Systematic benchmarking of tools for structural variation detection using short- and long-read sequencing data in pigs

文献类型： 外文期刊

第一作者： He, Sang

作者： He, Sang;Song, Bangmin;Tang, Yueting;Qu, Xiaolu;Li, Xingzheng;Yang, Xintong;Bao, Qi;Tang, Zhonglin;Yi, Guoqiang;He, Sang;Tang, Zhonglin;Yi, Guoqiang;Fang, Lingzhao;Jiang, Jicai;Tang, Zhonglin;Yi, Guoqiang

作者机构：

期刊名称：ISCIENCE （ 影响因子：4.1； 五年影响因子：4.7 ）

ISSN：

年卷期： 2025 年 28 卷 3 期

页码：

收录情况： SCI

摘要： Evaluating diverse structural variation (SV) detection-relevant programs leveraging different algorithms has become a pressing need in humans and farm animals. We addressed this by sequencing five genetically diverse pig individuals (breeds) with short- and long-read DNA-sequencing platforms. We created the SV benchmark set for each breed and assessed the performance of 16 SV calling-relevant tools. Results showed that long-read platforms enabled detecting many SVs missed by short-read platforms with similar precision. Benchmark SVs, mainly 200-500 bp insertions/deletions, had high validation rates. The assembly-based SV calling program SVIM-asm showed superior detection performance and resource consumption. The SVs with more supporting reads, sizes under 1 kb, outside simple repeat area, in low GC content and runs of homozygosity regions, had higher detection accuracy. Alignment-based tools performed well even at 5 3 depth. Our study provides systematic guidance for an optimal SV calling pipeline in pigs and other farm animals.

分类号：

  • 相关文献
作者其他论文 更多>>
  • Complete Genomic Landscape Reveals Hidden Evolutionary History and Selection Signature in Asian Water Buffaloes (Bubalus bubalis)

    作者：Si, Jingfang;Dai, Dongmei;Dhakal, Aashish;Omar, Abdullah Ibne;Zhang, Yi;Gorkhali, Neena Amatya;Sapkota, Saroj;Wang, Mingshan;Wang, Sheng;Wu, Dong-Dong;Kadel, Ram Chandra;Sadaula, Amir;Faruque, Md Omar;Sari, Eka Meutia;Ashari, Hidayat;Dagong, Muhammad Ihsan Andi;Yindee, Marnoch;Rushdi, Hossam E.;Amin, Ahmed;Radwan, Mohamed A.;Elregalaty, Hussein;Pham, Lan Doan;Hulugalla, W. M. M. P.;Silva, G. L. L. Pradeepa;Zheng, Wei;Mansoor, Shahid;Ali, Muhammad Basil;Mansoor, Shahid;Vahidi, Farhad;Al-Bayatti, Sahar Ahmed;Pauciullo, Alfredo;Lenstra, Johannes A.;Barker, J. Stuart F.;Fang, Lingzhao;Han, Jianlin

    关键词：buffalo; CSN2; MC1R; population genomics; selection; single-cell RNA-seq

  • PIGOME: An Integrated and Comprehensive Multi-omics Database for Pig Functional Genomics Studies

    作者：Han, Guohao;Yang, Peng;Li, Qiaowei;Fan, Xinhao;Chen, Ruipu;Yan, Chao;Zeng, Mu;Yang, Yalan;Tang, Zhonglin;Han, Guohao;Yang, Peng;Zhang, Yongjin;Li, Qiaowei;Fan, Xinhao;Chen, Ruipu;Yan, Chao;Zeng, Mu;Yang, Yalan;Tang, Zhonglin;Han, Guohao;Yang, Peng;Zhang, Yongjin;Li, Qiaowei;Fan, Xinhao;Chen, Ruipu;Yan, Chao;Zeng, Mu;Yang, Yalan;Tang, Zhonglin;Yang, Peng;Tang, Zhonglin;Yang, Peng;Li, Qiaowei;Zeng, Mu

    关键词：Pig; Multi-omics; Genome; Gene expression; Epigenetics; Database

  • Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of 232 complex traits in pigs

    作者：Xu, Zhiting;Lin, Qing;Cai, Xiaodian;Zhong, Zhanming;Teng, Jinyan;Zeng, Haonan;Gao, Yahui;Wei, Chen;Zhou, Jun;Zhang, Wenjing;Zhang, Xiaoke;Shi, Shaolei;Wu, Jun;Diao, Shuqi;Liu, Yuqiang;Pan, Xiangchun;Feng, Xueyan;Liu, Ruiqi;Su, Zhanqin;Chang, Chengjie;Zhu, Qianghui;Wu, Yuwei;Zhang, Hao;Yuan, Xiaolong;Li, Jiaqi;Zhang, Zhe;Li, Bingjie;Gao, Yahui;Liu, George E.;Gao, Yahui;Ma, Li;Cai, Zexi;Bai, Zhonghao;Su, Guosheng;Sahana, Goutam;Lund, Mogens Sando;Fang, Lingzhao;Wang, Xiaoqing;Shi, Liangyu;Zhao, Fuping;Wang, Xue;Wang, Yi;Zhang, Zipeng;Ding, Xiangdong;Lin, Yu;Tang, Guoqing;Li, Mingzhou;Li, Xuewei;Liu, Shuli;Yin, Hongwei;Bai, Lijing;Li, Kui;Zhou, Zhongyin;Wang, Qishan;Pan, Yuchun;Xu, Zhong;Peng, Xianwen;Mei, Shuqi;Mo, Delin;Liu, Xiaohong;Chen, Yaosheng;Liu, Yang;Xiang, Ruidong;Xiang, Ruidong;Shen, Xia;Shen, Xia;Shen, Xia;Li, Pinghua;Huang, Ruihua;Li, Pinghua;Huang, Ruihua;Ballester, Maria;Crespo-Piazuelo, Daniel;Amills, Marcel;Clop, Alex;Amills, Marcel;Karlskov-Mortensen, Peter;Fredholm, Merete;Zhang, Qin;Zhao, Yunxiang

    关键词：pig; meta-GWAS; PigGTEx; molQTL; complex traits

  • A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigs

    作者：Yin, Hongwei;Zhao, Qianyi;Yang, Liu;Yi, Guoqiang;Yao, Wenye;Bai, Lijing;Fang, Lingzhao;Yao, Wenye

    关键词：Pig; TADs; Gene expression; Biological functions

  • Single-nucleus transcriptional and chromatin accessible profiles reveal critical cell types and molecular architecture underlying chicken sex determination

    作者：Li, Jianbo;Zhang, Xiuan;Wang, Xiqiong;Zheng, Jiangxia;Li, Junying;Xu, Guiyun;Sun, Congjiao;Yang, Ning;Li, Jianbo;Zhang, Xiuan;Wang, Xiqiong;Zheng, Jiangxia;Li, Junying;Xu, Guiyun;Sun, Congjiao;Yang, Ning;Li, Jianbo;Zhang, Xiuan;Wang, Xiqiong;Zheng, Jiangxia;Li, Junying;Xu, Guiyun;Sun, Congjiao;Yang, Ning;Wang, Zhen;Li, Xingzheng;Yi, Guoqiang

    关键词：Chicken; Embryonic gonad; Sex determination and differentiation; Single-nucleus RNA-seq; Single-nucleus ATAC-seq

  • Multi-dimensional annotation of porcine variants using genomic and epigenomic features in pigs

    作者：Yin, Hongwei;Yang, Liu;Zhao, Qianyi;Yao, Wenye;Bai, Lijing;Li, Kui;Fang, Lingzhao;Yao, Wenye;Groenen, Martien A. M.;Madsen, Ole;Teng, Jinyan;Gao, Yahui;Xu, Zhiting;Lin, Qing;Diao, Shuqi;Li, Jiaqi;Zhang, Zhe;Zhou, Huaijun;Guan, Dailu;Liu, Xiaohong;Zhao, Fuping;Zhou, Zhongyin;Wang, Qishan

    关键词：Genomic variants; Gene expression and splicing; Complex traits; Non-coding regions; Epigenome

  • DPImpute: A Genotype Imputation Framework for Ultra-Low Coverage Whole-Genome Sequencing and its Application in Genomic Selection

    作者：Zheng, Weigang;Wang, Chao;Dong, Wenjun;Liu, Yuwen;Zheng, Weigang;Wang, Chao;Dong, Wenjun;Liu, Yuwen;Zheng, Weigang;Ma, Wenlong;Chen, Zhilong;Wang, Chao;Sun, Tao;Dong, Wenjun;Zhang, Song;Tang, Zhonglin;Li, Kui;Liu, Yuwen;Zheng, Weigang;Ma, Wenlong;Chen, Zhilong;Wang, Chao;Sun, Tao;Dong, Wenjun;Zhang, Song;Tang, Zhonglin;Li, Kui;Liu, Yuwen;Zhang, Wenjing;Tang, Zhonglin;Liu, Yuwen;Zhao, Yunxiang

    关键词：breeding models; genetic screening of embryos; genomic selection; genotype imputation; single cell genotype

微信小程序