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浙江大学学报（农业与生命科学版）
浙江大学学报(农业与生命科学版)  2015, Vol. 41 Issue (4): 394-406    DOI: 10.3785/j.issn.1008-9209.2014.12.291
生物科学与技术     
基于Illumina平台的厚壳贻贝外套膜转录组从头测序
鲍林飞，王新星，何健瑜，范美华，高鹏，廖智
浙江海洋学院海洋科学与技术学院，海洋生物资源及分子工程实验室，浙江 舟山 316022
Illumina-based transcriptome sequencing of mussel Mytilus coruscus mantle
Bao Linfei, Wang Xinxing, He Jianyu, Fan Meihua, Gao Peng, Liao Zhi
(Laboratory of Marine Biological Source and Molecular Engineering, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, Zhejiang, China)
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摘要： 为了解贻贝贝壳基质蛋白的分子多样性，采用Illumina高通量测序平台，对厚壳贻贝(Mytilus coruscus)外套膜组织开展转录组文库构建及从头测序研究，总计产出6 970 102 920 nt数据,共77 445 588条干净阅读子；经序列拼接与组装，获得厚壳贻贝外套膜转录组单一基因共计106 452个,总长55 222 289 nt，平均长度519 nt，N50达到754 nt；并对上述单一基因进行了生物学功能注释和聚类分析.为进一步挖掘贻贝贝壳基质蛋白相关基因，通过对单一基因的序列注释以及利用已知贝壳基质蛋白序列进行本地搜索，共鉴定出与12种已知贝壳基质蛋白同源的厚壳贻贝外套膜单一基因124条。通过对厚壳贻贝贝壳基质蛋白单一基因进行序列分析和比较，发现厚壳贻贝与其他软体动物，如鲍属、牡蛎属和珠母贝属等在贝壳基质蛋白组成以及序列上具有一定的保守性，暗示着贝壳基质蛋白可能具有共同的起源；同时，首次从贻贝属中发现了3种贝壳棱柱层特异的贝壳基质蛋白单一基因.这为后续贻贝贝壳基质蛋白的大规模鉴定以及对贝壳形成机制的探讨奠定了基础.
Abstract: Mollusk shell is an exoskeleton made up of organic mineral particles and its function is to protect the inner soft body from predators and environmental damage. Due to its superior mechanical properties, such as stiffness, fracture toughness, and tensile strength, the mollusk shell has been investigated as an excellent biomaterial and as biomineralization model over the past decades. Previous studies have revealed that mollusk shell was consist of a mineral phase (calcium carbonate) and an organic matrix (proteins, polysaccharides and lipids). The organic matrix intercalated in a shell is generally assumed to play an important role in crystal nucleation, crystal orientation, crystal size regulation, and crystal polymorphism and contributing to the shell’s mechanical properties. Recent advances on ease and availability of high throughput RNA-sequencing have resulted in a sharp increase in transcriptome data for invertebrate biominerals. However, for -Mytilus, bio-mineralization mechanisms and shell formation were restricted to obtain by deficiency of transcriptome information. 
To understand the molecular diversity of matrix proteins from mussel shell and to develop a transcriptome from the adult mantle tissue of M. coruscus, the transcriptome sequencing of M. coruscus mantle was performed by Illumina platform. A total of 77 445 588 paired end reads amounting to 6 Gb of sequence data were generated and further assembled de novo with Trinity software. A transcriptome was produced after filtering and quality checking, yielded a final set of 106 425 high quality mantle unigenes for analysis. To obtain an integrated view of the transcriptional events of bio-mineralization related processes in M. coruscus mantle, the unique transcript library was screened for reported shell matrix proteins (SMPs). Taken together, 124 unigenes were identified with significant hits (E value <10-5) to 12 reported bio-mineralization related proteins including all known Mytilus SMPs. The most abundant unigenes out of 124 matched ones were annotated as calponin, followed by fibronectin, perlucin, nacrein, and Shematrin. Most of homologues were from Crassostrea, Pinctada, Haliotis, and Mytilus, which showed that M. coruscus mantle unigene encoded putative proteins exhibiting sequence similarities with previously characterized SMPs of other Bivalvias, indicating a common originate for these SMPs. 
In conclusion, a comprehensive transcriptomic resource for the Mytilus SMPs was presented in this paper, providing insight into the protein composition of the shell. The transcriptomic resource can also provide a foundation for further investigations on the formation and bio-mineralization of mussel shell.
出版日期: 2015-07-20
CLC:  Q 71  
通讯作者: 廖智(http://orcid.org/0000-0003-0688-7346)     E-mail: liaozhi@zjou.edu.cn
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鲍林飞
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引用本文:

鲍林飞，王新星，何健瑜，范美华，高鹏，廖智. 基于Illumina平台的厚壳贻贝外套膜转录组从头测序[J]. 浙江大学学报(农业与生命科学版), 2015, 41(4): 394-406.

Bao Linfei, Wang Xinxing, He Jianyu, Fan Meihua, Gao Peng, Liao Zhi. Illumina-based transcriptome sequencing of mussel Mytilus coruscus mantle. Journal of Zhejiang University (Agriculture and Life Sciences), 2015, 41(4): 394-406.

链接本文:

http://www.zjujournals.com/agr/CN/10.3785/j.issn.1008-9209.2014.12.291    或    http://www.zjujournals.com/agr/CN/Y2015/V41/I4/394

[1] 柯野， 曾松荣， 郑秋桦. 总状毛霉丝氨酸蛋白酶基因结构和功能的生物信息学分析[J]. 浙江大学学报(农业与生命科学版), 2012, 38(4): 370-376.