Transcriptome Sequencing and Characterization of Japanese Scallop Patinopecten yessoensis from Different Shell Color Lines

Transcriptome Sequencing and Characterization of Japanese Scallop Patinopecten yessoensis from Different Shell Color Lines

Shell color is an important trait that is used in breeding the Japanese scallop Patinopecten yessoensis, the most economically important scallop species in China. We constructed four transcriptome libraries from different shell color lines of P. yessoensis: the left and right shell mantles of ordina...

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Main Authors: Ding, Jun, Zhao, Le, Chang, Yaqing, Zhao, Wenming, Du, Zhenlin, Hao, Zhenlin
Format: Online
Language:English
Published: Public Library of Science 2015
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332496/
id pubmed-4332496
recordtype oai_dc
spelling pubmed-43324962015-02-24 Transcriptome Sequencing and Characterization of Japanese Scallop Patinopecten yessoensis from Different Shell Color Lines Ding, Jun Zhao, Le Chang, Yaqing Zhao, Wenming Du, Zhenlin Hao, Zhenlin Research Article Shell color is an important trait that is used in breeding the Japanese scallop Patinopecten yessoensis, the most economically important scallop species in China. We constructed four transcriptome libraries from different shell color lines of P. yessoensis: the left and right shell mantles of ordinary strains of P. yessoensis and the left shell mantles of the ‘Ivory’ and ‘Maple’ strains. These four libraries were paired-end sequenced using the Illumina HiSeq 2000 platform and contained 54,802,692 sequences, 40,798,962 sequences, 74,019,262 sequences, and 44,466,166 sequences, respectively. A total of 214,087,082 expressed sequence tags were assembled into 73,522 unigenes with an average size of 1,163 bp. When the data were compared against the public Nr and Swiss-Prot databases using BlastX, nearly 30.55% (22,458) of the unigenes were significantly matched to known unique proteins. Gene Ontology annotation and pathway mapping analysis using the Kyoto Encyclopedia of Genes and Genomes categorized unigenes according to their diverse biological functions and processes and identified candidate genes that were potentially involved in growth, pigmentation, metal transcription, and immunity. Expression profile analysis was performed on all four libraries and many differentially expressed genes were identified. In addition, 5,772 simple sequence repeats were obtained from the P. yessoensis transcriptomes, and 464,197, 395,646, and 310,649 single nucleotide polymorphisms were revealed in the ordinary strains, the ‘Ivory’ strain, and the ‘Maple’ strain, respectively. These results provide valuable information for future genomic studies on P. yessoensis and improve our understanding of the molecular mechanisms involved in the growth, immunity, shell coloring, and shell biomineralization of this species. These resources also may be used in a variety of applications, such as trait mapping, marker-assisted breeding, studies of population genetics and genomics, and work on functional genomics. Public Library of Science 2015-02-13 /pmc/articles/PMC4332496/ /pubmed/25680107 http://dx.doi.org/10.1371/journal.pone.0116406 Text en © 2015 Ding et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author Ding, Jun
Zhao, Le
Chang, Yaqing
Zhao, Wenming
Du, Zhenlin
Hao, Zhenlin
spellingShingle Ding, Jun
Zhao, Le
Chang, Yaqing
Zhao, Wenming
Du, Zhenlin
Hao, Zhenlin
Transcriptome Sequencing and Characterization of Japanese Scallop Patinopecten yessoensis from Different Shell Color Lines
author_facet Ding, Jun
Zhao, Le
Chang, Yaqing
Zhao, Wenming
Du, Zhenlin
Hao, Zhenlin
author_sort Ding, Jun
title Transcriptome Sequencing and Characterization of Japanese Scallop Patinopecten yessoensis from Different Shell Color Lines
title_short Transcriptome Sequencing and Characterization of Japanese Scallop Patinopecten yessoensis from Different Shell Color Lines
title_full Transcriptome Sequencing and Characterization of Japanese Scallop Patinopecten yessoensis from Different Shell Color Lines
title_fullStr Transcriptome Sequencing and Characterization of Japanese Scallop Patinopecten yessoensis from Different Shell Color Lines
title_full_unstemmed Transcriptome Sequencing and Characterization of Japanese Scallop Patinopecten yessoensis from Different Shell Color Lines
title_sort transcriptome sequencing and characterization of japanese scallop patinopecten yessoensis from different shell color lines
description Shell color is an important trait that is used in breeding the Japanese scallop Patinopecten yessoensis, the most economically important scallop species in China. We constructed four transcriptome libraries from different shell color lines of P. yessoensis: the left and right shell mantles of ordinary strains of P. yessoensis and the left shell mantles of the ‘Ivory’ and ‘Maple’ strains. These four libraries were paired-end sequenced using the Illumina HiSeq 2000 platform and contained 54,802,692 sequences, 40,798,962 sequences, 74,019,262 sequences, and 44,466,166 sequences, respectively. A total of 214,087,082 expressed sequence tags were assembled into 73,522 unigenes with an average size of 1,163 bp. When the data were compared against the public Nr and Swiss-Prot databases using BlastX, nearly 30.55% (22,458) of the unigenes were significantly matched to known unique proteins. Gene Ontology annotation and pathway mapping analysis using the Kyoto Encyclopedia of Genes and Genomes categorized unigenes according to their diverse biological functions and processes and identified candidate genes that were potentially involved in growth, pigmentation, metal transcription, and immunity. Expression profile analysis was performed on all four libraries and many differentially expressed genes were identified. In addition, 5,772 simple sequence repeats were obtained from the P. yessoensis transcriptomes, and 464,197, 395,646, and 310,649 single nucleotide polymorphisms were revealed in the ordinary strains, the ‘Ivory’ strain, and the ‘Maple’ strain, respectively. These results provide valuable information for future genomic studies on P. yessoensis and improve our understanding of the molecular mechanisms involved in the growth, immunity, shell coloring, and shell biomineralization of this species. These resources also may be used in a variety of applications, such as trait mapping, marker-assisted breeding, studies of population genetics and genomics, and work on functional genomics.
publisher Public Library of Science
publishDate 2015
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332496/
_version_ 1613189835086888960

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