Jingfa Xiao

Beijing Institute of Genomics

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Jun Yu

Chinese Academy of Sciences

Jiayan Wu

Sun Yat-sen University

Zhang Zhang

Chinese Academy of Sciences

Meili Chen

Beijing Institute of Genomics

Yīmíng Bào

Chinese Academy of Sciences

Wenming Zhao

Beijing Institute of Genomics

Zhenglin Du

Beijing Institute of Genomics

Jingyao Zeng

Beijing Institute of Genomics

Zhewen Zhang

Chinese Academy of Sciences

Dong Zou

Beijing Institute of Genomics

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Chinese Academy of Sciences

529

University of Chinese Academy of Sciences

356

Beijing Institute of Genomics

236

Real Sociedad Española de Química

135

Robert Bosch (Germany)

133

Shanghai Center For Bioinformation Technology

125

Real Academia Española

109

Weatherford College

109

Chinese Academy of Medical Sciences & Peking Union Medical College

108

Huazhong University of Science and Technology

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Additional file 2: Figure S2. of GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes

Lina Yuan Yang Yu Yanmin Zhu Yulai Li Changqing Li

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The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types

Genomics Proteomics & Bioinformatics (2021)

Tingting Chen Xu Chen Sisi Zhang Junwei Zhu Bixia Tang

The Genome Sequence Archive (GSA) is a data repository for archiving raw sequence data, which provides data storage and sharing services for worldwide scientific communities. Considering explosive data growth with diverse data types, here we present the GSA family by expanding into a set of resources for raw data archive with different purposes, namely, GSA (https://ngdc.cncb.ac.cn/gsa/), GSA for Human (GSA-Human, https://ngdc.cncb.ac.cn/gsa-human/), and Open Archive for Miscellaneous Data (OMIX, https://ngdc.cncb.ac.cn/omix/). Compared with the 2017 version, GSA has been significantly updated in data model, online functionalities, and web interfaces. GSA-Human, as a new partner of GSA, is a data repository specialized in human genetics-related data with controlled access and security. OMIX, as a critical complement to the two resources mentioned above, is an open archive for miscellaneous data. Together, all these resources form a family of resources dedicated to archiving explosive data with diverse types, accepting data submissions from all over the world, and providing free open access to all publicly available data in support of worldwide research activities.

Data Sharing

Data set

Data access

10.1016/j.gpb.2021.08.001

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Genome sequence and genetic diversity of the common carp, Cyprinus carpio

Nature Genetics (2014)

Peng Xu Xiaofeng Zhang Xumin Wang Jiong-Tang Li Guiming Liu

Xiaowen Sun and colleagues report the whole-genome sequencing of the common carp, Cyprinus carpio. They also resequenced 33 representative accessions from a worldwide collection and provide insights into population structure and evolution. The common carp, Cyprinus carpio, is one of the most important cyprinid species and globally accounts for 10% of freshwater aquaculture production. Here we present a draft genome of domesticated C. carpio (strain Songpu), whose current assembly contains 52,610 protein-coding genes and approximately 92.3% coverage of its paleotetraploidized genome (2n = 100). The latest round of whole-genome duplication has been estimated to have occurred approximately 8.2 million years ago. Genome resequencing of 33 representative individuals from worldwide populations demonstrates a single origin for C. carpio in 2 subspecies (C. carpio Haematopterus and C. carpio carpio). Integrative genomic and transcriptomic analyses were used to identify loci potentially associated with traits including scaling patterns and skin color. In combination with the high-resolution genetic map, the draft genome paves the way for better molecular studies and improved genome-assisted breeding of C. carpio and other closely related species.

Common carp

Bovine genome

10.1038/ng.3098

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The C-Terminal Repeat Units of SpaA Mediate Adhesion of Erysipelothrix rhusiopathiae to Host Cells and Regulate Its Virulence

Biology (2022)

Chao Wu Zhewen Zhang Chao Kang Qiang Zhang Weifeng Zhu

Erysipelothrix rhusiopathiae is a causative agent of erysipelas in animals and erysipeloid in humans. However, current information regarding E. rhusiopathiae pathogenesis remains limited. Previously, we identified two E. rhusiopathiae strains, SE38 and G4T10, which were virulent and avirulent in pigs, respectively. Here, to further study the pathogenic mechanism of E. rhusiopathiae, we sequenced and assembled the genomes of strains SE38 and G4T10, and performed a comparative genomic analysis to identify differences or mutations in virulence-associated genes. Next, we comparatively analyzed 25 E. rhusiopathiae virulence-associated genes in SE38 and G4T10. Compared with that of SE38, the spaA gene of the G4T10 strain lacked 120 bp, encoding repeat units at the C-terminal of SpaA. To examine whether these deletions or splits influence E. rhusiopathiae virulence, these 120 bp were successfully deleted from the spaA gene in strain SE38 by homologous recombination. The mutant strain ΔspaA displayed attenuated virulence in mice and decreased adhesion to porcine iliac artery endothelial cells, which was also observed using the corresponding mutant protein SpaA'. Our results demonstrate that SpaA-mediated adhesion between E. rhusiopathiae and host cells is dependent on its C-terminal repeat units.

Erysipelothrix rhusiopathiae

Strain (injury)

10.3390/biology11071010

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国家基因组科学数据中心：现状及展望

Scientia Sinica Vitae (2024)

Meili Chen Yanqing Wang Rujiao Li Wei Ma Sisi Zhang

10.1360/ssv-2023-0150

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CCLHunter: An efficient toolkit for cancer cell line authentication

Computational and Structural Biotechnology Journal (2023)

Congfan Bu Xinchang Zheng Jialin Mai Zhi Nie Jingyao Zeng

Cancer cell lines are essential in cancer research, yet accurate authentication of these cell lines can be challenging, particularly for consanguineous cell lines with close genetic similarities. We introduce a new Cancer Cell Line Hunter (CCLHunter) method to tackle this challenge. This approach utilizes the information of single nucleotide polymorphisms, expression profiles, and kindred topology to authenticate 1389 human cancer cell lines accurately. CCLHunter can precisely and efficiently authenticate cell lines from consanguineous lineages and those derived from other tissues of the same individual. Our evaluation results indicate that CCLHunter has a complete accuracy rate of 93.27%, with an accuracy of 89.28% even for consanguineous cell lines, outperforming existing methods. Additionally, we provide convenient access to CCLHunter through standalone software and a web server at https://ngdc.cncb.ac.cn/cclhunter.

Cancer cell lines

10.1016/j.csbj.2023.09.040

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Future Directions of the Prokaryotic Chromosome Field

Molecular Microbiology (2025)

Elio A. Abbondanzieri Anjana Badrinarayanan Daniela Barillà Stephen D. Bell Fabian Blombach

In September 2023, the Biology and Physics of Prokaryotic Chromosomes meeting ran at the Lorentz Center in Leiden, The Netherlands. As part of the workshop, those in attendance developed a series of discussion points centered around current challenges for the field, how these might be addressed, and how the field is likely to develop over the next 10 years. The Lorentz Center staff facilitated these discussions via tools aimed at optimizing productive interactions. This Perspective article is a summary of these discussions and reflects the state-of-the-art of the field. It is expected to be of help to colleagues in advancing their own research related to prokaryotic chromosomes and inspiring novel interdisciplinary collaborations. This forward-looking perspective highlights the open questions driving current research and builds on the impressive recent progress in these areas as represented by the accompanying reviews, perspectives, and research articles in this issue. These articles underline the multi-disciplinary nature of the field, the multiple length scales at which chromatin is studied in vitro and in and highlight the differences and similarities of bacterial and archaeal chromatin and chromatin-associated processes.

10.1111/mmi.15347

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A comprehensive evaluation of the potential of three next-generation short-read-based plant pan-genome construction strategies for the identification of novel non-reference sequence

Frontiers in Plant Science (2024)

Meiye Jiang Meili Chen Jingyao Zeng Zhenglin Du Jingfa Xiao

Pan-genome studies are important for understanding plant evolution and guiding the breeding of crops by containing all genomic diversity of a certain species. Three short-read-based strategies for plant pan-genome construction include iterative individual, iteration pooling, and map-to-pan. Their performance is very different under various conditions, while comprehensive evaluations have yet to be conducted nowadays. Here, we evaluate the performance of these three pan-genome construction strategies for plants under different sequencing depths and sample sizes. Also, we indicate the influence of length and repeat content percentage of novel sequences on three pan-genome construction strategies. Besides, we compare the computational resource consumption among the three strategies. Our findings indicate that map-to-pan has the greatest recall but the lowest precision. In contrast, both two iterative strategies have superior precision but lower recall. Factors of sample numbers, novel sequence length, and the percentage of novel sequences’ repeat content adversely affect the performance of all three strategies. Increased sequencing depth improves map-to-pan’s performance, while not affecting the other two iterative strategies. For computational resource consumption, map-to-pan demands considerably more than the other two iterative strategies. Overall, the iterative strategy, especially the iterative pooling strategy, is optimal when the sequencing depth is less than 20X. Map-to-pan is preferable when the sequencing depth exceeds 20X despite its higher computational resource consumption.

Pooling

Identification

10.3389/fpls.2024.1371222

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CCAS: One-stop and comprehensive annotation system for individual cancer genome at multi-omics level

Frontiers in Genetics (2022)

Xinchang Zheng Wenting Zong Zhaohua Li Yingke Ma Yanling Sun

Due to the explosion of cancer genome data and the urgent needs for cancer treatment, it is becoming increasingly important and necessary to easily and timely analyze and annotate cancer genomes. However, tumor heterogeneity is recognized as a serious barrier to annotate cancer genomes at the individual patient level. In addition, the interpretation and analysis of cancer multi-omics data rely heavily on existing database resources that are often located in different data centers or research institutions, which poses a huge challenge for data parsing. Here we present CCAS (Cancer genome Consensus Annotation System, https://ngdc.cncb.ac.cn/ccas/#/home), a one-stop and comprehensive annotation system for the individual patient at multi-omics level. CCAS integrates 20 widely recognized resources in the field to support data annotation of 10 categories of cancers covering 395 subtypes. Data from each resource are manually curated and standardized by using ontology frameworks. CCAS accepts data on single nucleotide variant/insertion or deletion, expression, copy number variation, and methylation level as input files to build a consensus annotation. Outputs are arranged in the forms of tables or figures and can be searched, sorted, and downloaded. Expanded panels with additional information are used for conciseness, and most figures are interactive to show additional information. Moreover, CCAS offers multidimensional annotation information, including mutation signature pattern, gene set enrichment analysis, pathways and clinical trial related information. These are helpful for intuitively understanding the molecular mechanisms of tumors and discovering key functional genes.

Omics

10.3389/fgene.2022.956781

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Applications and challenges of high performance computing in genomics

CCF Transactions on High Performance Computing (2021)

Meiye Jiang Congfan Bu Jingyao Zeng Zhenglin Du Jingfa Xiao

10.1007/s42514-021-00081-w

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Citations (7)