title: A de novo transcriptome of the noble scallop, Chlamys nobilis, focusing on mining transcripts for carotenoid-based coloration.
abstract: BACKGROUND
  The noble scallop Chlamys nobilis Reeve displays polymorphism in shell and muscle colors. Previous research showed that the orange scallops with orange shell and muscle had a significantly higher carotenoid content than the brown ones with brown shell and white muscle. There is currently a need to identify candidate genes associated with carotenoid-based coloration.
  
  
  RESULTS
  In the present study, 454 GS-FLX sequencing of noble scallop transcriptome yielded 1,181,060 clean sequence reads, which were assembled into 49,717 isotigs, leaving 110,158 reads as the singletons. Of the 159,875 unique sequences, 11.84% isotigs and 9.35% singletons were annotated. Moreover, 3,844 SSRs and over 120,000 high confidence variants (SNPs and INDELs) were identified. Especially, one class B scavenge receptor termed SRB-like-3 was discovered to express only in orange scallops and absent in brown ones, suggesting a significant association with high carotenoid content. Down-regulation of SRB-like-3 mRNA by RNA interference remarkably decreased blood carotenoid, providing compelling evidence that SRB-like-3 is an ideal candidate gene controlling carotenoid deposition and determining orange coloration.
  
  
  CONCLUSIONS
  Transcriptome analysis of noble scallop reveals a novel scavenger receptor significantly associated with orange scallop rich in carotenoid content. Our findings pave the way for further functional elucidation of this gene and molecular basis of carotenoid deposition in orange scallop.
authors: Key Laboratory of Marine Biotechnology of Guangdong Province, Shantou University, Shantou, 515063, China. 08glliu@stu.edu.cn.|Department of Education of Guangdong Province, Mariculture Research Center for Subtropical Shellfish & Algae, Shantou, 515063, China. 08glliu@stu.edu.cn.|Sanya Institute of Deep-sea Science and Engineering, Chinese Academy of Science, Sanya, 572000, China. 08glliu@stu.edu.cn.
authors: Helu
authors: H
authors: Liu
authors: Key Laboratory of Marine Biotechnology of Guangdong Province, Shantou University, Shantou, 515063, China. hpzheng@stu.edu.cn.|Department of Education of Guangdong Province, Mariculture Research Center for Subtropical Shellfish & Algae, Shantou, 515063, China. hpzheng@stu.edu.cn.
authors: Huaiping
authors: H
authors: Zheng
authors: Key Laboratory of Marine Biotechnology of Guangdong Province, Shantou University, Shantou, 515063, China. 13hkzhang@stu.edu.cn.|Department of Education of Guangdong Province, Mariculture Research Center for Subtropical Shellfish & Algae, Shantou, 515063, China. 13hkzhang@stu.edu.cn.
authors: Hongkuan
authors: H
authors: Zhang
authors: Key Laboratory of Marine Biotechnology of Guangdong Province, Shantou University, Shantou, 515063, China. 11lhdeng1@stu.edu.cn.|Department of Education of Guangdong Province, Mariculture Research Center for Subtropical Shellfish & Algae, Shantou, 515063, China. 11lhdeng1@stu.edu.cn.
authors: Longhui
authors: L
authors: Deng
authors: Key Laboratory of Marine Biotechnology of Guangdong Province, Shantou University, Shantou, 515063, China. whliu@stu.edu.cn.|Department of Education of Guangdong Province, Mariculture Research Center for Subtropical Shellfish & Algae, Shantou, 515063, China. whliu@stu.edu.cn.
authors: Wenhua
authors: W
authors: Liu
authors: Key Laboratory of Marine Biotechnology of Guangdong Province, Shantou University, Shantou, 515063, China. sqw@stu.edu.cn.|Department of Education of Guangdong Province, Mariculture Research Center for Subtropical Shellfish & Algae, Shantou, 515063, China. sqw@stu.edu.cn.
authors: Shuqi
authors: S
authors: Wang
authors: Key Laboratory of Marine Biotechnology of Guangdong Province, Shantou University, Shantou, 515063, China. 11fmeng@stu.edu.cn.|Department of Education of Guangdong Province, Mariculture Research Center for Subtropical Shellfish & Algae, Shantou, 515063, China. 11fmeng@stu.edu.cn.
authors: Fang
authors: F
authors: Meng
authors: Key Laboratory of Marine Biotechnology of Guangdong Province, Shantou University, Shantou, 515063, China. 11yjwang@stu.edu.cn.|Department of Education of Guangdong Province, Mariculture Research Center for Subtropical Shellfish & Algae, Shantou, 515063, China. 11yjwang@stu.edu.cn.
authors: Yajun
authors: Y
authors: Wang
authors: Key Laboratory of Marine Biotechnology of Guangdong Province, Shantou University, Shantou, 515063, China. 12zcguo1@stu.edu.cn.|Department of Education of Guangdong Province, Mariculture Research Center for Subtropical Shellfish & Algae, Shantou, 515063, China. 12zcguo1@stu.edu.cn.
authors: Zhicheng
authors: Z
authors: Guo
authors: Key Laboratory of Marine Biotechnology of Guangdong Province, Shantou University, Shantou, 515063, China. lisk@stu.edu.cn.|Department of Education of Guangdong Province, Mariculture Research Center for Subtropical Shellfish & Algae, Shantou, 515063, China. lisk@stu.edu.cn.
authors: Shengkang
authors: S
authors: Li
authors: Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China. gfzhang@qdio.ac.cn.
authors: Guofan
authors: G
authors: Zhang
mesh_terms: D000818:Animals; D002338:Carotenoids / Q000235:genetics*; D005786:Gene Expression Regulation; D054643:INDEL Mutation; D058977:Molecular Sequence Annotation; D049897:Pectinidae / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics; D017422:Sequence Analysis, DNA; D012880:Skin Pigmentation / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*
chemical_list: D012333:RNA, Messenger; D002338:Carotenoids
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