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Cui T, Bai Q, Yu W, Guo D, Ban Y, Chen K, Raza A, Zhou G, Wu Q. Chromosome-level genome assembly and population genomic analysis provide novel insights into the immunity and evolution of Sogatella furcifera. Genomics 2023; 115:110729. [PMID: 37852332 DOI: 10.1016/j.ygeno.2023.110729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/10/2023] [Accepted: 10/15/2023] [Indexed: 10/20/2023]
Abstract
Sogatella furcifera is a destructive agricultural pest causing large threats to rice production in China and Southeast Asian countries. Despite recent breakthroughs in long-read sequencing, high quality genomic data are very limited in S. furcifera. In present study, a chromosome-level assembly of the S. furcifera genome was completed (0.64 GB), comprising 15 chromosomes covered 95.04% of the estimated genome size, along with other 624 small scaffolds making up the remaining 4.96% of the genome of S. furcifera. A total of 24,669 protein-coding genes, 1211 long noncoding RNA and 7595 circular RNA transcripts were predicted in this study. Comparative genomic analysis revealed rapidly evolved genes were associated with multiple immune-related pathways in S. furcifera. Genome resequencing of 44 individuals from 12 geographic populations revealed frequent gene flow among populations. The systemic genomic analysis will provide more insights into the understanding of the immunity and evolutionary adaptation of S. furcifera.
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Affiliation(s)
- Ting Cui
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Qing Bai
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China.
| | - Weiqiang Yu
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Dongyang Guo
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yawen Ban
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Kun Chen
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Ali Raza
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Guohui Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Qingfa Wu
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China; Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.
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Yang N, Dong Z, Chen A, Yin Y, Li X, Chu D. Migration of Sogatella furcifera between the Greater Mekong Subregion and northern China revealed by mtDNA and SNP. BMC Evol Biol 2020; 20:154. [PMID: 33213363 PMCID: PMC7678102 DOI: 10.1186/s12862-020-01722-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 11/10/2020] [Indexed: 11/10/2022] Open
Abstract
Background The white-backed planthopper (WBPH), Sogatella furcifera (Horváth) (Hemiptera, Delphacidae), is a migratory pest of rice in Asia. Shandong Province, in northern China, is located on the migration pathway of WBPH between southern and northeast China. The potential sources of WBPH in northern China are poorly understood. We studied the sources of WBPH in Shandong Province by determining the population genetic structure of WBPH in 18 sites distributed in Shandong and in six regions of the Greater Mekong Subregion (GMS). We used mitochondrial gene and single-nucleotide polymorphism (SNP) markers for analysis. Results All of the WBPH populations studied in the seven regions had low genetic diversity. Pairwise FST values based on mtDNA ranged from − 0.061 to 0.285, while FST based on SNP data ranged from − 0.007 to 0.009. These two molecular markers revealed that 4.40% (mtDNA) and 0.19% (SNP) genetic variation could be explained by the interpopulation variation, while the rest came from intrapopulation variation. The populations in the seven geographic regions comprised four hypothetical genetic clusters (K = 4) not associated with geographic location. Eighty-four of 129 individuals distributed across the given area were designated as recent migrants or of admixed ancestry. Although the substantial migration presented, a weak but significant correlation between genetic and geographic distances was found (r = 0.083, P = 0.004). Conclusion The Greater Mekong Subregion was the main genetic source of WBPH in Shandong, while other source populations may also exist. The genetic structure of WBPH is shaped by both migration and geographic barriers. These results help clarify the migration route and the source of WBPH in northern China.
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Affiliation(s)
- Nan Yang
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Zhaoke Dong
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Aidong Chen
- Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Yanqiong Yin
- Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Xiangyong Li
- Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Dong Chu
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109, China.
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Hu S, Sun S, Fu D, Lü J, Wang X, Yu Y, Dong L, Chen S, Ye H. Migration sources and pathways of the pest species Sogatella furcifera in Yunnan, China, and across the border inferred from DNA and wind analyses. Ecol Evol 2020; 10:8235-8250. [PMID: 32788975 PMCID: PMC7417236 DOI: 10.1002/ece3.6531] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/20/2020] [Accepted: 06/03/2020] [Indexed: 01/31/2023] Open
Abstract
The migration sources and pathways of Sogatella furcifera (Horváth) in topologically complex regions like Yunnan, China, and adjacent montane areas have long been a challenging task and a bottleneck in effective pest forecast and control. The present research reinvestigated this issue using a combination of mtDNA and long-term historical wind field data in an attempt to provide new insights. Genetic analyses showed that the 60 populations of S. furcufera collected across Myanmar, Thailand, Laos, Vietnam, Yunnan, Guizhou, and Sichuan lack genetic structure and geographic isolation, while spatial analysis of haplotype and diversity indices discovered geographic relevance between populations. Migration rate analysis combined with high-resolution 10-year wind field analysis detected the following migration sources, pathways, and impacted areas which could explain the outbreak pattern in Yunnan. (a) Dominating stepwise northward migrations originated from northern Indochina, southern Yunnan, and central-eastern Yunnan, impacting their northern areas. (b) Concurring summer-autumn southward (return) migration originated from nearly all latitude belts of Sichuan and Yunnan mainly impacting central and southern Yunnan. (c) Regular eastward and summer-autumn westward migrations across Yunnan. The northward migration reflects the temporal rhythm of gradual outbreaks from the south to the north in a year, while the return migration may explain the repeated or very severe outbreaks in the impacted areas. To form a better pest forecast and control network, attention must also be paid to the northern part of Yunnan to suppress the impact of return migration in summers and autumns.
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Affiliation(s)
- Shao‐Ji Hu
- Yunnan Key Laboratory of International Rivers and Transboundary Eco‐securityYunnan UniversityKunmingChina
- Institute of International Rivers and Eco‐securityYunnan UniversityKunmingChina
| | - Shan‐Shan Sun
- Department of Atmospheric SciencesSchool of Resource Environment and Earth ScienceYunnan UniversityKunmingChina
| | - Da‐Ying Fu
- School of Life SciencesSouthwest Forest UniversityKunmingChina
| | - Jian‐Ping Lü
- Plant Protection and Quarantine Station of Yunnan ProvinceKunmingChina
| | - Xue‐Ying Wang
- School of Life SciencesYunnan UniversityKunmingChina
| | - Yan‐Ping Yu
- School of Life SciencesYunnan UniversityKunmingChina
| | - Li‐Min Dong
- School of Life SciencesYunnan UniversityKunmingChina
| | - Sui‐Yun Chen
- Biocontrol Engineering Research Centre of Crop Disease and PestYunnan UniversityKunmingChina
- Biocontrol Engineering Research Centre of Plant Disease and PestYunnan UniversityKunmingChina
| | - Hui Ye
- School of AgricultureYunnan UniversityKunmingChina
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