Chromosome-level genome assembly and population genomic analysis provide novel insights into the immunity and evolution of Sogatella furcifera

Ting Cui; Qing Bai; Weiqiang Yu; Dongyang Guo; Yawen Ban; Kun Chen; Ali Raza; Guohui Zhou; Qingfa Wu

doi:10.1016/j.ygeno.2023.110729

Chromosome-level genome assembly and population genomic analysis provide novel insights into the immunity and evolution of Sogatella furcifera

Genomics. 2023 Nov;115(6):110729. doi: 10.1016/j.ygeno.2023.110729. Epub 2023 Oct 17.

Authors

Ting Cui¹, Qing Bai², Weiqiang Yu¹, Dongyang Guo¹, Yawen Ban¹, Kun Chen¹, Ali Raza¹, Guohui Zhou³, Qingfa Wu⁴

Affiliations

¹ 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.
² 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. Electronic address: baiqing@ustc.edu.cn.
³ Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China.
⁴ 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. Electronic address: wuqf@ustc.edu.cn.

PMID: 37852332
DOI: 10.1016/j.ygeno.2023.110729

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.

Keywords: Chromosome-level genome assembly; Comparative genomics; Immunity and evolution; Population genomics; Sogatella furcifera.

MeSH terms

Animals
Asia
China
Chromosomes
Genomics
Hemiptera* / genetics
Humans
Metagenomics*