GSA: Genome Sequence Archive

Wang, Yanqing; Song, Fuhai; Zhu, Junwei; Zhang, Sisi; Yang, Yadong; Chen, Tingting; Tang, Bixia; Dong, Lili; Ding, Nan; Zhang, Qian; Bai, Zhouxian; Dong, Xunong; Chen, Huanxin; Sun, Mingyuan; Zhai, Shuang; Sun, Yuan; Yu, Lei; Li, Lan; Xiao, Jingfa; Fang, Xiangdong; Lei, Hongxing; Zhang, Zhang; Zhao, Wenming

doi:10.1016/j.gpb.2017.01.001

Cited by 547 publications

(392 citation statements)

References 13 publications

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“…An Analysis of the overall functional profiles in the present study indicated that the gut microbes associated with these two bird species exhibited high metabolic activities. These results were consistent with earlier studies on the gut metagenomes of bar‐headed geese ( Anser indicus ) (Wang, Zheng, et al., ; Wang, Song, et al., ). This high metabolic rate may be related to the energy consumption required to fulfill the demands of flight.…”

Section: Discussionsupporting

confidence: 93%

“…The results presented in this study represent the first gut metagenomic characterizations of both greylag geese and ruddy shelducks. To date, although several datasets are available for the gut metagenomes of domestic birds (e.g., chickens and ducks) (Day, Ballard, Duke, Scheffler, & Zsak, ; Delforno et al., ; Lu et al., ), relatively little information is available concerning the metagenomes of wild birds’ gut microbiota (Godoy‐Vitorino et al., , ; Wang, Zheng, et al., ; Wang, Song, et al., ). Therefore, this study provides a significant contribution to the vast, yet little explored, field of wild birds’ gut microbiome.…”

Section: Discussionmentioning

confidence: 99%

“…Analyses of these datasets will help to elucidate the composition of microbial communities and are valuable resources for identifying carbohydrate‐active enzymes and antibiotics resistance genes present in gut communities. To the best of our knowledge, only very limited metagenomic analyses of the functional aspects of avian gut microbiota have been reported (Danzeisen, Kim, Isaacson, Tu, & Johnson, ; Godoy‐Vitorino et al., ; Lu, Santo Domingo, & Shanks, ; Wang, Zheng, et al., ; Wang, Song, et al., ). A meta‐analysis of these studies showed that the gut microbiota of birds were dominated by four major phyla, Firmicutes , Proteobacteria , Actinobacteria, and Bacteroidetes (Waite & Taylor, , ).…”

Section: Introductionmentioning

confidence: 99%

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Comparative metagenomics of the gut microbiota in wild greylag geese (Anser anser) and ruddy shelducks (Tadorna ferruginea)

Wen

Zheng

et al. 2018

MicrobiologyOpen

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Gut microbiome contributes to host health by maintaining homeostasis, increasing digestive efficiency, and facilitating the development of immune system. Wild greylag geese ( Anser anser ) and ruddy shelducks ( Tadorna ferruginea ), migrating along the central Asian flyway, appear to be one of the most popular species in the rare birds rearing industries of China. However, the structure and function of the gut microbial communities associated with these two bird species remain poorly understood. Here, for the first time, we compared gut metagenomes from greylag geese to ruddy shelducks and investigated the similarities and differences between these two bird species in detail. Taxonomic classifications revealed the top three bacterial phyla, Firmicutes , Proteobacteria, and Fusobacteria , in both greylag geese and ruddy shelducks. Furthermore, between the two species, 12 bacterial genera were found to be more abundant in ruddy shelducks and 41 genera were significantly higher in greylag geese. A total of 613 genera (approximately 70%) were found to be present in both groups. Metabolic categories related to carbohydrate metabolism, metabolism of cofactors and vitamins, lipid metabolism, amino acid metabolism, and glycan biosynthesis and metabolism were significantly more abundant in ruddy shelducks, while greylag geese were enriched in nucleotide metabolism and energy metabolism. The herbivorous greylag geese gut microbiota harbored more carbohydrate‐active enzymes than omnivorous ruddy shelducks. In our study, a range of antibiotic resistance categories were also identified in the gut microbiota of greylag geese and ruddy shelducks. In addition to providing a better understanding of the composition and function of wild birds gut microbiome, this comparative study provides reference values of the artificial domestication of these birds.

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Section: Discussionsupporting

confidence: 93%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Comparative metagenomics of the gut microbiota in wild greylag geese (Anser anser) and ruddy shelducks (Tadorna ferruginea)

Wen

Zheng

et al. 2018

MicrobiologyOpen

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“…All data could be available in this article and its additional files. The raw sequence data reported in this paper have been deposited in the Genome Sequence Archive (Genomics, Proteomics & Bioinformatics 2017) (Wang et al, ) in BIG Data Center (Nucleic Acids Res 2018) (BIG Data Center Members, ), Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, under accession numbers , , that are publicly accessible at http://bigd.big.ac.cn/gsa.…”

Section: Data Availability Statementmentioning

confidence: 99%

PTCH1 alterations are frequent but other genetic alterations are rare in sporadic odontogenic keratocysts

Zhang

et al. 2019

Oral Diseases

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Objective Odontogenic keratocysts (OKCs) are benign jaw lesions with high growth potential and propensity for recurrence. Our previous study revealed that PTCH1 mutations, which were frequently detected in sporadic OKCs, might be underestimated due to the masking effect of the stromal components within the tested tissues. We aimed to confirm these results in larger scale and further present the unbiased view of the genomic basis of sporadic OKCs except PTCH1. Materials and methods We analyzed PTCH1 mutations in additional 19 samples. Using whole‐exome sequencing (WES), we further characterized the mutational landscape of five sporadic OKC samples lacking PTCH1 mutation and loss of heterozygosity (LOH). Results Combined with our previously reported 19 cases, thirty of 38 (79%) cases harbored PTCH1 mutations. Through whole‐exome sequencing and integrative analysis, 22 novel mutations were confirmed among five PTCH1‐negative samples. No recurrent mutations were identified in the WES samples and validation cohort of 10 OKCs. Conclusions Our data further confirmed the frequent PTCH1 mutation and other rare genetic alterations in sporadic OKCs, highlighting the central role of SHH signaling pathway. In PTCH1‐negative cases, other rare mutations scattered in a subset of OKCs were independent of the SHH pathway. These results suggested that an SHH inhibitor may be effective to treat the majority of OKCs.

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“…Nucleosome occupancy of a nucleotide was defined as the number of read pairs uniquely mapped to the genome region covering the nucleotide. The raw sequencing data of MNase-seq have been deposited to the Genome Sequence Archive [49] in BIG Data Center (http://bigd.big.ac.cn/gsa), Beijing Institute of Genomics, Chinese Academy of Sciences, under accession number CRA000570.…”

Section: Estimation Of Nucleosome Occupancymentioning

confidence: 99%

DNA local structure decreases mutation rates

Duan

Huan

Chen³

et al. 2018

Preprint

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Running title: Intrinsic DNA curvature decreases local mutation rates 2 ABSTRACT Background Mutation rates vary across the genome. Whereas many trans factors that influence mutation rates have been identified, as have specific sequence motifs at the 1-7 bp scale, cis elements remain poorly characterized. The lack of understanding why different sequences have different mutation rates hampers our ability to identify positive selection in evolution and to identify driver mutations in tumorigenesis. ResultsHere we show, using a combination of synthetic genes and sequencing of thousands of isolated yeast colonies, that intrinsic DNA curvature is the major cis determinant of mutation rate. Mutation rate negatively correlates with DNA curvature within genes, and a 10% decrease in curvature results in a 70% increase in mutation rate. Consistently, both yeast cells and human tumors accumulate mutations in regions with small curvature. We further show that this effect is due to differences in the intrinsic mutation rate, likely due to differences in mutagen sensitivity, and not due to differences in the local activity of DNA repair. ConclusionsOur study establishes a framework in understanding the cis properties of DNA sequence in modulating the local mutation rate and identifies a novel causal source of non-uniform mutation rates across the genome.

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GSA: Genome Sequence Archive

Cited by 547 publications

References 13 publications

Comparative metagenomics of the gut microbiota in wild greylag geese (Anser anser) and ruddy shelducks (Tadorna ferruginea)

Comparative metagenomics of the gut microbiota in wild greylag geese (Anser anser) and ruddy shelducks (Tadorna ferruginea)

PTCH1 alterations are frequent but other genetic alterations are rare in sporadic odontogenic keratocysts

DNA local structure decreases mutation rates

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