Development of SSR primers for <em>Simulium (Eusimulium) angustipes</em> (Diptera: Simuliidae) based on RNA-seq dataset
昆虫学报
       Home | About Journal | Editorial Board | Subscription | Instruction | Advertisement | Contact Us | Chinese
ACTA ENTOMOLOGICA SINICA  2018, Vol. 61 Issue (7): 815-824    DOI: 10.16380/j.kcxb.2018.07.008
RESEARCH PAPERS Current Issue | Next Issue | Archive | Adv Search Previous Articles  |  Next Articles  
Development of SSR primers for Simulium (Eusimulium) angustipes (Diptera: Simuliidae) based on RNA-seq dataset
GUO Huan, WANG Gang, ZHANG Shu-Tian, HUANG Min 
(Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi 712100, China)
 Download: PDF (1693 KB)   HTML (1 KB)   Export: BibTeX | EndNote (RIS)      Supporting Info
Abstract 【Aim】 Simulium (Eusimulium) angustipes is a bloodthirsty species that transmits poultry diseases. In this study, S. (E.) angustipes transcriptomes were sequenced using RNA-seq technology, and the SSRs were developed using transcriptome datasets, which may serve as reliable molecular markers for population genetics research of simuliids. 【Methods】 Transcriptome database of S. (E.) angustipes larvae collected from Baoji of Shaanxi and Altay of Xinjiang was constructed. The software MISA was used to explore all the microsatellite loci in the unigene database of S. (E.) angustipes. Primers were designed using software Primer Premier 5.0 and Oligo 6.7 from the SSR loci chosen randomly. After PCR procedure and electrophoresis detection, the primers with polymorphism for SSR were screened and analyzed using Cervus 3.0.7 and other bioinformatics softwares. Unigenes with polymorphic SSR loci were annotated using BlastX against Nr and Swiss-Prot databases. 【Results】 A total of 29 471 SSRs were identified in S. (E.) angustipes transcriptome. The most frequent repeat motifs were mononucleotide motifs (87.05%), followed by trinucleotide motifs (7.95%). Among all the 34 SSR motifs, (A/T)n was the most abundant mononucleotide motif (86.93%). SSR primers were synthesized, and 15 primers were amplified successfully, of which 12 loci were polymorphic. BlastX results indicated that seven SSR loci were identified from the annotated genes. 【Conclusion】 Based on RNA-seq sequencing technology, we can better realize the development of SSRs for S. (E.) angustipes, which is of great significance to the study of population genetics of this group.
Service
E-mail this article
Add to my bookshelf
Add to citation manager
E-mail Alert
RSS
Articles by authors
GUO Huan
WANG Gang
ZHANG Shu-Tian
HUANG Min
Key wordsSimulium (Eusimulium) angustipes   RNA-seq dataset   microsatellite DNA   SSR molecular marker   polymorphism     
Cite this article:   
GUO Huan,WANG Gang,ZHANG Shu-Tian et al. Development of SSR primers for Simulium (Eusimulium) angustipes (Diptera: Simuliidae) based on RNA-seq dataset[J]. ACTA ENTOMOLOGICA SINICA, 2018, 61(7): 815-824.
URL:  
http://www.insect.org.cn/EN/10.16380/j.kcxb.2018.07.008      or     http://www.insect.org.cn/EN/Y2018/V61/I7/815
 
No references of article
[1] GUO Hui-Ping, ZHOU Shu-Jing, ZHU Xiang-Jie, XU Xin-Jian, YU Ying-Long, YANG Kai-Jie, CHEN Dao-Yin, ZHOU Bing-Feng. Population genetic analysis of Apis cerana cerana from the Qinling-Daba Mountain Areas based on microsatellite DNA[J]. ACTA ENTOMOLOGICA SINICA, 2016, 59(3): 337-345.
[2] HE Qiang, LIU Shao-Lun, MA Zheng-Gang, ZHANG You-Yi, Charles R. VOSSBRIN. Comparative genomics of three geographical strains reveals genetic diversity in Antheraea pernyi nucleopolyhedrovirus (AnpeNPV)(In English[J]. ACTA ENTOMOLOGICA SINICA, 2015, 58(5): 535-545.
[3] ZHANG Bo, HE Yu-Rong, CHEN Ting, QI Guo-Jun, LU Li-Hua. Dietary composition of foragers of the red imported fire ant, Solenopsis invicta Buren (Hymenoptera: Formicidae) in two habitats, mulberry orchard and barren land, in South China[J]. ACTA ENTOMOLOGICA SINICA, 2015, 58(4): 382-390.
[4] LUO Mei, ZHANG He, BIN Shu-Ying, LIN Jin-Tian. High-throughput discovery of SSR genetic markers in the mealybug, Phenacoccus solenopsis (Hemiptera: Pseudococcidae), from its transcriptome database[J]. ACTA ENTOMOLOGICA SINICA, 2014, 57(4): 395-400.
[5] ZHENG Yan, WANG Kang, LI Yu-Ting, QIAO Xian-Feng, CHEN Mao-Hua. Amplification stability and polymorphism of microsatellite loci in the oriental fruit moth, Grapholita molesta (Lepidoptera: Tortricidae) in China[J]. ACTA ENTOMOLOGICA SINICA, 2014, 57(11): 1335-1342.
[6] . Variation of mtCOI gene in Bemisia tabaci (Hemiptera: Aleyrodidae) cryptic species Q and B and its effects on cryptic species identification based on cleavage amplified polymorphic sequence (CAPS) markers[J]. ACTA ENTOMOLOGICA SINICA, 2014, 57(10): 1238-1244.
[7] HE Chun-Ling , NIU Ze-Qing, LUO A-Rong, ZHU Chao-Dong, WU Yan-Ru. In-nest ethology and mating strategies of the carpenter bees Xylocopa spp. (Hymenoptera: Apidae)[J]. ACTA ENTOMOLOGICA SINICA, 2013, 56(9): 1047-1054.
[8] XU Xin-Jian, ZHOU Shu-Jing, ZHU Xiang-Jie, ZHOU Bing-Feng. Microsatellite DNA analysis of genetic diversity of Apis cerana cerana in Hainan Island, southern China[J]. ACTA ENTOMOLOGICA SINICA, 2013, 56(5): 554-560.
[9] . Genotypic polymorphism of Spodoptera litura nucleopolyhedrovirus (SpltNPV) in the wild[J]. ACTA ENTOMOLOGICA SINICA, 2013, 56(4): 372-378.
[10] DONG De-Zhen, DONG Yan-Fei, GE Zhou-Miao, WANG Dong-Mei, CHEN Jie, LU Yong-Quan. Effects of imidacloprid on DNA methylation polymorphism in the brown planthopper, Nilaparvata lugens (Hemiptera: Delphacidae)[J]. ACTA ENTOMOLOGICA SINICA, 2013, 56(1): 39-46.
[11] HUANG Li, ZHANG Chun-Lin, JIANG Ying-Hai, CHEN Han-Bin. Polytene chromosomes of Simulium (Wilhelmia) xingyiense (Diptera: Simuliidae) from China[J]. ACTA ENTOMOLOGICA SINICA, 2012, 55(8): 988-993.
[12] DUAN Hui-Sheng, ZHANG An-Sheng, ZHAO Chuan-Zhi, YU Yi, CHU Dong. Characterization and molecular marker screening of EST-SSRs and their polymorphism compared with Genomic-SSRs in Frankliniella occidentalis (Thysanoptera: Thripidae)[J]. ACTA ENTOMOLOGICA SINICA, 2012, 55(6): 634-640.
[13] ZHU Yan-Bin, MA Ji-Fang, DONG Li, LI Li-Tao, JIANG Jing-Yu, LI Zhi-Hui, DONG Zhi-Ping, DONG Jin-Gao, WANG Qin-Ying. Analysis of genetic polymorphism of Athetis lepigone (Lepidoptera: Noctuidae) populations from China based on mtDNA COⅠ gene sequences[J]. ACTA ENTOMOLOGICA SINICA, 2012, 55(4): 457-465.
[14] LU Si-Xing, LIU Ji-Ping, TANG Li, LI Xiang-Lin, MI Hong-Xia, YANG Ji-Long, YAN Yu-Wei, XU Shu-Lan. Genetic diversity of Beauveria bassiana in different silkworm populations from Guangdong and Guangxi, southern China, based on SSRs[J]. ACTA ENTOMOLOGICA SINICA, 2012, 55(10): 1142-1148.
[15] MI Zhi, LI Ao-Xiang, RUAN Cheng-Long, LI Guan-Nan, DU Wen-Hua, LONG Yao-Hang, ZHU Yong. Searching and analysis of EST-SSR markers from linkage group 12 of the silkworm, Bombyx mori
[J]. ACTA ENTOMOLOGICA SINICA, 2011, 54(11): 1223-1230.
Copyright © 2011 ACTA ENTOMOLOGICA SINICA
Supported by:Beijing Magtech