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Transcriptome de novo assembly and differentially expressed genes related to cytoplasmic male sterility in kenaf (Hibiscus cannabinus L.)

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Abstract

Cytoplasmic male sterility (CMS) is a maternally inherited trait in which plants do not produce functional pollen during anther development; it plays a key role in hybrid seed production. CMS in kenaf (Hibiscus cannabinus L.) was first found by our group, but little is known about its molecular mechanism. To reveal the possible mechanism, a comparative transcriptome analysis of kenaf anthers from a CMS line and its maintainer was conducted using Solexa sequencing. We obtained 29,656,489 and 30,712,685 raw paired-end reads from the CMS and maintainer lines, respectively. These reads were eventually assembled into 54,563 unigenes with a mean size of 1,015 bp. As a result, 45,930 (84 %) sequences were annotated against the nr protein database. 15,977 (29 %) sequences were assigned to 286 kyoto encyclopedia of genes and genomes (KEGG) pathways, 20,289 (37 %) sequences have Clusters of Orthologous Groups classifications, and 38,611 unigenes (71 %) have at least one gene ontology (GO) term assigned and could be categorized into 50 functional groups. By using the digital gene expression (DGE) method, 4,584 transcripts were detected with at least twofold differences between CMS and maintainer lines. A total of 838 genes were increased and 528 genes decreased by at least fivefold in the CMS line. We performed GO and KEGG pathway enrichment analysis of differentially expressed genes (DEGs). The DEGs were assigned to 155 GO terms and enriched to 74 KEGG pathways. Twenty-eight genes were randomly selected and their expression levels were confirmed by quantitative real-time PCR, and 22 of them showed expression patterns consistent with the DGE data. The results provide a comprehensive foundation for understanding anther development and the CMS mechanism in kenaf.

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Abbreviations

CMS:

Cytoplasmic male sterility

nr:

Non-redundant protein sequences

CTAB:

Cetyltrimethyl ammonium bromide

DEG:

Differential expressed gene (unigenes)

DGE:

Digital gene expression

qRT-PCR:

Quantitative real time PCR

KEGG:

Kyoto encyclopedia of genes and genomes

TCA:

Cycle, tricarboxylic acid cycle

PPR:

Pentatricopeptide repeat

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (Grant No. 31260341).

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Authors and Affiliations

  1. College of Agriculture, Guangxi University, Daxue Road 100, Nanning, 530004, China

    Peng Chen, Shanmin Ran, Zhipeng Huang, Jinghua Qian, Mingli Yu & Ruiyang Zhou

  2. College of Life Science and Technology, Guangxi University, Daxue Road 100, Nanning, 530004, China

    Ru Li

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  1. Peng Chen
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Correspondence to Peng Chen or Ruiyang Zhou.

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11032_2014_146_MOESM1_ESM.jpg

Effects of quality-based K-mer correction on overall quality improvement. The left shows per-base quality graph of the reads before correction; the right shows per-base quality graph of the reads after correction. The X-axis indicates the bp position along the reads; the Y-axis indicates the Phred-based quality score. The average quality score at each bp position is plotted. The central red line is the median value. The yellow box represents the inter-quartile range (25-75 %). The upper and lower whiskers represent the 10 % and 90 % points. The blue line represents the mean quality (JPEG 64 kb)

11032_2014_146_MOESM2_ESM.jpg

Length distribution of the assembled sequences. “Unigenes_CDS” are Unigenes with a predicated ORF; “Unigenes_No_CDS” are Unigenes without any predicated ORF. (JPEG 161 kb)

11032_2014_146_MOESM3_ESM.jpg

Gap distribution of the assembled sequences. “Unigenes_CDS” are Unigenes with a predicated ORF; “Unigenes_No_CDS” are Unigenes without any predicated ORF (JPEG 134 kb)

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Chen, P., Ran, S., Li, R. et al. Transcriptome de novo assembly and differentially expressed genes related to cytoplasmic male sterility in kenaf (Hibiscus cannabinus L.). Mol Breeding 34, 1879–1891 (2014). https://doi.org/10.1007/s11032-014-0146-8

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