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. 2015 Jul 23;10(7):e0133312.
doi: 10.1371/journal.pone.0133312. eCollection 2015.

De Novo Assembly and Annotation of the Chinese Chive (Allium tuberosum Rottler ex Spr.) Transcriptome Using the Illumina Platform

Shu-Mei Zhou  1 , Li-Mei Chen  2 , Shi-Qi Liu  2 , Xiu-Feng Wang  2 , Xiu-Dong Sun  2
Affiliations

De Novo Assembly and Annotation of the Chinese Chive (Allium tuberosum Rottler ex Spr.) Transcriptome Using the Illumina Platform

Shu-Mei Zhou et al. PLoS One. .

Abstract

Chinese chive (A. tuberosum Rottler ex Spr.) is one of the most widely cultivated Allium species in China. However, minimal transcriptomic and genomic data are available to reveal its evolution and genetic diversity. In this study, de novo transcriptome sequencing was performed to produce large transcript sequences using an Illumina HiSeq 2000 instrument. We produced 51,968,882 high-quality clean reads and assembled them into 150,154 contigs. A total of 60,031 unigenes with an average length of 631 bp were identified. Of these, 36,523 unigenes were homologous to existing database sequences, 35,648 unigenes were annotated in the NCBI non-redundant (Nr) sequence database, and 23,509 unigenes were annotated in the Swiss-Prot database. A total of 26,798 unigenes were assigned to 57 Gene Ontology (GO) terms, and 13,378 unigenes were assigned to Cluster of Orthologous Group categories. Using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database, we mapped 21,361 unigenes onto 128 pathways. Furthermore, 2,125 sequences containing simple sequence repeats (SSRs) were identified. This new dataset provides the most comprehensive resource currently available for gene expression, gene discovery, and future genomic research on Chinese chive. The sequence resources developed in this study can be used to develop molecular markers that will facilitate further genetic research on Chinese chive and related species.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Overview of the transcriptome assembly for A. tuberosum Rottler ex Spr.
(A) Size distribution of contigs; (B) size distribution of unigenes.
Fig 2
Fig 2. Unigene homology searches against the NR database.
(A) The E-value distribution of BLAST hits for the assembled unigenes in the NR database. (B) The similarity distribution of BLAST hits against the NR database for each unigene. (C) Species distribution of the top BLASTx hits against the NR database for each unigene.
Fig 3
Fig 3. GO classification of assembled sequences.
A total of 13,897 unigenes were grouped into three main GO categories: ‘Biological Processes’, ‘Cellular Component’, and ‘Molecular Function’.
Fig 4
Fig 4. COG functional classification of unigenes.
A total of 950 assembled unigenes were annotated and assigned to 24 functional categories.
See this image and copyright information in PMC

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