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De novo sequencing and a comprehensive analysis of purple sweet potato (Impomoea batatas L.) transcriptome

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Abstract

High-throughput RNA sequencing was performed for comprehensively analyzing the transcriptome of the purple sweet potato. A total of 58,800 unigenes were obtained and ranged from 200 nt to 10,380 nt with an average length of 476 nt. The average expression of one unigene was 34 reads per kb per million reads (RPKM) with a maximum expression of 1,935 RPKM. At least 40,280 (68.5%) unigenes were identified to be protein-coding genes, in which 11,978 and 5,184 genes were homologous to Arabidopsis and rice proteins, respectively. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analysis showed that 19,707 (33.5%) unigenes were classified to 1,807 terms of GO including molecular functions, biological processes, and cellular components and 9,970 (17.0%) unigenes were enriched to 11,119 KEGG pathways. We found that at least 3,553 genes may be involved in the biosynthesis pathways of starch, alkaloids, anthocyanin pigments, and vitamins. Additionally, 851 potential simple sequence repeats (SSRs) were identified in all unigenes. Transcriptome sequencing on tuberous roots of the sweet potato yielded substantial transcriptional sequences and potentially useful SSR markers which provide an important data source for sweet potato research. Comparison of two RNA-sequence datasets from the purple and the yellow sweet potato showed that UDP-glucose-flavonoid 3-O-glucosyltransferase was one of the key enzymes in the pathway of anthocyanin biosynthesis and that anthocyanin-3-glucoside might be one of the major components for anthocyanin pigments in the purple sweet potato. This study contributes to the molecular mechanisms of sweet potato development and metabolism and therefore that increases the potential utilization of the sweet potato in food nutrition and pharmacy.

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Abbreviations

AFLP:

Amplified fragment-length polymorphism

bHLH:

Helix-loop-helix

CHI:

Chalcone isomerase

CHS:

Chalcone synthase

COG:

Clusters of orthologous groups

EST:

Expression sequence tag

F3′5′H:

Flavonoid 3′ 5′-hydroxylase

F3H:

Flavonoid 3′ hydroxylase

GO:

Gene ontology

KEGG:

Kyoto encyclopedia of genes and genomes

RNA-seq:

RNA sequencing

RPKM:

Reads per kb per million reads

SRA:

Short read archive

SSR:

Simple sequence repeat

UFGT:

UDP-glucose-flavonoid 3-O-glucosyltransferase

VNTR:

Variable number of tandem repeat

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Authors and Affiliations

  1. Department of Biology, East Carolina University, Greenville, NC, 27858, USA

    Fuliang Xie, Caitlin E. Burklew & Baohong Zhang

  2. The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China

    Yanfang Yang & Deyou Qiu

  3. State Key Lab of Tree Genetics and Breeding, No. 2 DongXiaoFu, Haidian District,, Beijing, 100091, China

    Yanfang Yang & Deyou Qiu

  4. College of Plant Science, Agriculture University of Beijing, Beijing, 102206, China

    Min Liu

  5. Department of Mathematics, East Carolina University, Greenville, NC, 27858, USA

    Peng Xiao

Authors
  1. Fuliang Xie
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  2. Caitlin E. Burklew
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  3. Yanfang Yang
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  4. Min Liu
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  5. Peng Xiao
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  6. Baohong Zhang
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  7. Deyou Qiu
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Correspondence to Baohong Zhang or Deyou Qiu.

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Xie, F., Burklew, C.E., Yang, Y. et al. De novo sequencing and a comprehensive analysis of purple sweet potato (Impomoea batatas L.) transcriptome. Planta 236, 101–113 (2012). https://doi.org/10.1007/s00425-012-1591-4

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  • DOI: https://doi.org/10.1007/s00425-012-1591-4

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