Genome-wide analysis reveals the genomic features of the turkey vulture (Cathartes aura) as a scavenger

Zhou, Chuang; Wang, Guannan; Yu, Haoran; Yang, Geng; Wu, Wei; Tu, Hongmei; Price, Megan; Fan, Zhenxin; Yang, Meng; Yue, Bisong

doi:10.1007/s00438-019-01541-3

Cited by 13 publications

(19 citation statements)

References 62 publications

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“…For the identification of OR genes in birds, we employed a consensus approach, because it was reported that different approaches and/or cutoffs would possibly cause systematic bias [13]. A homology search was conducted to identify OR genes in these ten avian genomes.…”

Section: Methodsmentioning

confidence: 99%

The Draft Genome of the Endangered Sichuan Partridge (Arborophila rufipectus) with Evolutionary Implications

Zhou

et al. 2019

Genes

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The Sichuan partridge (Arborophila rufipectus, Phasianidae, Galliformes) is distributed in south-west China, and classified as endangered grade. To examine the evolution and genomic features of Sichuan partridge, we de novo assembled the Sichuan partridge reference genome. The final draft assembly consisted of approximately 1.09 Gb, and had a scaffold N50 of 4.57 Mb. About 1.94 million heterozygous single-nucleotide polymorphisms (SNPs) were detected, 17,519 protein-coding genes were predicted, and 9.29% of the genome was identified as repetitive elements. A total of 56 olfactory receptor (OR) genes were found in Sichuan partridge, and conserved motifs were detected. Comparisons between the Sichuan partridge genome and chicken genome revealed a conserved genome structure, and phylogenetic analysis demonstrated that Arborophila possessed a basal phylogenetic position within Phasianidae. Gene Ontology (GO) enrichment analysis of positively selected genes (PSGs) in Sichuan partridge showed over-represented GO functions related to environmental adaptation, such as energy metabolism and behavior. Pairwise sequentially Markovian coalescent analysis revealed the recent demographic trajectory for the Sichuan partridge. Our data and findings provide valuable genomic resources not only for studying the evolutionary adaptation, but also for facilitating the long-term conservation and genetic diversity for this endangered species.

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Section: Methodsmentioning

confidence: 99%

The Draft Genome of the Endangered Sichuan Partridge (Arborophila rufipectus) with Evolutionary Implications

Zhou

et al. 2019

Genes

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“…The mutations in the target sites of insects, insecticide metabolism by detoxification enzymes and tegumental changes inhibiting insecticide penetration were the main mechanisms related to resistance development (Georghiou ). Reduction in the sequencing costs and an increasing number of whole genomes facilitated by next generation sequencing (NGS) technologies have greatly advanced genomic studies in nonmodel organisms, which increased the possibility of recovering important biological information from complete genomes (Zhou et al ). Crucially, the sequencing of FAWs chromosome‐scale whole genome allows investigation of the genetic mechanisms of adaptive evolution, such as insecticide resistance which is a biologically complex phenomena and vital for insect survival (Perry et al ).…”

Section: Resultsmentioning

confidence: 99%

“…Insect protein sequences of P450s, GSTs, CCEs, UGTs, ABCs, and five AMPs were obtained from NCBI (Bethesda, MD, USA) and used as a query after removing the redundant sequences through cd‐hit (Li and Godzik, ). TBLASTN (Kent ), SOLAR (Zhou et al ), and GeneWise (Birney et al ) were then employed as the previous study (Zhou et al ) described. We then searched for P450s, GSTs, CCEs, UGTs, ABCs, and five AMPs in the translated set of FAW predicted proteins using the hmmscan program from the HMMER3 software package (http://hmmer.janelia.org) with the P450 HMM model (PF00135.23), GST HMM model (PF00043 and PF02798), CCE HMM model (PF00135.23), UGT HMM model (PF00201.13), ABC HMM model (PF00005), attacin HMM model (PF03768.15 and PF03769.15), cecropin HMM model (PF00272.19), defensin HMM model (PF01097.18), gloverin HMM model (PF10793.9), and moricin HMM model (PF06451.11) obtained from the PFAM website (http://pfam.xfam.org).…”

Section: Methodsmentioning

confidence: 99%

“…We referred to the previous study (Zhou et al ; Vega et al ) and developed a consensus approach to screen P450s, GSTs, CCEs, UGTs, ABCs, and five AMPs (i.e. attacin, cecropin, defensin, gloverin, and moricin).…”

Section: Methodsmentioning

confidence: 99%

Section: Identification Of P450s Gsts Cces Ugts Abcs and Ampsmentioning

confidence: 99%

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Genomic features of the fall armyworm (Spodoptera frugiperda) (J.E. Smith) yield insights into its defense system and flight capability

Zhou

Price

et al. 2020

Entomological Research

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The fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith) is an agriculturally important insect pest and causes significant economic loss due to its resistance to insecticide and high dispersal ability (i.e. long‐distance flyer). We performed comparative genomics analysis based on the recently released chromosome‐scale genome of the FAW to investigate the genetic mechanisms of FAWs defense system and flight ability. The gene families encoding receptors for bitter or toxic substances and detoxification enzymes, such as cytochrome P450, carboxylesterase and glutathione‐S‐transferase, were expanded in FAW, enabling its ability to detect and detoxify many plant secondary compounds. The chromosomal locations of five detoxification‐related genes (i.e. ABC, CCE, GST, P450, and UGT) were analyzed, which revealed the density of these genes across the FAW genome. Several genes like Mio, Sik2, CRTC, and Lpin were positively selected in FAW, which were associated with energy metabolism, lipid metabolism, and/or muscle development, and thus possibly contributed to the high flight ability of FAW. We also analyzed the homologs to antimicrobial genes reported in the Drosophila genome, and identified 2 attacins, 6 cecropins, 3 gloverins, and 2 moricins in FAW. The findings of this study will broadly expand our knowledge on the biology of the devastating FAW, and contribute to the development of new pest management strategies for the control of major agricultural pests like FAW.

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Vultures as a model for testing molecular adaptations of dietary specialization in birds

Chen,

Xiang,

Chen

et al. 2023

Avian Research

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Genome-wide analysis reveals the genomic features of the turkey vulture (Cathartes aura) as a scavenger

Cited by 13 publications

References 62 publications

The Draft Genome of the Endangered Sichuan Partridge (Arborophila rufipectus) with Evolutionary Implications

The Draft Genome of the Endangered Sichuan Partridge (Arborophila rufipectus) with Evolutionary Implications

Genomic features of the fall armyworm (Spodoptera frugiperda) (J.E. Smith) yield insights into its defense system and flight capability

Vultures as a model for testing molecular adaptations of dietary specialization in birds

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