Chromosome-level genome assembly of the razor clam Sinonovacula constricta (Lamarck, 1818)

被引:51
作者
Ran, Zhaoshou [1 ,2 ]
Li, Zhenzhen [3 ]
Yan, Xiaojun [2 ]
Liao, Kai [1 ]
Kong, Fei [1 ]
Zhang, Lin [1 ]
Cao, Jiayi [1 ]
Zhou, Chengxu [1 ]
Zhu, Peng [1 ]
He, Shan [1 ]
Huang, Wanlong [3 ]
Xu, Jilin [1 ,4 ]
机构
[1] Ningbo Univ, Minist Educ China, Key Lab Appl Marine Biotechnol, Ningbo 315211, Zhejiang, Peoples R China
[2] Ningbo Univ, Collaborat Innovat Ctr Zhejiang Marine High Effic, Ningbo 315211, Zhejiang, Peoples R China
[3] Novogene Bioinformat Inst, Beijing, Peoples R China
[4] Fujian Baozhi Aquat Sci & Technol Co LTD, Zhangzhou, Peoples R China
关键词
aquatic ecology; chromosome-level genome assembly; evolutionary adaptation; Sinonovacula constricta; TRANSCRIPTOME ANALYSIS; PEARL OYSTER; GENE; PREDICTION; IDENTIFICATION; ALIGNMENT; PROGRAM; POPULATIONS; ADAPTATION; FRAMEWORK;
D O I
10.1111/1755-0998.13086
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Bivalves, a highly diverse and the most evolutionarily successful class of invertebrates native to aquatic habitats, provide valuable molecular resources for understanding the evolutionary adaptation and aquatic ecology. Here, we reported a high-quality chromosome-level genome assembly of the razor clam Sinonovacula constricta using Pacific Bioscience single-molecule real-time sequencing, Illumina paired-end sequencing, 10X Genomics linked-reads and Hi-C reads. The genome size was 1,220.85 Mb, containing scaffold N50 of 65.93 Mb and contig N50 of 976.94 Kb. A total of 899 complete (91.92%) and seven partial (0.72%) matches of the 978 metazoa Benchmarking Universal Single-Copy Orthologs were determined in this genome assembly. And Hi-C scaffolding of the genome resulted in 19 pseudochromosomes. A total of 28,594 protein-coding genes were predicted in the S. constricta genome, of which 25,413 genes (88.88%) were functionally annotated. In addition, 39.79% of the assembled genome was composed of repetitive sequences, and 4,372 noncoding RNAs were identified. The enrichment analyses of the significantly expanded and contracted genes suggested an evolutionary adaptation of S. constricta to highly stressful living environments. In summary, the genomic resources generated in this work not only provide a valuable reference genome for investigating the molecular mechanisms of S. constricta biological functions and evolutionary adaptation, but also facilitate its genetic improvement and disease treatment. Meanwhile, the obtained genome greatly improves our understanding of the genetics of molluscs and their comparative evolution.
引用
收藏
页码:1647 / 1658
页数:12
相关论文
共 78 条
[1]   In vitro, long-range sequence information for de novo genome assembly via transposase contiguity [J].
Adey, Andrew ;
Kitzman, Jacob O. ;
Burton, Joshua N. ;
Daza, Riza ;
Kumar, Akash ;
Christiansen, Lena ;
Ronaghi, Mostafa ;
Amini, Sasan ;
Gunderson, Kevin L. ;
Steemers, Frank J. ;
Shendure, Jay .
GENOME RESEARCH, 2014, 24 (12) :2041-2049
[2]   Pinctada radiata (pearl oyster): A bioindicator for metal pollution monitoring in the Qatari waters (Arabian Gulf) [J].
Al-Madfa, H ;
Abdel-Moati, MAR ;
Al-Gimaly, FH .
BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY, 1998, 60 (02) :245-251
[3]   BASIC LOCAL ALIGNMENT SEARCH TOOL [J].
ALTSCHUL, SF ;
GISH, W ;
MILLER, W ;
MYERS, EW ;
LIPMAN, DJ .
JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410
[4]  
Apweiler R, 2004, NUCLEIC ACIDS RES, V32, pD115, DOI [10.1093/nar/gkw1099, 10.1093/nar/gkh131]
[5]   Repbase Update, a database of repetitive elements in eukaryotic genomes [J].
Bao, Weidong ;
Kojima, Kenji K. ;
Kohany, Oleksiy .
MOBILE DNA, 2015, 6
[6]   Tandem repeats finder: a program to analyze DNA sequences [J].
Benson, G .
NUCLEIC ACIDS RESEARCH, 1999, 27 (02) :573-580
[7]   Discovering and detecting transposable elements in genome sequences [J].
Bergman, Casey M. ;
Quesneville, Hadi .
BRIEFINGS IN BIOINFORMATICS, 2007, 8 (06) :382-392
[8]   GeneWise and genomewise [J].
Birney, E ;
Clamp, M ;
Durbin, R .
GENOME RESEARCH, 2004, 14 (05) :988-995
[9]   Prediction of complete gene structures in human genomic DNA [J].
Burge, C ;
Karlin, S .
JOURNAL OF MOLECULAR BIOLOGY, 1997, 268 (01) :78-94
[10]   BIOLOGICAL MONITORING OF AMBIENT WATER-QUALITY - THE CASE FOR USING BIVALVES AS SENTINEL ORGANISMS FOR MONITORING PETROLEUM POLLUTION IN COASTAL WATERS [J].
BURNS, KA ;
SMITH, JL .
ESTUARINE COASTAL AND SHELF SCIENCE, 1981, 13 (04) :433-443