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
Rough LemonRough Lemonaccession
ShatianShatianaccession
Shimennongjia pummeloShimennongjia pummeloaccession
Shuijing pummeloShuijing pummeloaccession
Siji pummeloSiji pummeloaccession
Sour OrangeSour Orangeaccession
Star RubyStar Rubyaccession
SuanyouSuanyouaccession
Washington navel orangeWashington navel orangeaccession
Wendan pummeloWendan pummeloaccession
Wusuan pummeloWusuan pummeloaccession
Zhenban pummeloZhenban pummeloaccession
Zipi pummeloZipi pummeloaccession
Trifoliate orangeTrifoliate orangeaccession

Pages

Features
This publication contains information about 6,177 features:
Feature NameUniquenameType
CgSSR0017-1CgSSR0017-1genetic_marker
CgSSR0017-2CgSSR0017-2genetic_marker
CgSSR0017-3CgSSR0017-3genetic_marker
CgSSR0017-4CgSSR0017-4genetic_marker
CgSSR0017-5CgSSR0017-5genetic_marker
CgSSR0123-1CgSSR0123-1genetic_marker
CgSSR0123-2CgSSR0123-2genetic_marker
CgSSR0123-3CgSSR0123-3genetic_marker
CgSSR0124-1CgSSR0124-1genetic_marker
CgSSR0124-2CgSSR0124-2genetic_marker
CgSSR0124-3CgSSR0124-3genetic_marker
CgSSR0124-4CgSSR0124-4genetic_marker
CgSSR0124-5CgSSR0124-5genetic_marker
CgSSR0125-1CgSSR0125-1genetic_marker
CgSSR0125-2CgSSR0125-2genetic_marker
CgSSR0125-3CgSSR0125-3genetic_marker
CgSSR0125-4CgSSR0125-4genetic_marker
CgSSR0125-5CgSSR0125-5genetic_marker
CgSSR0153-1CgSSR0153-1genetic_marker
CgSSR0153-2CgSSR0153-2genetic_marker
CgSSR0153-3CgSSR0153-3genetic_marker
CgSSR0153-4CgSSR0153-4genetic_marker
CgSSR0153-5CgSSR0153-5genetic_marker
CgSSR0155-1CgSSR0155-1genetic_marker
CgSSR0155-2CgSSR0155-2genetic_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