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| Transcriptome Sequencing and Bio-information Analysis of Colaphellus bowringi |
| Junxue Sha, , , , , , , |
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Abstract Abstract Colaphellus bowringi is a common vegetable pest. As the current Colaphellus bowringi full genome has not yet been announced, the various related gene information can not be known, leading to the Colaphellus bowringi gene function research is slow. The complete transcriptome data of Colaphellus bowringi was obtained by a new generation of high-throughput sequencing. Transcriptome data was analyzed with bioinformatics analysis. A complete transcriptomic database of Colaphellus bowringi was obtained, and the obtained original data was uploaded to National Center for Biotechnology Information (NCBI), and accession number is of SRP125298. Blast X tool was used to search the unigenes against NR (NCBI non-redundant protein sequences), NT (NCBI nucleotide sequences), KEGG (Kyoto Encyclopedia of Genes and Genomes), Swiss-Prot(Manually Annotated and Reviewed Protein Sequence Database), Pfam (Protein Family), GO (Gene Ontology) and KOG (enKaryotic Ortholog Groups) databases to perform gene function and pathway annotation. In this study, 40 489 unigenes were de novo assembled. 19 955 unigenes were annotated in the public protein databases. A total of 17 437, 4 158, 6 817, 12 129, 15 890, 8 641, 11 416 unigenes had NR, NT, KEGG, Swiss-Prot, Pfam, GO, KOG database classification. The microsatellite (SSR) analysis, which found a total of 2 992 SSR exist in 2 692 unigenes, the average length of 14.61 bp. The most abundant type of repeat motif was mononucleotide (65.51%) and trinucleotide (21.76%). The most frequent motifs in mononucleotide and trinucleotide were A/T (94.95%) and TTA/TAA (8.45%). A total of 115 repetitive primers were found, of which 12, 60 and 38 of the dinucleotide, trinucleotide and tetranucleotide were found, respectively. The repetition frequency of the motif was between 5 and 50 times, and the length of the motif was mainly in the range of 10 ~ 20 bp. This study provides basic data for species identification and genetic diversity analysis through the acquisition of the primary data of the transcriptome of the Colaphellus bowringi.
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Received: 13 July 2017
Published: 21 May 2018
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