasold ◽  
Sarah W. Burge ◽  
Maria Ninova ◽  
Jana Hertel ◽  
...  
Keyword(s):  
Non Coding Rnas ◽  
Avian Genomes
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