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Article: Chromosomal-level reference genome of the moth Heortia vitessoides (Lepidoptera: Crambidae), a major pest of agarwood-producing trees

TitleChromosomal-level reference genome of the moth Heortia vitessoides (Lepidoptera: Crambidae), a major pest of agarwood-producing trees
Authors
KeywordsAquilaria
Lepidopteran
microRNA
Sesquiterpenoid
Issue Date26-Jul-2022
PublisherElsevier
Citation
Genomics, 2022, v. 114, n. 4 How to Cite?
Abstract

The moth Heortia vitessoides Moore (Lepidoptera: Crambidae) is a major pest of ecologically, commercially and culturally important agarwood-producing trees in the genus Aquilaria. In particular, H. vitessoides is one of the most destructive defoliating pests of the incense tree Aquilaria sinesis, which produces a valuable fragrant wood used as incense and in traditional Chinese medicine [33]. Nevertheless, a genomic resource for H. vitessoides is lacking. Here, we present a chromosomal-level assembly for H. vitessoides, consisting of a 517 megabase (Mb) genome assembly with high physical contiguity (scaffold N50 of 18.2 Mb) and high completeness (97.9% complete BUSCO score). To aid gene annotation, 8 messenger RNA transcriptomes from different developmental stages were generated, and a total of 16,421 gene models were predicted. Expansion of gene families involved in xenobiotic metabolism and development were detected, including duplications of cytosolic sulfotransferase (SULT) genes shared among lepidopterans. In addition, small RNA sequencing of 5 developmental stages of H. vitessoides facilitated the identification of 85 lepidopteran conserved microRNAs, 94 lineage-specific microRNAs, as well as several microRNA clusters. A large proportion of the H. vitessoides genome consists of repeats, with a 29.12% total genomic contribution from transposable elements, of which long interspersed nuclear elements (LINEs) are the dominant component (17.41%). A sharp decrease in the genome-wide percentage of LINEs with lower levels of genetic distance to family consensus sequences suggests that LINE activity has peaked in H. vitessoides. In contrast, opposing patterns suggest a substantial recent increase in DNA and LTR element activity. Together with annotations of essential sesquiterpenoid hormonal pathways, neuropeptides, microRNAs and transposable elements, the high-quality genomic and transcriptomic resources we provide for the economically important moth H. vitessoides provide a platform for the development of genomic approaches to pest management, and contribute to addressing fundamental research questions in Lepidoptera.


Persistent Identifierhttp://hdl.handle.net/10722/337939
ISSN
2023 Impact Factor: 3.4
2023 SCImago Journal Rankings: 0.850
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorLaw, STS-
dc.contributor.authorNong, W-
dc.contributor.authorSo, WL-
dc.contributor.authorBaril, T-
dc.contributor.authorSwale, T-
dc.contributor.authorChan, CB-
dc.contributor.authorTobe, SS-
dc.contributor.authorKai, ZP-
dc.contributor.authorBendena, WG-
dc.contributor.authorHayward, A-
dc.contributor.authorHui, JHL-
dc.date.accessioned2024-03-11T10:25:04Z-
dc.date.available2024-03-11T10:25:04Z-
dc.date.issued2022-07-26-
dc.identifier.citationGenomics, 2022, v. 114, n. 4-
dc.identifier.issn0888-7543-
dc.identifier.urihttp://hdl.handle.net/10722/337939-
dc.description.abstract<p>The moth Heortia vitessoides Moore (Lepidoptera: Crambidae) is a major pest of ecologically, commercially and culturally important agarwood-producing trees in the genus Aquilaria. In particular, H. vitessoides is one of the most destructive defoliating pests of the incense tree Aquilaria sinesis, which produces a valuable fragrant wood used as incense and in traditional Chinese medicine [33]. Nevertheless, a genomic resource for H. vitessoides is lacking. Here, we present a chromosomal-level assembly for H. vitessoides, consisting of a 517 megabase (Mb) genome assembly with high physical contiguity (scaffold N50 of 18.2 Mb) and high completeness (97.9% complete BUSCO score). To aid gene annotation, 8 messenger RNA transcriptomes from different developmental stages were generated, and a total of 16,421 gene models were predicted. Expansion of gene families involved in xenobiotic metabolism and development were detected, including duplications of cytosolic sulfotransferase (SULT) genes shared among lepidopterans. In addition, small RNA sequencing of 5 developmental stages of H. vitessoides facilitated the identification of 85 lepidopteran conserved microRNAs, 94 lineage-specific microRNAs, as well as several microRNA clusters. A large proportion of the H. vitessoides genome consists of repeats, with a 29.12% total genomic contribution from transposable elements, of which long interspersed nuclear elements (LINEs) are the dominant component (17.41%). A sharp decrease in the genome-wide percentage of LINEs with lower levels of genetic distance to family consensus sequences suggests that LINE activity has peaked in H. vitessoides. In contrast, opposing patterns suggest a substantial recent increase in DNA and LTR element activity. Together with annotations of essential sesquiterpenoid hormonal pathways, neuropeptides, microRNAs and transposable elements, the high-quality genomic and transcriptomic resources we provide for the economically important moth H. vitessoides provide a platform for the development of genomic approaches to pest management, and contribute to addressing fundamental research questions in Lepidoptera.</p>-
dc.languageeng-
dc.publisherElsevier-
dc.relation.ispartofGenomics-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.subjectAquilaria-
dc.subjectLepidopteran-
dc.subjectmicroRNA-
dc.subjectSesquiterpenoid-
dc.titleChromosomal-level reference genome of the moth Heortia vitessoides (Lepidoptera: Crambidae), a major pest of agarwood-producing trees-
dc.typeArticle-
dc.identifier.doi10.1016/j.ygeno.2022.110440-
dc.identifier.scopuseid_2-s2.0-85135415613-
dc.identifier.volume114-
dc.identifier.issue4-
dc.identifier.eissn1089-8646-
dc.identifier.isiWOS:000837420100002-
dc.identifier.issnl0888-7543-

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