Apolygus lucorum genome provides insights into omnivorousness and mesophyll feeding

Abstract

Apolygus lucorum (Miridae) is an omnivorous pest that occurs worldwide and is notorious for the serious damage it causes to various crops and substantial economic losses. Although some studies have examined the biological characteristics of the mirid bug, no reference genome is available in Miridae, limiting in‐depth studies of this pest. Here, we present a chromosome‐scale reference genome of A. lucorum, the first sequenced Miridae species. The assembled genome size was 1.02 Gb with a contig N50 of 785 kb. With Hi‐C scaffolding, 1,016 Mb contig sequences were clustered, ordered and assembled into 17 large scaffolds with scaffold N50 length 68 Mb, each corresponding to a natural chromosome. Numerous transposable elements occur in this genome and contribute to the large genome size. Expansions of genes associated with omnivorousness and mesophyll feeding such as those related to digestion, chemosensory perception, and detoxification were observed in A. lucorum, suggesting that gene expansion contributed to its strong environmental adaptability and severe harm to crops. We clarified that a salivary enzyme polygalacturonase is unique in mirid bugs and has significantly expanded in A. lucorum, which may contribute to leaf damage from this pest. The reference genome of A. lucorum not only facilitates biological studies of Hemiptera as well as an understanding of the damage mechanism of mesophyll feeding, but also provides a basis on which to develop efficient control technologies for mirid bugs.

Chromosomal-Level Genome Assembly of a True Bug, Aspongopus chinensis Dallas, 1851 (Hemiptera: Dinidoridae)

“…1 c ). The phylogenetic tree and divergence time were consistent with hemipteran taxonomy and results from a previous study ( Liu et al 2021 ). As shown in the tree, two suborders of Hemiptera, namely Fulgoromorpha and Heteroptera, diverged from a recent common ancestor at 225–242 Ma and from Aphidomorpha approximately at 265–280 Ma.…”

“…Next, we concatenated the orthologous genes to a single alignment using RAxML v1.5.5 ( Jarvis et al 2014 ) (-m PROTGAMMAJTT -# 1000). The MCMCTree v4.9 of PAML ( Yang 2007 ) was used to perform the divergence time analysis and calibration time was based on three nodes: D. melanogaster with A. lucorum (320–390 Ma) ( Misof et al 2014 ), A. pisum with A. lucorum (260–280 Ma) ( International Aphid Genomics Consortium 2010 ; Liu et al 2021 ), and H. halys with R. prolixus (144–338 Ma) ( www.timetree.org/ ). The expansion/contraction of gene families was estimated using CAFÉ v4.2.1 ( Han et al 2013 ), with the single birth–death parameter lambda and a significance level of 0.01.…”

A widely diverged locus involved in locomotor adaptation in Heliconius butterflies

“…Using BlastP ( 63 ), we identified the orthology of genes at the L locus, including Col4 α 1 , Vkg , Oseg4 , and na , in multiple insect reference genomes, including H. e. demophoon v1 ( 24 ), D. plexippus v3 ( 64 ), P. xuthus v1.0 ( 65 ), B. mori ( 66 ), D. melanogaster v6.22 ( 67 ), T. castaneum v5.2 ( 68 ), A. mellifera HAv3.1 ( 69 ), A. lucorum ( 70 ), and L. migratoria ( 71 ). We extracted 200-kb regions containing these four orthologous genes and performed multiple alignments to the reference genomes of H. melpomene v2.5 ( 23 ) to determine locally collinear blocks using Mauve ( 72 ) with default parameters.…”

Identification and Expression Analysis of G Protein-Coupled Receptors in the Miridae Insect Apolygus lucorum

“…A. lucorum protein sequences were retrieved from the NCBI Genome database (https://www.ncbi.nlm.nih.gov/assembly/ GCA_009739505.2/) (32). Based on previous studies and records in Flybase (http://www.flybase.org/) (33), the GPCRs of Drosophila melanogaster (34), A. pisum (22), Bombyx mori (17), Tribolium castaneum (16), and Pediculus humanus humanus (18) were collected.…”

“…Apolygus lucorum (Miridae) is an omnivorous pest that occurs worldwide and is notorious for the serious damage it causes in various crops and its substantial economic losses (30,31). Recently, the genome of A. lucorum had been reported, which provided convenient in-depth studies of this pest (32). In the present research, using bioinformatics analysis, we screened the genes encoding GPCRs from the genome of A. lucorum.…”