Dataset Information

Population expansion and genomic adaptation to agricultural environments of the soybean looper, Chrysodeixis includens.

ABSTRACT: Evolutionary studies of insect pests improve our ability to anticipate problems in agricultural ecosystems, such as pest outbreaks, control failures, or expansions of the host range. Here, we investigated the mechanisms underlying the evolutionary processes behind the recent census size expansion and local adaptation of Chrysodeixis includens. First, we sequenced mitochondrial markers to conduct a phylogeographic investigation of C. includens historical processes. Then, we combined a de novo genotyping-by-sequencing approach with a study of agricultural landscapes to uncover recent processes of adaptation. Primarily, we found low genetic diversity across all markers and clear indications of a recent demographic expansion. We also found a lack of significant isolation by distance (IBD), and weak or absent genetic structure considering geographic locations. However, we did find initial signs of population differentiation that were associated with host plant types (i.e., soybean and cotton). Agricultural landscape attributes, including soybean crops, were significantly associated with putative markers under positive selection. Moreover, positive selection associated with host differentiation was putatively linked to digestive enzymes. This study showed how landscape composition and host plants can affect the evolutionary process of agricultural pest insects such as C. includens.

SUBMITTER: Silva CS

PROVIDER: S-EPMC7463353 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized genetic information from organisms that lack of gene sequencing data. Sequences of transcriptomic or genomic data of C. includens are no longer available to conduct relevant and applied studies to agriculture, such as, characterize biological process, screening for resistance and identification of new target genes. In this sense, we constructed a reference transcriptome of C. includens from head and body tissues of third instar larvae and we performed and analysis of gene expression functionality of transcripts between head and body. Methods: Two replicates of pool 5 larvae (third instar) were dissected into two parts: head (enriched with neural tissue) and body (enriched with adipose and gut tissues). Paired-end libraries of head and body tissues, with an approximate average insert length of 300 bp, were sequenced on an Illumina HiSeq platform with 150 bp paired-end sequencing. Trimmed RNA-Seq reads from transcriptomes of head and body larvae were used for de novo assembly using de Bruijn graph-based assembler (Trinity). All contig sequences built on the reference transcriptome assembled were annotated using Blast2GO pipeline. For the expression analysis RNA-seq reads were mapped to the built reference transcriptome using TopHat and expression values of transcripts in FPKM (fragments per kilobase per million mapped reads) between head and body tissues were estimated on Cufflinks. Results: The assembled transcriptome from reads of head and body tissues of C. includens larvae generated a fasta file format (136.2MB) containing 102,249 transcript sequences and 60,347 “genes”. The length distribution of transcripts was between a minimum of 200bp and a maximum of 37,230bp with an average of 1,005bp. As the RNA extraction of body included enriched tissues of tegument, gut, and hemolymph of third instar larvae, the transcripts were found to be involved on transmembrane transport, proteolysis, cation transport and many types of metabolic process. These biological processes in soybean looper were related to the cellular functionality of oxidoreductase, transmembrane transporter and serine-type endopeptidase activities and many types of binding functions. In the head tissue of C. includens we found most transcripts with gene ontology related to signal transduction. This biological process could be associated with the functionality of genes related to odorant binding, signaling receptor binding, DNA binding and other types of molecular binding. As we found, we suggest that these genes expressed only in the head tissue might be involved mainly in the detection of a signal and subsequent cascade expression of biological processes. Conclusions: Our study represents the first detailed transcriptome of Chrysodeixis includens of different larvae tissues, with biologic replicates, generated by RNA-seq technology. Our results show that NGS offers a comprehensive and accurate sequencing data to species with reference genome not available. Also, RNA-seq data offer a global gene expression analysis between tissues and permit understand some biological process involved in insect physiology.

Dataset Information

Population expansion and genomic adaptation to agricultural environments of the soybean looper, Chrysodeixis includens.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure