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 citronaccession
Chandler pummeloChandler pummeloaccession
Citron1Citron1accession
Citron2Citron2accession
Clementine tangerineClementine tangerineaccession
Dianjiangbai pummeloDianjiangbai pummeloaccession
Fenghuang pummeloFenghuang pummeloaccession
Gaoban pummeloGaoban pummeloaccession
Guanxi pummeloGuanxi pummeloaccession
HB PummeloHB Pummeloaccession
Honghe papedaHonghe papedaaccession
HongjuHongjuaccession
Huanonghongxin pummeloHuanonghongxin pummeloaccession
HuyouHuyouaccession
Ichang papedaIchang papedaaccession
Jincheng orangeJincheng orangeaccession
Liangping pummeloLiangping pummeloaccession
LimoniaLimoniaaccession
Lisbon lemonLisbon lemonaccession
Longan pummeloLongan pummeloaccession
Majia pummeloMajia pummeloaccession
Mexican limeMexican limeaccession
Nanfeng mandarinNanfeng mandarinaccession
Pingshan pummeloPingshan pummeloaccession
Qingjia ponkanQingjia ponkanaccession

Pages

Features
This publication contains information about 6,177 features:
Feature NameUniquenameType
CgSSR0443-2CgSSR0443-2genetic_marker
CgSSR0443-3CgSSR0443-3genetic_marker
CgSSR0443-4CgSSR0443-4genetic_marker
CgSSR0443-5CgSSR0443-5genetic_marker
CgSSR0534-1CgSSR0534-1genetic_marker
CgSSR0534-2CgSSR0534-2genetic_marker
CgSSR0534-3CgSSR0534-3genetic_marker
CgSSR0534-4CgSSR0534-4genetic_marker
CgSSR0534-5CgSSR0534-5genetic_marker
CgSSR0544-1CgSSR0544-1genetic_marker
CgSSR0544-2CgSSR0544-2genetic_marker
CgSSR0544-3CgSSR0544-3genetic_marker
CgSSR0544-4CgSSR0544-4genetic_marker
CgSSR0544-5CgSSR0544-5genetic_marker
CgSSR0579-1CgSSR0579-1genetic_marker
CgSSR0579-2CgSSR0579-2genetic_marker
CgSSR0579-3CgSSR0579-3genetic_marker
CgSSR0579-4CgSSR0579-4genetic_marker
CgSSR0579-5CgSSR0579-5genetic_marker
CgSSR0609-1CgSSR0609-1genetic_marker
CgSSR0609-2CgSSR0609-2genetic_marker
CgSSR0609-3CgSSR0609-3genetic_marker
CgSSR0609-4CgSSR0609-4genetic_marker
CgSSR0609-5CgSSR0609-5genetic_marker
CgSSR0612-1CgSSR0612-1genetic_marker

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
This publication is also available in the following databases:
DatabaseAccession
PMID: PubMedPMID:25799271