Acta Entomologica Sinica ›› 2022, Vol. 65 ›› Issue (1): 31-43.doi: 10.16380/j.kcxb.2022.01.004

• RESEARCH PAPERS • Previous Articles     Next Articles

Analysis of the transcriptome and development of novel SSR markers in Notonecta chinensis (Hemiptera: Notonectidae)

LI Min1, ZHANG Dan-Li1, LI Rong-Rong1, LEI Ting1, SONG Xian-Mei1, BU Wen-Jun2,*   

  1.  (1. Department of Biology, Taiyuan Normal University, Jinzhong, Shanxi 030619, China; 2. Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China)
  • Online:2022-01-20 Published:2022-01-17

Abstract: 【Aim】Notonecta chinensis, distributed in China and Okinawa of Japan, is an important aquatic natural enemy insect which can be used for biological control of mosquitoes. The purpose of this study is to establish the transcriptome database of N. chinensis, and to mine its genetic information. 【Methods】The transcriptome of N. chinensis was sequenced, de novo assembled and subjected to bioinformatics analysis by using the Illumina NextSeq500 high-throughput sequencing platform. New SSR molecular markers were selected by using MISA software based on the transcriptome unigenes data. Polymorphism of SSRs was detected by capillary electrophoresis. 【Results】A total of 34 782 282 clean reads (NCBI SRA accession number: SRR13259254) were obtained, and assembled into 37 801 unigenes with the N50 length of 913 bp. All unigenes were aligned against the known databases for gene function annotation, and 36 474, 32 470, 27 781, 35 079 and 5 638 sequences were annotated in nr, SwissProt, GO, eggNOG and KEGG databases, respectively. According to GO database annotation, the function of the unigenes can be divided into three categories including biological process, cellular component and molecular function, among which unigenes involved in cell, cell part and binding were enriched to a higher degree. eggNOG database annotation results showed that 37 801 unigenes were classified into 25 gene families, with the most annotated to function unknown. Enrichment analysis of KEGG metabolic pathways showed that 5 638 unigenes were annotated to 245 metabolic pathways, and the number of annotations to ribosome was the largest. Moreover, a large-scale SSR search was performed for 37 801 unigenes on the transcriptome sequencing data using the software MISA, and a total of 3 124 SSR loci (accounting for 8.26%) were identified, with a frequency of 7.07%. A total of 16 SSR loci were screened by PCR. The polymorphic information content (PIC) of the three loci NcCF/NcCR, NcKF/NcKR and NcLF/NcLR in seven geographical populations of N. chinensis were 0.870, 0.902 and 0.857, respectively, indicating high polymorphism. 【Conclusion】In this study, we successfully obtained the reference transcriptome of N. chinensis, which provides a molecular theoretical basis for its gene function analysis. The development of these potential SSR markers could provide a set of candidate molecular markers for genetic diversity analysis, cryptic species identification and genetic mapping construction of N. chinensis.

Key words: Notonecta chinensis, transcriptome, SSR, gene annotation, Illumina NextSeq