NDLI: SNP Mining in Crassostrea gigas EST Data: Transferability to Four Other Crassostrea Species, Phylogenetic Inferences and Outlier SNPs under Selection

Content Provider	PubMed Central
Author	Zhong, Xiaoxiao Li, Qi Yu, Hong Kong, Lingfeng
Editor	Colgan, Donald James
Copyright Year	2014
Abstract	Oysters, with high levels of phenotypic plasticity and wide geographic distribution, are a challenging group for taxonomists and phylogenetics. Our study is intended to generate new EST-SNP markers and to evaluate their potential for cross-species utilization in phylogenetic study of the genus Crassostrea. In the study, 57 novel SNPs were developed from an EST database of C. gigas by the HRM (high-resolution melting) method. Transferability of 377 SNPs developed for C. gigas was examined on four other Crassostrea species: C. sikamea, C. angulata, C. hongkongensis and C. ariakensis. Among the 377 primer pairs tested, 311 (82.5%) primers showed amplification in C. sikamea, 353 (93.6%) in C. angulata, 254 (67.4%) in C. hongkongensis and 253 (67.1%) in C. ariakensis. A total of 214 SNPs were found to be transferable to all four species. Phylogenetic analyses showed that C. hongkongensis was a sister species of C. ariakensis and that this clade was sister to the clade containing C. sikamea, C. angulata and C. gigas. Within this clade, C. gigas and C. angulata had the closest relationship, with C. sikamea being the sister group. In addition, we detected eight SNPs as potentially being under selection by two outlier tests (fdist and hierarchical methods). The SNPs studied here should be useful for genetic diversity, comparative mapping and phylogenetic studies across species in Crassostrea and the candidate outlier SNPs are worth exploring in more detail regarding association genetics and functional studies.
Related Links	http://dx.doi.org/10.1371/journal.pone.0108256
Starting Page	108256
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	9
Volume Number	9
Language	English
Publisher	Public Library of Science
Publisher Date	2014-09-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Genetic Variation and Breeding Signature in Mass Selection Lines of the Pacific Oyster (Crassostrea gigas) Assessed by SNP Markers

Development of Fifty-one novel EST-SSR loci in the Pacific oyster, Crassostrea gigas by data mining from the public EST database

BAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences, and Perspectives for Genetic Mapping

Reactive Oxygen Species in Unstimulated Hemocytes of the Pacific Oyster Crassostrea gigas: A Mitochondrial Involvement

Eight SSR loci from Oyster Crassostrea gigas EST database and cross-species amplification in C. plicatula

Adult Pacific Oyster (Crassostrea gigas) May Have Light Sensitivity

Data from: Genetic evidence for the uncoupling of local aquaculture activities and a population of an invasive species – a case study of Pacific oysters (Crassostrea gigas) (Dataset)

Identification and Functional Characterization of Two Executioner Caspases in Crassostrea gigas

Transcriptomic Responses to Salinity Stress in the Pacific Oyster Crassostrea gigas

SNP Mining in Crassostrea gigas EST Data: Transferability to Four Other Crassostrea Species, Phylogenetic Inferences and Outlier SNPs under Selection

Similar Documents

Genetic Variation and Breeding Signature in Mass Selection Lines of the Pacific Oyster (Crassostrea gigas) Assessed by SNP Markers

Development of Fifty-one novel EST-SSR loci in the Pacific oyster, Crassostrea gigas by data mining from the public EST database

BAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences, and Perspectives for Genetic Mapping

Reactive Oxygen Species in Unstimulated Hemocytes of the Pacific Oyster Crassostrea gigas: A Mitochondrial Involvement

Eight SSR loci from Oyster Crassostrea gigas EST database and cross-species amplification in C. plicatula

Adult Pacific Oyster (Crassostrea gigas) May Have Light Sensitivity

Data from: Genetic evidence for the uncoupling of local aquaculture activities and a population of an invasive species – a case study of Pacific oysters (Crassostrea gigas) (Dataset)

Identification and Functional Characterization of Two Executioner Caspases in Crassostrea gigas

Transcriptomic Responses to Salinity Stress in the Pacific Oyster Crassostrea gigas

SNP Mining in Crassostrea gigas EST Data: Transferability to Four Other Crassostrea Species, Phylogenetic Inferences and Outlier SNPs under Selection