Genome and metagenome analyses reveal adaptive evolution of the host and interaction with the gut microbiota in the goose

Gao, Guangliang; Zhao, Xianzhi; Qin, Li; He, Chuan; Zhao, Wenjing; Liu, Shuyun; Ding, Jinmei; Ye, Weixing; Wang, Jun; Chen, Ye; Wang, Haiwei; Li, Jing; Luo, Yi; Su, Jian; Huang, Yong; Liu, Zuohua; Dai, Ronghua; Shi, Yixiang; Meng, He; Wang, Qigui

doi:10.1038/srep32961

Cited by 42 publications

(37 citation statements)

References 59 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…After ltering, a total of 2.891 Tb of high-quality sequence data were mapped to a goose genome sequence, with an average mapping rate of 98.15% (96.58%-98.38%) ( Table S2). The average GC content was 42.85%, which is consistent with that previously reported for the goose genome [26][27][28]. A total of 9,279,339 SNPs identi ed in goose genome were used for further analysis ( Figure S1).…”

Section: Whole-genome Resequencing and Snp Callingsupporting

confidence: 83%

Genome-Wide Association Study to Identify SNPs and Haplotypes Associated with Reproductive Performance and Egg Quality Traits in Geese

Gao¹,

Gao²,

Zhao³

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

Background: Geese are one of the most economically important waterfowl worldwide. However, suboptimal reproductive performance hinders the development of the goose rearing industry. With the increasing public concern surrounding animal health and the regulation of the goose rearing industry, reproductive performance and egg quality have become a major focus for researchers. To promote the accuracy of selective breeding and identify important candidate genes associated with reproductive performance and egg quality traits, we examined the birth body weight (BBW), egg number at 48 weeks (EN48), egg number at 60 weeks (EN60) and egg yolk color (EYC) among 209 Sichuan White geese using a genome-wide association study (GWAS).Results: In this study, we obtained 2.896 Tb of raw whole-genome sequencing data with a mean depth coverage of 12.44. A total of 9,279,339 single nucleotide polymorphisms (SNPs) were identified in the goose genome. The GWAS analysis showed that 26 SNPs were significantly associated with the examined birth body weight (BBW), egg number in 48- and 60-week-old geese (EN48 and EN60) traits and egg yolk color (EYC), respectively. Notably, two genomic regions, a 28.85 kb genomic region (4512855bp ~ 4541709bp) on chromosome 35, and 294.57kb genomic region (21069009 b ~ 21363580 bp) located on chromosome 5, were significantly associated with egg number in 48- and 60-week-old geese (EN40 and EN60) egg yolk color (EYC), respectively. In addition, we performed the MALDI-TOP MS method to detected SNPs and haplotypes markers for EN48, EN60 and EYC traits were identified in the candidate gene TMEM161A, CALCR, TFPI2, and GLP1R, respectivelyConclusions: The SNPs, haplotypes markers and genes identified in this study can be used for marker-assisted selection of reproductive performance and egg quality traits in geese, promoting the accuracy of selective breeding. In addition, the identified candidate genes significantly associated with the traits provide a foundation for a better understanding of the mechanisms underlying reproduction and egg quality in geese.

show abstract

Section: Whole-genome Resequencing and Snp Callingsupporting

confidence: 83%

Genome-Wide Association Study to Identify SNPs and Haplotypes Associated with Reproductive Performance and Egg Quality Traits in Geese

Gao¹,

Gao²,

Zhao³

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…The average GC content of the bar-headed goose genome was around 41.87%, similar to that of the other birds such as Sichuan white goose (Anser cygnoides Linn. var domestica) (Gao et al, 2016) and buff-throated partridge (Tetraophasis szechenyii) (Zhou et al, 2019). Repeat sequences comprised approximately 8.9% of the bar-headed goose genome, which was higher than that of the Sichuan white goose genome at 6.9%.…”

Section: Discussionmentioning

confidence: 96%

First de novo whole genome sequencing and assembly of the bar-headed goose

Wang

Hao

et al. 2020

PeerJ

View full text Add to dashboard Cite

Background The bar-headed goose (Anser indicus) mainly inhabits the plateau wetlands of Asia. As a specialized high-altitude species, bar-headed geese can migrate between South and Central Asia and annually fly twice over the Himalayan mountains along the central Asian flyway. The physiological, biochemical and behavioral adaptations of bar-headed geese to high-altitude living and flying have raised much interest. However, to date, there is still no genome assembly information publicly available for bar-headed geese. Methods In this study, we present the first de novo whole genome sequencing and assembly of the bar-headed goose, along with gene prediction and annotation. Results 10X Genomics sequencing produced a total of 124 Gb sequencing data, which can cover the estimated genome size of bar-headed goose for 103 times (average coverage). The genome assembly comprised 10,528 scaffolds, with a total length of 1.143 Gb and a scaffold N50 of 10.09 Mb. Annotation of the bar-headed goose genome assembly identified a total of 102 Mb (8.9%) of repetitive sequences, 16,428 protein-coding genes, and 282 tRNAs. In total, we determined that there were 63 expanded and 20 contracted gene families in the bar-headed goose compared with the other 15 vertebrates. We also performed a positive selection analysis between the bar-headed goose and the closely related low-altitude goose, swan goose (Anser cygnoides), to uncover its genetic adaptations to the Qinghai-Tibetan Plateau. Conclusion We reported the currently most complete genome sequence of the bar-headed goose. Our assembly will provide a valuable resource to enhance further studies of the gene functions of bar-headed goose. The data will also be valuable for facilitating studies of the evolution, population genetics and high-altitude adaptations of the bar-headed geese at the genomic level.

show abstract

“…For example, the propanoate metabolism belongs to the carbohydrate metabolic pathways, including the malonate semialdehyde pathway and propanoyl-CoA pathway. It has been documented that propanoate metabolism is highly enriched simultaneously between the gut microbiota and the host 31 , and that the Streptomyces , which is the significant resource for antibiotic production, harbors the complete pathway of propanoate metabolism 32 . These studies suggest that propanoate metabolism plays an important role in the interaction between the host and its gut microbes and is necessary for normal metabolism.…”

Section: Discussionmentioning

confidence: 99%

Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants

Zhu

Xiao

et al. 2017

Sci Rep

View full text Add to dashboard Cite

The early postnatal period is the most dynamic and vulnerable stage in the assembly of intestinal microbiota. Antibiotics are commonly prescribed to newborn preterm babies and are frequently used for a prolonged duration in China. We hypothesized that the prolonged antibiotic therapy would affect the early development of intestinal microbiota and their metabolites. To test this hypothesis, we analyzed the stool microbiota and metabolites in 36 preterm babies with or without antibiotic treatment. These babies were divided into three groups, including two groups treated with the combination of penicillin and moxalactam or piperacillin-tazobactam for 7 days, and the other group was free of antibiotics. Compared to the antibiotic-free group, both antibiotic-treated groups had distinct gut microbial communities and metabolites, including a reduction of bacterial diversity and an enrichment of harmful bacteria such as Streptococcus and Pseudomonas. In addition, there was a significant difference in the composition of gut microbiota and their metabolites between the two antibiotic-treated groups, where the piperacillin-tazobactam treatment group showed an overgrowth of Enterococcus. These findings suggest that prolonged antibiotic therapy affects the early development of gut microbiota in preterm infants, which should be considered when prescribing antibiotics for this population.

show abstract

Genome and metagenome analyses reveal adaptive evolution of the host and interaction with the gut microbiota in the goose

Cited by 42 publications

References 59 publications

Genome-Wide Association Study to Identify SNPs and Haplotypes Associated with Reproductive Performance and Egg Quality Traits in Geese

Genome-Wide Association Study to Identify SNPs and Haplotypes Associated with Reproductive Performance and Egg Quality Traits in Geese

First de novo whole genome sequencing and assembly of the bar-headed goose

Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants

Contact Info

Product

Resources

About