Data from: Assessing the local adaptative changes associated with range expansion of the pink stem borer
Data files
Sep 05, 2023 version files 228.20 MB
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README.md
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Sesamia_inferens.snp.nexus
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Sesamia_inferens.snp.vcf.gz
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Sesamia_inferens.sv.nexus
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Sesamia_inferens.sv.vcf.gz
Abstract
Understanding the genetic basis of adaptive evolution following habitat expansion can have important implications for pest management. The pink stem borer (PSB), Sesamia inferens (Walker), is a destructive pest of rice that historically restricted to regions south of N34° latitude in China. However, with changes in global climate and farming practices, the distribution of this moth has progressively exceeded its traditional limit of 34° N and encompassed most regions in North China. However, the evolutionary processes and local adaptative changes of this species, are not yet fully understood. Here, we employed genome resequencing to genotype over 1 million of high‐quality SNPs and 20,000 SVs from 14 geographical populations across China. Three highly differentiated genetic groups were formed, corresponding to Northern, Southern China regions and Yunnan-Guizhou Plateau. The pairwise genetic distance between locations was highly correlated with geographic and environmental distance. Our estimates of evolutionary history indicate asymmetric migration with varying population sizes across three genetic groups. Selective sweep analyses highlight the strong selected insect cuticle GRP genes enhanced desiccation adaptability of the northern group and SETMAR gene associated with range expansion and local adaptation in Shandong population. Based on an integrated analysis of transcriptome and enGWAS, we also identified the CYP321A7 gene was involved in the PSB adaption to desiccation climates. Our findings revealed the phylogeography, demographic dynamics and evolutionary forces of PSB and identified potential candidate genes to explore the genetic adaptation to novel environments, which have significant implications for the development of effective strategies to control this pest.
README: Assessing the local adaptative changes associated with range expansion of the pink stem borer
Whole-genome variant files (snp & sv) and the whole genome phylogenetic tree of pink stem borer Populations
Description of the data and file structure
All whole-genome structural variant calls
The final product of our structural variant calling pipeline; obtained as described under: "SNP and SV calling" in Materials and Methods. This file includes both high-quality SVs.
Sesamia_inferens.sv.vcf.gz
All whole-genome SNP variant calls
The final product of our structural variant calling pipeline; obtained as described under: "SNP and SV calling" in Materials and Methods. This file includes high-quality SNPs.
Sesamia_inferens.snp.vcf.gz
Main whole genome phylogenetic tree using SNP dataset
Figure 1A
Sesamia_inferens.snp.nexus
Main whole genome phylogenetic tree using SV dataset
Figure 1D
Sesamia_inferens.sv.nexus
Sharing/Access information
The sequence data have been submitted to the National Center for Biotechnology Information (NCBI). The raw data used for genome resequencing analysis are available at PRJNA979934.
Links to other publicly accessible locations of the data:
https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA979934
Data was derived from the following sources:
https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA979934
Code/Software
no code or software