›› 2015, Vol. 58 ›› Issue (10): 1037-1045.

• RESEARCH PAPERS •     Next Articles

Distribution patterns of microsatellites in the genome of the German cockroach (Blattella germanica)

WANG Chen1,#, DU Lian-Ming1,#, LI Peng1, YANG Ming-Yu1, LI Wu-Jiao1, SHEN Yong-Mei2, ZHANG Xiu-Yue1, YUE Bi-Song1,*   

  1. (1. Key Laboratory of Bioresources and Ecoenvironment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China; 2. Sichuan Key Laboratory of Medicinal Periplaneta America, Chengdu 610081, China)
  • Online:2015-10-20 Published:2015-10-20

Abstract: 【Aim】 The objective of this study is to analyze the number and distribution of microsatellites in the whole genome of the German cockroach, Blattella germanica, and get the functional annotation information of genes containing microsatellites in exons. 【Methods】 The microsatellite number, repetition and location information were calculated by using microsatellite search tool. The distribution information of microsatellites in the genome was calculated by custom Python scripts, and all genes containing microsatellites were annotated by using the programs of Blast2Go and KAAS. 【Results】 A total of 604 386 simple sequence repeats (SSRs) with 1-6 bp nucleotide motifs were identified, with a total length of 15 301 255 bp, indicating that about 0.75% of the B. germancia genome (2.04 Gb) is occupied by SSRs and that there is a locus per 3.37 kb. The length of the microsatellite sequences mainly ranges from 12 to 60 bp. Among different types of microsatellites, trinucleotide microsatellites (226 876, 37.54%) are the most abundant SSRs, followed by tetranucleotide microsatellites (150 355, 24.88%), mononucleotide microsatellites (141 167, 23.36%), dinucleotide microsatellites (60 877, 10.07%), pentanucleotide microsatellites (21 570, 3.57%) and hexa-nucleotide microsatellites (3 541, 0.59%). The predominant repeat types are ATT, AAT, A, T, AAAT, ATTT and AT, with a total number of 411 789, accounting for 68.13% of the total SSRs. The number of each of these 7 categories is greater than 30 000. There are 2 372 microsatellites in the exons of 1 481 genes. The results of GO annotation indicated that 434 GO terms are classified as cellular component, 402 GO terms are related to molecular function and 660 GO terms are related to the biological process. Aligned to KEGG database, most of these genes are associated with metabolism, followed by genes related to organismal system, and genes related to genetic information processing are the least. 【Conclusion】 This study lays a foundation for further in-depth analysis of microsatellite function and developing microsatellite markers of B. germanica.

Key words: Blattella germanica, microsatellite, bioinformatics, functional annotation, genome, exon