Telomere-to-telomere gap-free genome assembly of the endangered Yangtze finless porpoise and East Asian finless porpoise
文献类型： 外文期刊
作者： Yin, Denghua 1 ; Chen, Chunhai 2 ; Lin, Danqing 1 ; Hua, Zhong 1 ; Ying, Congping 1 ; Zhang, Jialu 1 ; Zhao, Chenxi 2 ; Liu, Yan 1 ; Cao, Zhichen 3 ; Zhang, Han 3 ; Wang, Chenhe 2 ; Liang, Liping 2 ; Xu, Pao 1 ; Jian, Jianbo 2 ; Liu, Kai 1 ;
作者机构： 1.Chinese Acad Fishery Sci, Freshwater Fisheries Res Ctr, Key Lab Freshwater Fisheries & Germplasm Resources, Minist Agr & Rural Affairs, Wuxi 214081, Peoples R China
2.BGI Genom, Shenzhen 518083, Peoples R China
3.Shanghai Ocean Univ, Natl Demonstrat Ctr Expt Fisheries Sci Educ, Shanghai 201306, Peoples R China
4.Nanjing Agr Univ, Wuxi Fisheries Coll, Wuxi 214081, Peoples R China
5.Shantou Univ, Guangdong Prov Key Lab Marine Biotechnol, Shantou 515063, Peoples R China
关键词： telomere-to-telomere; genome assembly; Yangtze finless porpoise; gap-free; HiFi sequencing; Hi-C sequencing
期刊名称：GIGASCIENCE （ 影响因子：3.9； 五年影响因子：11.1 ）
ISSN： 2047-217X
年卷期： 2024 年 13 卷
页码：
收录情况： SCI
摘要： Background The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis, YFP) and the East Asian finless porpoise (Neophocaena asiaeorientalis sunameri, EFP) are 2 subspecies of the narrow-ridged finless porpoise that live in freshwater and saltwater, respectively. The main objective of this study was to provide contiguous chromosome-level genome assemblies for YFP and EFP.Results Here, we generated and upgraded the genomes of YFP and EFP at the telomere-to-telomere level through the integration of PacBio HiFi long reads, ultra-long ONT reads, and Hi-C sequencing data with a total size of 2.48 Gb and 2.50 Gb, respectively. The scaffold N50 of 2 genomes was 125.12 Mb (YFP) and 128 Mb (EFP) with 1 contig for 1 chromosome. The telomere repeat and centromere position were clearly identified in both YFP and EFP genomes. In total, 5,480 newfound genes were detected in the YFP genome, including 56 genes located in the newly identified centromere regions. Additionally, synteny blocks, structural similarities, phylogenetic relationships, gene family expansion, and inference of selection were studied in connection with the genomes of other related mammals.Conclusions Our research findings provide evidence for the gradual adaptation of EFP in a marine environment and the potential sensitivity of YFP to genetic damage. Compared to the 34 cetacean genomes sourced from public databases, the 2 new assemblies demonstrate superior continuity with the longest contig N50 and scaffold N50 values, as well as the lowest number of contigs. The improvement of telomere-to-telomere gap-free reference genome resources supports conservation genetics and population management for finless porpoises.
- 相关文献
作者其他论文 更多>>
-
Temporal-Spatial Variations in Physicochemical Factors and Assessing Water Quality Condition in River-Lake System of Chaohu Lake Basin, China
作者：Wu, Li;Wang, Ziqi;Yang, Yujie;Sang, Rui;Zhu, Haoyue;Wang, Xitong;Pang, Yuqing;Tong, Jiangshan;Liu, Xiangting;Ma, Mingyue;Wang, Qianqian;Ma, Kaijun;Liu, Fan;Liu, Kai;Liu, Kai
关键词：water quality index; trophic level index; Chaohu Lake; spatiotemporal water quality pattern
-
Genetic Diversity and Population Structure of Largefin Longbarbel Catfish (Hemibagrus macropterus) Inferred by mtDNA and Microsatellite DNA Markers
作者：Hou, Yanling;Ye, Huan;Li, Chuangju;Ye, Huan;Yue, Huamei;Li, Junyi;Huang, Ling;Qu, Ziling;Ruan, Rui;Li, Chuangju;Lin, Danqing;Liang, Zhiqiang;Xie, Yong
关键词：largefin longbarbel catfish; mitochondrial cytochrome
b (Cytb ); microsatellite; conservation genetics -
Chromosome-level genome assembly of the freshwater bivalve Anodonta woodiana
作者：Chen, Xiubao;Jiang, Tao;Xue, Junren;Liu, Kai;Gu, Mengying;Wang, Meiyi
关键词：
-
Yam glycoprotein promotes white adipose tissue browning, enhances metabolism, and boosts exercise tolerance in mice: A novel Strategy for metabolic disease prevention
作者：Li, Weiye;Shi, Jian;Mei, Meijuan;Qiu, Hongyong;Liu, Yan;Liu, Chunhong;Li, Weiye;Shi, Jian;Mei, Meijuan;Qiu, Hongyong;Liu, Yan;Liu, Chunhong;Rang, Yifeng;Liang, Boji
关键词：Browning of white adipose tissue; Muscle-fat crosstalk; exercise tolerance; Lipid metabolism; Obesity; IL-6
-
Estuarine plastic dynamics: Analyzing export patterns from a typical semi-enclosed bay in Asia
作者：Wei, Nian;Lu, Jungang;Jiao, Meng;Zong, Changxing;Zhang, Feng;Jiang, Chunhua;Zhu, Lixin;Liu, Kai;Cui, Tiefeng;Li, Daoji;Wei, Nian;Lu, Jungang;Jiao, Meng;Zong, Changxing;Zhang, Feng;Jiang, Chunhua;Zhu, Lixin;Liu, Kai;Cui, Tiefeng;Li, Daoji;Wei, Nian;Lu, Jungang;Jiao, Meng;Zong, Changxing;Zhang, Feng;Jiang, Chunhua;Zhu, Lixin;Liu, Kai;Cui, Tiefeng;Li, Daoji;Wei, Nian;Liu, Kai
关键词：Microplastic (MPs); Spatial distribution; Principal Coordinate Analysis (PCoA); Semi-enclosed bays; Hydrodynamic processes; Pollution management
-
Integrating population genetics and species distribution models to predict red seabream distribution under climate change
作者：Shan, Binbin;Zhang, Mengyi;Wang, Liangming;Liu, Yan;Yan, Changping;Liu, Manting;Xie, Qijian;Sun, Dianrong;Shan, Binbin;Zhang, Mengyi;Wang, Liangming;Liu, Yan;Yan, Changping;Liu, Manting;Xie, Qijian;Sun, Dianrong;Huang, Wenhao;Zhao, Linlin;Huang, Wenhao;Zou, Jianwei
关键词：Global climate change; Pagrus major; Mitochondrial DNA; Migration; Marine fishery resources management
-
The molecular mechanism of ovary development in Thamnaconus septentrionalis induced by rising temperature via transcriptomics and metabolomics analysis
作者：Liu, Yan;Xu, Wengang;Zhang, Xueli;Wang, Jiulong;Liu, Liming;Liu, Yan;Xu, Wengang;Wang, Jiulong;Liu, Liming;Liu, Yan;Xu, Wengang;Wang, Jiulong;Liu, Liming;Chen, Xiaoling;Yu, Xiaoyan;Zeng, Jun;Wu, Yanqing
关键词：
Thamnaconus septentrionalis ; ovary development; molecular mechanism; transcriptomics; metabolomics
