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Li C, Song Y, Li L, Tessnow AE, Zhu J, Guan X, Guo W, Cui H, Lu Z, Lv S, Yu Y, Men X. Two Microsatellite Types Within NAD6 Gene Help to Distinguish Populations and Infer the Migratory Route of the Invasive Fall Armyworm, Spodoptera frugiperda, (Lepidoptera, Noctuidae) in China. JOURNAL OF ECONOMIC ENTOMOLOGY 2022; 115:1409-1416. [PMID: 35899806 DOI: 10.1093/jee/toac114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Indexed: 06/15/2023]
Abstract
Spodoptera frugiperda is a major agricultural pest that has invaded China since January 2019. Given that most of the individuals present in China carried the diagnostic rice-strain mtDNA (COI-RS), there was no efficient method to distinguish populations of S. frugiperda. In this study, we identified and characterized two variant microsatellite alleles in the mitochondrial NAD6 gene of S. frugiperda retrieved from the National Center for Biotechnology Center GenBank. We then sequenced partial NAD6 genes containing the microsatellite region and the diagnostic COI barcoding gene (used to distinguish the corn-strain and the rice-strain) of 429 invasive S. frugiperda individuals that were collected from the main infested regions in China during 2019-2020. Our data indicates that two kinds of interrupted repeat sequences, (ATA)4T(ATA)3 and (ATA)5T(ATA)3, exist in the microsatellite region which we defined as the deletion type (NAD6-D), and the insertion type (NAD6-I) based on the repeat units' differentiation, respectively. The presence of these two microsatellite types in the mtDNA genome of S. frugiperda was further confirmed with the sequencing results in 429 samples. Moreover, NAD6-I and NAD6-D types were both present in individuals with COI-RS, while only NAD6-D type was detected in the COI-CS individuals. Interestingly, the two microsatellite types suggested a possible geographic distribution: the western migratory route (Yunan and Chongqing) was comprised exclusively of NAD6-I type, while both NAD6-I and NAD6-D types were identified in the predicted eastern migration trajectories (Hainan, Guangxi, Shandong, etc.). These results suggested that NAD6-D and NAD6-I types may be useful in distinguishing between populations, analyzing the evolutionary mechanism of mtDNA microsatellite polymorphism, inferring the migratory route of S. frugiperda in China, and developing precise and integrated control strategies for S. frugiperda.
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Affiliation(s)
- Chao Li
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Shandong, Jinan, China
| | - Yingying Song
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Shandong, Jinan, China
| | - Lili Li
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Shandong, Jinan, China
| | - Ashley E Tessnow
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Junsheng Zhu
- Shandong Plant Protection Station, Shandong, Jinan, China
| | - Xiumin Guan
- Shandong Plant Protection Station, Shandong, Jinan, China
| | - Wenxiu Guo
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Shandong, Jinan, China
| | - Hongying Cui
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Shandong, Jinan, China
| | - Zengbin Lu
- Maize Research Institute, Shandong Academy of Agricultural Science, Shandong, Jinan, China
| | - Suhong Lv
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Shandong, Jinan, China
| | - Yi Yu
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Shandong, Jinan, China
| | - Xingyuan Men
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Shandong, Jinan, China
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Nagpure NS, Rashid I, Pathak AK, Singh M, Pati R, Singh SP, Sarkar UK. FMiR: A Curated Resource of Mitochondrial DNA Information for Fish. PLoS One 2015; 10:e0136711. [PMID: 26317619 PMCID: PMC4552752 DOI: 10.1371/journal.pone.0136711] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 08/07/2015] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial genome sequences have been widely used for evolutionary and phylogenetic studies. Among vertebrates, fish are an important, diverse group, and their mitogenome sequences are growing rapidly in public repositories. To facilitate mitochondrial genome analysis and to explore the valuable genetic information, we developed the Fish Mitogenome Resource (FMiR) database to provide a workbench for mitogenome annotation, species identification and microsatellite marker mining. The microsatellites are also known as simple sequence repeats (SSRs) and used as molecular markers in studies on population genetics, gene duplication and marker assisted selection. Here, easy-to-use tools have been implemented for mining SSRs and for designing primers to identify species/habitat specific markers. In addition, FMiR can analyze complete or partial mitochondrial genome sequence to identify species and to deduce relational distances among sequences across species. The database presently contains curated mitochondrial genomes from 1302 fish species belonging to 297 families and 47 orders reported from saltwater and freshwater ecosystems. In addition, the database covers information on fish species such as conservation status, ecosystem, family, distribution and occurrence downloaded from the FishBase and IUCN Red List databases. Those fish information have been used to browse mitogenome information for the species belonging to a particular category. The database is scalable in terms of content and inclusion of other analytical modules. The FMiR is running under Linux operating platform on high performance server accessible at URL http://mail.nbfgr.res.in/fmir.
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Affiliation(s)
- Naresh Sahebrao Nagpure
- Division of Molecular Biology and Biotechnology, National Bureau of Fish Genetic Resources, Lucknow-226002, India
| | - Iliyas Rashid
- Division of Molecular Biology and Biotechnology, National Bureau of Fish Genetic Resources, Lucknow-226002, India
| | - Ajey Kumar Pathak
- Division of Fish Taxonomy and Resources, National Bureau of Fish Genetic Resources, Lucknow-226002, India
| | - Mahender Singh
- Division of Molecular Biology and Biotechnology, National Bureau of Fish Genetic Resources, Lucknow-226002, India
- * E-mail:
| | - Rameshwar Pati
- Division of Molecular Biology and Biotechnology, National Bureau of Fish Genetic Resources, Lucknow-226002, India
| | - Shri Prakash Singh
- Division of Fish Taxonomy and Resources, National Bureau of Fish Genetic Resources, Lucknow-226002, India
| | - Uttam Kumar Sarkar
- Division of Fish Taxonomy and Resources, National Bureau of Fish Genetic Resources, Lucknow-226002, India
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