Cloning and bioinformatics analysis of an ubiquitin gene of the rice stem borer, Chilo suppressalis Walker (Lepidoptera: Pyralidae)

Abstract

Ubiquitin which has the function of selective protein degradation may play an important role in the regulation of insect growth and development. The coding sequence of an ubiquitin gene from the larvae of the rice stem borer, Chilo suppressalis Walker (Lepidoptera: Pyralidae) named CsUB (GenBank Accession No. GU238420) was cloned by RT-PCR and sequenced in this study, with primers according to the sequences of ubiquitin genes  from Homo sapiens, Drosophila melanogaster and Lepidopteran insects. Sequence analysis showed that the length of the coding sequence is 228 bp, encoding 76 amino acids with calculated molecular weight of 8.50 kDa and the theoretical isoeletric point of 5.26. Signal sequence and transmembrane domain had not been found. Multiple sequence alignment indicated that CsUB gene sequence with other known gene sequences of invertebrates and vertebrates had a high degree of homology (more than 72% similarity) and a shorter genetic distance (lower than 0.360). During the genetic diversity analysis, the total of 104 polymorphic sites was detected from 18 ubiquitin gene sequences and 18 haplotypes were sorted. Abundant genetic diversity and strong codon usage bias were found by the haplotype diversity (1.000), average number of nucleotide differences (47.475), nucleotide diversity (0.20866), effective number of codons (44.526), codon bias index (0.559) and scaled Chi-square (0.779). The predicated secondary structure composition of CsUB protein had about 32.89% extended strands, 36.84% random colis, 15.79% alpha helixes and 14.47% beta turns. Subcellular localization analysis showed that CsUB protein of cytoplasm, cell nucleus, mitochondrion, cell skeleton and plasma membrane occupied about 47.80, 26.10, 17.40, 4.30 and 4.30%, respectively. Sequence, homology and structural analysis confirmed that CsUB gene was highly conserved during evolution and belonged to ubiquitin gene family. The results might provide some fundamental data for further studies on expressed characteristics and physiological functions of CsUB gene.

Key words: Chilo suppressalis Walker, ubiquitin, gene cloning, bioinformatics.