A Barakat

A Conesa

A Mortazavi

AJ Molendijk

AP Weber

B Wang

Boping Fang

C Iseli

C Sun

CA Maher

DA Hahn

DL Wheeler

DR Bentley

E Meyer

E Novaes

F Alagna

GM Cordeiro

GZ Kang

H Li

J Wang

J Ye

JC Vega-Arreguin

JC Vera

Jingyi Chen

JJ Hu

JK Yu

JR Andersen

K Nobuta

L Gilbert

LC Hannah

Lifei Huang

LJ Collins

M Bevan

M Cameron

M Chatterjee

M Kanehisa

M Tanaka

M Trick

M Zagrobelny

MC Hale

MC Saha

MD Bennett

MF Berger

MI Buteler

ML Metzker

MV Ruchko

NH Roosens

NM Jacob

O Morozova

PA Pevzner

PK Gupta

PK Wall

R Li

R Rosenkranz

R Schafleitner

RK Varshney

S Biastoff

S Comparot-Moss

SF Altschul

SK Hahn

T Thiel

T Wu

TL Parchman

U Nagalakshmi

VV Baranenko

W Wang

WB Barbazuk

Xinliang Chen

Xiongjian Zhang

XW Wang

Yujun Li

YW Huang

Z Hegedus

Zhangying Wang

Zhongxia Luo

BMC Genomics

English

PubMed

Springer - Publisher Connector

De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas)

Abstract
          
            Background
            The tuberous root of sweetpotato is an important agricultural and biological organ. There are not sufficient transcriptomic and genomic data in public databases for understanding of the molecular mechanism underlying the tuberous root formation and development. Thus, high throughput transcriptome sequencing is needed to generate enormous transcript sequences from sweetpotato root for gene discovery and molecular marker development.
          
          
            Results
            In this study, more than 59 million sequencing reads were generated using Illumina paired-end sequencing technology. De novo assembly yielded 56,516 unigenes with an average length of 581 bp. Based on sequence similarity search with known proteins, a total of 35,051 (62.02%) genes were identified. Out of these annotated unigenes, 5,046 and 11,983 unigenes were assigned to gene ontology and clusters of orthologous group, respectively. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) indicated that 17,598 (31.14%) unigenes were mapped to 124 KEGG pathways, and 11,056 were assigned to metabolic pathways, which were well represented by carbohydrate metabolism and biosynthesis of secondary metabolite. In addition, 4,114 cDNA SSRs (cSSRs) were identified as potential molecular markers in our unigenes. One hundred pairs of PCR primers were designed and used for validation of the amplification and assessment of the polymorphism in genomic DNA pools. The result revealed that 92 primer pairs were successfully amplified in initial screening tests.
          
          
            Conclusion
            This study generated a substantial fraction of sweetpotato transcript sequences, which can be used to discover novel genes associated with tuberous root formation and development and will also make it possible to construct high density microarrays for further characterization of gene expression profiles during these processes. Thousands of cSSR markers identified in the present study can enrich molecular markers and will facilitate marker-assisted selection in sweetpotato breeding. Overall, these sequences and markers will provide valuable resources for the sweetpotato community. Additionally, these results also suggested that transcriptome analysis based on Illumina paired-end sequencing is a powerful tool for gene discovery and molecular marker development for non-model species, especially those with large and complex genome.
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De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas)

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