De novo transcriptome assembly of pummelo and molecular marker development

Publication Overview
TitleDe novo transcriptome assembly of pummelo and molecular marker development
AuthorsLiang M, Yang X, Li H, Su S, Yi H, Chai L, Deng X
TypeJournal Article
Journal NamePloS one
Volume10
Issue3
Year2015
Page(s)e0120615
CitationLiang M, Yang X, Li H, Su S, Yi H, Chai L, Deng X. De novo transcriptome assembly of pummelo and molecular marker development. PloS one. 2015; 10(3):e0120615.

Abstract

Pummelo (Citrus grandis) is an important fruit crop worldwide because of its nutritional value. To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. Here, we obtained a 12-Gb transcriptome dataset of pummelo through a mixture of RNA from seven tissues using Illumina pair-end sequencing, assembled into 57,212 unigenes with an average length of 1010 bp. The annotation and classification results showed that a total of 39,584 unigenes had similar hits to the known proteins of four public databases, and 31,501 were classified into 55 Gene Ontology (GO) functional sub-categories. The search for putative molecular markers among 57,212 unigenes identified 10,276 simple sequence repeats (SSRs) and 64,720 single nucleotide polymorphisms (SNPs). High-quality primers of 1174 SSR loci were designed, of which 88.16% were localized to nine chromosomes of sweet orange. Of 100 SSR primers that were randomly selected for testing, 87 successfully amplified clear banding patterns. Of these primers, 29 with a mean PIC (polymorphic information content) value of 0.52 were effectively applied for phylogenetic analysis. Of the 20 SNP primers, 14 primers, including 54 potential SNPs, yielded target amplifications, and 46 loci were verified via Sanger sequencing. This new dataset will be a valuable resource for molecular biology studies of pummelo and provides reliable information regarding SNP and SSR marker development, thus expediting the breeding program of pummelo.

Stocks
This publication contains information about 39 stocks:
Stock NameUniquenameType
Buddha's hand citronBuddha's hand citroncultivar
Chandler pummeloChandler pummelocultivar
Citron1Citron1cultivar
Citron2Citron2cultivar
Clementine tangerineClementine tangerinecultivar
Dianjiangbai pummeloDianjiangbai pummelocultivar
Fenghuang pummeloFenghuang pummelocultivar
Gaoban pummeloGaoban pummelocultivar
Guanxi pummeloGuanxi pummelocultivar
HB PummeloHB Pummelocultivar
Honghe papedaHonghe papedacultivar
HongjuHongjucultivar
Huanonghongxin pummeloHuanonghongxin pummelocultivar
HuyouHuyoucultivar
Ichang papedaIchang papedacultivar
Jincheng orangeJincheng orangecultivar
Liangping pummeloLiangping pummelocultivar
LimoniaLimoniacultivar
Lisbon lemonLisbon lemonbreeding_research_material
Longan pummeloLongan pummelocultivar
Majia pummeloMajia pummelocultivar
Mexican limeMexican limebreeding_research_material
Nanfeng mandarinNanfeng mandarincultivar
Pingshan pummeloPingshan pummelocultivar
Qingjia ponkanQingjia ponkancultivar

Pages

Properties
Additional details for this publication include:
Property NameValue
Publication ModelElectronic-eCollection
ISSN1932-6203
eISSN1932-6203
Publication Date2015
Journal AbbreviationPLoS ONE
DOI10.1371/journal.pone.0120615
Elocation10.1371/journal.pone.0120615
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
Journal CountryUnited States
Cross References
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DatabaseAccession
PMID: PubMedPMID:25799271