基于新一代测序技术的昆虫转录组学研究进展

新一代测序技术具有快速、 高通量和低成本的特点, 为“组学”研究带来了新方法、 新方案, 正在深刻地改变着当前生物学的研究模式。近年来, 新一代测序技术极大促进了昆虫特别是无参考基因组信息昆虫的转录组学研究。自2008年至今, 采用新一代测序技术已对7个目的68种昆虫进行了转录组测序, 其中由我国学者完成了6个目的22种昆虫的转录组测序。目前, 昆虫转录组学研究主要集中在基因挖掘、 分子标记开发、 基因表达分析等方面, 为全面揭示昆虫生命活动中相关基因功能、 系统发生与进化以及昆虫与其他生物相互作用等奠定了基础。本文总结了当前昆虫转录组学研究的已有成果, 分析了其今后的发展趋势, 讨论了采用新一代测序技术开展昆虫转录组学研究中存在的诸如研究对象相对局限、 测序准确性不够高等不足, 并指出开展昆虫转录组学研究时需充分思考所要回答的科学问题, 选择合适的研究策略, 评估性价比, 以及开发转录组信息高效利用的方法等。作者建议未来的研究方向侧重于： （1）大规模开展基于新一代测序技术的昆虫转录组学研究, 特别是对其他目以及独特生态环境中的代表性昆虫应予以重点关注; （2）开发昆虫转录组数据存储及分析的软硬件; （3）合理利用新一代测序技术研究昆虫转录组并充分挖掘已测昆虫转录组中的遗传信息。     

Two calcium‐binding chaperones from the fat body of the Colorado potato beetle,Leptinotarsa decemlineata (Coleoptera: Chrysomelidae) involved in diapause

Molecular chaperones are crucial for the correct folding of newly synthesized polypeptides, in particular, under stress conditions. Various studies have revealed the involvement of molecular chaperones, such as heat shock proteins, in diapause maintenance and starvation; however, the role of other chaperones in diapause and starvation relatively is unknown. In the current study, we identified two lectin‐type chaperones with calcium affinity, a calreticulin (LdCrT) and a calnexin (LdCnX), that were present in the fat body of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae) during diapause. Both proteins possessed an N‐globular domain, a P‐arm domain, and a highly charged C‐terminal domain, while an additional transmembrane domain was present in LdCnX. Phylogenetic analysis revealed distinction at the order level. Both genes were expressed in multiple tissues in larval and adult stages, and constitutively throughout development, though a starvation response was detected only for LdCrT. In females, diapause‐related expression analysis in the whole body revealed an upregulation of both genes by post‐diapause, but a downregulation by diapause only for LdCrT. By contrast, males revealed no alteration in their diapause‐related expression pattern in the entire body for both genes. Fat body‐specific expression analysis of both genes in relation to diapause revealed the same expression pattern with no alteration in females and downregulation in males by post‐diapause. This study suggests that calcium‐binding chaperones play similar and possibly gender‐specific roles during diapause.     

Protein Domain Analysis of Genomic Sequence Data Reveals Regulation of LRR Related Domains in Plant Transpiration in Ficus

Predicting protein domains is essential for understanding a protein’s function at the molecular level. However, up till now, there has been no direct and straightforward method for predicting protein domains in species without a reference genome sequence. In this study, we developed a functionality with a set of programs that can predict protein domains directly from genomic sequence data without a reference genome. Using whole genome sequence data, the programming functionality mainly comprised DNA assembly in combination with next-generation sequencing (NGS) assembly methods and traditional methods, peptide prediction and protein domain prediction. The proposed new functionality avoids problems associated with de novo assembly due to micro reads and small single repeats. Furthermore, we applied our functionality for the prediction of leucine rich repeat (LRR) domains in four species of Ficus with no reference genome, based on NGS genomic data. We found that the LRRNT_2 and LRR_8 domains are related to plant transpiration efficiency, as indicated by the stomata index, in the four species of Ficus. The programming functionality established in this study provides new insights for protein domain prediction, which is particularly timely in the current age of NGS data expansion.