The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures

Chung, Oksung; Jin, Shil; Cho, Yun Sung; Lim, Jeongheui; Kim, Hyunho; Jho, Sungwoong; Kim, Hak-Min; Jun, JeHoon; Lee, Hye-Jin; Chon, Alvin; Ko, Junsu; Edwards, Jeremy S.; Weber, Jessica A.; Han, Kyudong; O’Brien, Stephen J.; Manica, Andrea; Bhak, Jong; Paek, Woon Kee

doi:10.1186/s13059-015-0780-4

Cited by 46 publications

(47 citation statements)

References 67 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Therefore, it is necessary to further investigate if the genetic signatures found in vertebrate meat eating carnivores are also shared in other carnivores and/or if the other carnivores show different patterns of evolutionary adaptation according to their major food types. Also, non-living or decaying material eating animals such as coprophagy (eating feces) and scavenger (eating carrion) could be a good subject for investigating evolutionary adaptations by diet patterns [62]. …”

Section: Discussionmentioning

confidence: 99%

Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly

et al. 2016

Self Cite

View full text Add to dashboard Cite

BackgroundThere are three main dietary groups in mammals: carnivores, omnivores, and herbivores. Currently, there is limited comparative genomics insight into the evolution of dietary specializations in mammals. Due to recent advances in sequencing technologies, we were able to perform in-depth whole genome analyses of representatives of these three dietary groups.ResultsWe investigated the evolution of carnivory by comparing 18 representative genomes from across Mammalia with carnivorous, omnivorous, and herbivorous dietary specializations, focusing on Felidae (domestic cat, tiger, lion, cheetah, and leopard), Hominidae, and Bovidae genomes. We generated a new high-quality leopard genome assembly, as well as two wild Amur leopard whole genomes. In addition to a clear contraction in gene families for starch and sucrose metabolism, the carnivore genomes showed evidence of shared evolutionary adaptations in genes associated with diet, muscle strength, agility, and other traits responsible for successful hunting and meat consumption. Additionally, an analysis of highly conserved regions at the family level revealed molecular signatures of dietary adaptation in each of Felidae, Hominidae, and Bovidae. However, unlike carnivores, omnivores and herbivores showed fewer shared adaptive signatures, indicating that carnivores are under strong selective pressure related to diet. Finally, felids showed recent reductions in genetic diversity associated with decreased population sizes, which may be due to the inflexible nature of their strict diet, highlighting their vulnerability and critical conservation status.ConclusionsOur study provides a large-scale family level comparative genomic analysis to address genomic changes associated with dietary specialization. Our genomic analyses also provide useful resources for diet-related genetic and health research.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1071-4) contains supplementary material, which is available to authorized users.

show abstract

Section: Discussionmentioning

confidence: 99%

Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly

et al. 2016

Self Cite

View full text Add to dashboard Cite

show abstract

“…Mode-shift, a graphical method, was also used to estimate an allele frequency distortion after a bottleneck (Luikart et al 1998). Generation time of the Cinereous Vulture is assumed to be 10 years (Chung et al 2015) and l was assumed to be 5 9 10 À4 per nucleotide per generation (Agudo et al 2010). 0.1-0.2) are expected to be more common than alleles with low frequencies (< 0.1; Ganapathi et al 2012).…”

Section: Genetic Diversity and Bottleneckmentioning

confidence: 99%

Genetic diversity is retained in a bottlenecked Cinereous Vulture population in Turkey

Çakmak

Pekşen

Kirazlı

et al. 2018

Ibis

View full text Add to dashboard Cite

Vulture populations worldwide have suffered precipitous declines in recent decades. The Cinereous Vulture Aegypius monachus, a highly philopatric scavenger distributed across southern Europe and the central Asian plateau, is threatened in many parts of its range. Turkey holds the second largest population of this species in the Western Palaearctic, but there has been no research on its genetic structure and the possible implications of this structure for the future of the species. Here we report nuclear diversity and relatedness determined by short tandem repeat genotyping of 81 individuals from the four largest colonies. Our results demonstrated no significant genetic structuring, suggesting a single panmictic metapopulation connected by frequent dispersal. Furthermore, we show that the study population has retained moderate levels of genetic diversity, despite passing through a recent demographic bottleneck. We estimated the effective population size to be 112 individuals (95% confidence interval 74–201). Our results imply that the observed lack of increase in population size since the 1990s has not been caused by lowered fitness due to genetic inbreeding but rather by increased mortality via demographic processes. In the short term, we suggest that conservation efforts should treat the Turkish subpopulations as a single management unit and aim to increase population size through effective protection, especially during the breeding season.

show abstract

“…With the advancements in sequencing technologies, the genomes of several avian species, including Peking ducks [30], passenger pigeons [15], and vultures [31], have been sequenced and characterized, whereby this inclusion has accelerated the research on functional genomics and improved our understanding of the genetic regulation of important traits. However, for some non-model organisms and minor species, it is not feasible to perform whole genome sequencing because of the expensive cost.…”

Section: Discussionmentioning

confidence: 99%

De novo transcriptome analysis shows differential expression of genes in salivary glands of edible bird’s nest producing swiftlets

et al. 2017

View full text Add to dashboard Cite

BackgroundEdible bird’s nest (EBN), produced from solidified saliva secretions of specific swiftlet species during the breeding season, is one of the most valuable animal by-products in the world. The composition and medicinal benefits of EBN have been extensively studied, however, genomic and transcriptomic studies of the salivary glands of these birds have not been conducted.ResultsThe study described the transcriptomes of salivary glands from three swiftlet species (28 samples) generated by RNASeq. A total of 14,835 annotated genes and 428 unmapped genes were cataloged. The current study investigated the genes and pathways that are associated with the development of salivary gland and EBN composition. Differential expression and pathway enrichment analysis indicated that the expression of CREB3L2 and several signaling pathways involved in salivary gland development, namely, the EGFR, BMP, and MAPK signaling pathways, were up-regulated in swiftlets producing white EBN (Aerodramus fuciphagus) and black EBN (Aerodramus maximus) compared with non-EBN-producing swiftlets (Apus affinis). Furthermore, MGAT, an essential gene for the biosynthesis of N-acetylneuraminic acid (sialic acid), was highly expressed in both white- and black-nest swiftlets compared to non-EBN-producing swiftlets. Interspecies comparison between Aerodramus fuciphagus and Aerodramus maximus indicated that the genes involved in N-acetylneuraminic and fatty acid synthesis were up-regulated in Aerodramus fuciphagus, while alanine and aspartate synthesis pathways were up-regulated in Aerodramus maximus. Furthermore, gender-based analysis revealed that N-glycan trimming pathway was significantly up-regulated in male Aerodramus fuciphagus from its natural habitat (cave) compared to their female counterpart.ConclusionsTranscriptomic analysis of salivary glands of different swiftlet species reveal differential expressions of candidate genes that are involved in salivary gland development and in the biosynthesis of various bioactive compounds found in EBN.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3861-9) contains supplementary material, which is available to authorized users.

show abstract

The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures

Cited by 46 publications

References 67 publications

Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly

Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly

Genetic diversity is retained in a bottlenecked Cinereous Vulture population in Turkey

De novo transcriptome analysis shows differential expression of genes in salivary glands of edible bird’s nest producing swiftlets

Contact Info

Product

Resources

About