1
|
Law STS, Nong W, So WL, Baril T, Swale T, Chan CB, Tobe SS, Kai ZP, Bendena WG, Hayward A, Hui JHL. Chromosomal-level reference genome of the moth Heortia vitessoides (Lepidoptera: Crambidae), a major pest of agarwood-producing trees. Genomics 2022; 114:110440. [PMID: 35905835 DOI: 10.1016/j.ygeno.2022.110440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/13/2022] [Accepted: 07/24/2022] [Indexed: 11/04/2022]
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.
Collapse
Affiliation(s)
- Sean T S Law
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Wai Lok So
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | | | | | - Chi Bun Chan
- School of Biological Science, The University of Hong Kong, Hong Kong, China
| | - Stephen S Tobe
- Department of Cell and Systems Biology, University of Toronto, Canada
| | - Zhen-Peng Kai
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, China
| | | | | | - Jerome H L Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
| |
Collapse
|
2
|
Gimenez S, Seninet I, Orsucci M, Audiot P, Nègre N, Nam K, Streiff R, d'Alençon E. Integrated miRNA and transcriptome profiling to explore the molecular determinism of convergent adaptation to corn in two lepidopteran pests of agriculture. BMC Genomics 2021; 22:606. [PMID: 34372780 PMCID: PMC8351448 DOI: 10.1186/s12864-021-07905-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 07/22/2021] [Indexed: 11/11/2022] Open
Abstract
Background The degree to which adaptation to same environment is determined by similar molecular mechanisms, is a topic of broad interest in evolutionary biology, as an indicator of evolutionary predictability. We wished to address if adaptation to the same host plant in phytophagous insects involved related gene expression patterns. We compared sRNA-Seq and RNA-Seq data between two pairs of taxa of Ostrinia and Spodoptera frugiperda sharing maize as host-plant. For the latter, we had previously carried out a reciprocal transplant experiment by feeding of the larvae of the Corn strain (Sf-C) and the Rice strain (Sf-R) on corn versus rice and characterized the mRNA and miRNA responses. Results First, we predicted the genes encoding miRNA in Ostrinia nubilalis (On) and O. scapulalis (Os). Respectively 67 and 65 known miRNA genes, as well as 196 and 190 novel ones were predicted with Os genome using sncRNAs extracted from whole larvae feeding on corn or mugwort. In On, a read counts analysis showed that 37 (55.22%) known miRNAs and 19 (9.84%) novel miRNAs were differentially expressed (DE) on mugwort compared to corn (in Os, 25 known miRs (38.46%) and 8 novel ones (4.34%)). Between species on corn, 8 (12.5%) known miRNAs and 8 (6.83%) novel ones were DE while only one novel miRNA showed expression variation between species on mugwort. Gene target prediction led to the identification of 2953 unique target genes in On and 2719 in Os, among which 11.6% (344) were DE when comparing species on corn. 1.8% (54) of On miR targets showed expression variation upon a change of host-plant. We found molecular changes matching convergent phenotype, i.e., a set of nine miRNAs that are regulated either according to the host-plant both in On and Sf-C or between them on the same plant, corn. Among DE miR target genes between taxa, 13.7% shared exactly the same annotation between the two pairs of taxa and had function related to insect host-plant interaction. Conclusion There is some similarity in underlying genetic mechanisms of convergent evolution of two distant Lepidopteran species having adopted corn in their host range, highlighting possible adaptation genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07905-7.
Collapse
Affiliation(s)
| | | | - Marion Orsucci
- DGIMI, Univ Montpellier, INRAE, Montpellier, France.,CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France.,Department of Plant Biology, Uppsala BioCenter and Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Philippe Audiot
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | | | - Kiwoong Nam
- DGIMI, Univ Montpellier, INRAE, Montpellier, France
| | - Réjane Streiff
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | | |
Collapse
|
3
|
Gschloessl B, Audiot P, Nidelet S, Kergoat GJ, Streiff R. Complete mitogenome data from a European specimen of Ostrinia scapulalis (Walker, 1859) (Lepidoptera, Pyraloidea, Crambidae, Pyraustinae). Data Brief 2020; 33:106427. [PMID: 33241091 PMCID: PMC7672281 DOI: 10.1016/j.dib.2020.106427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/14/2020] [Indexed: 11/29/2022] Open
Abstract
We present an assembly and annotation of the mitogenome of a European specimen of the Adzuki bean borer, Ostrinia scapulalis (Walker, 1859). The data were obtained by combining WGS data issue of a de novo and a previously published sequence library (Gschloessl et al., 2018). We also provide the phylogenetic positioning of the mitogenome within the Ostrinia genus, the Crambidae family and with more distant Lepidoptera species.
Collapse
Affiliation(s)
- Bernhard Gschloessl
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Philippe Audiot
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Sabine Nidelet
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Gael J Kergoat
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Réjane Streiff
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| |
Collapse
|
4
|
Borges dos Santos L, Paulo Gomes Viana J, José Biasotto Francischini F, Victoria Fogliata S, L. Joyce A, Pereira de Souza A, Gabriela Murúa M, J. Clough S, Imaculada Zucchi M. A first draft genome of the Sugarcane borer, Diatraea saccharalis. F1000Res 2020. [DOI: 10.12688/f1000research.26614.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: The sugarcane borer (Diatraea saccharalis), a widely distributed moth throughout the Americas, is a pest that affects economically important crops such as sugarcane, sorghum, wheat, maize and rice. Given its significant impact on yield reduction, whole-genome information of the species is needed. Here, we report the first draft assembly of the D. saccharalis genome. Methods: The genomic sequences were obtained using the Illumina HiSeq 2500 whole-genome sequencing of a single adult male specimen. We assembled the short-reads using the SPAdes software and predicted protein-coding genes using MAKER. Genome assembly completeness was assessed through BUSCO and the repetitive content by RepeatMasker. Results: The 453 Mb assembled sequences contain 1,445 BUSCO gene orthologs and 1,161 predicted gene models identified based on homology evidence to the domestic silk moth, Bombyx mori. The repeat content composes 41.18% of the genomic sequences which is in the range of other lepidopteran species. Conclusions: Functional annotation reveals that predicted gene models are involved in important cellular mechanisms such as metabolic pathways and protein synthesis. Thus, the data generated in this study expands our knowledge on the genomic characteristics of this devastating pest and provides essential resources for future genetic studies of the species.
Collapse
|
5
|
Noriega DD, Arraes FBM, Antonino JD, Macedo LLP, Fonseca FCA, Togawa RC, Grynberg P, Silva MCM, Negrisoli AS, Morgante CV, Grossi-de-Sa MF. Comparative gut transcriptome analysis of Diatraea saccharalis in response to the dietary source. PLoS One 2020; 15:e0235575. [PMID: 32745084 PMCID: PMC7398519 DOI: 10.1371/journal.pone.0235575] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/17/2020] [Indexed: 12/21/2022] Open
Abstract
The sugarcane borer (Diatraea saccharalis, Fabricius, 1794) is a devastating pest that causes millions of dollars of losses each year to sugarcane producers by reducing sugar and ethanol yields. The control of this pest is difficult due to its endophytic behavior and rapid development. Pest management through biotechnological approaches has emerged in recent years as an alternative to currently applied methods. Genetic information about the target pests is often required to perform biotechnology-based management. The genomic and transcriptomic data for D. saccharalis are very limited. Herein, we report a tissue-specific transcriptome of D. saccharalis larvae and a differential expression analysis highlighting the physiological characteristics of this pest in response to two different diets: sugarcane and an artificial diet. Sequencing was performed on the Illumina HiSeq 2000 platform, and a de novo assembly was generated. A total of 27,626 protein-coding unigenes were identified, among which 1,934 sequences were differentially expressed between treatments. Processes such as defence, digestion, detoxification, signaling, and transport were highly represented among the differentially expressed genes (DEGs). Furthermore, seven aminopeptidase genes were identified as candidates to encode receptors of Cry proteins, which are toxins of Bacillus thuringiensis used to control lepidopteran pests. Since plant-insect interactions have produced a considerable number of adaptive responses in hosts and herbivorous insects, the success of phytophagous insects relies on their ability to overcome challenges such as the response to plant defences and the intake of nutrients. In this study, we identified metabolic pathways and specific genes involved in these processes. Thus, our data strongly contribute to the knowledge advancement of insect transcripts, which can be a source of target genes for pest management.
Collapse
Affiliation(s)
- Daniel D. Noriega
- Embrapa Genetic Resources and Biotechnology, Brasília-DF, Brazil
- Department of Cellular Biology, University of Brasília, Brasília-DF, Brazil
- Catholic University of Brasília, Brasília-DF, Brazil
| | - Fabricio B. M. Arraes
- Embrapa Genetic Resources and Biotechnology, Brasília-DF, Brazil
- Biotechnology Center, UFRGS, Porto Alegre-RS, Brazil
| | - José Dijair Antonino
- Embrapa Genetic Resources and Biotechnology, Brasília-DF, Brazil
- Departamento de Agronomia/Entomologia, UFRPE, Recife-PE, Brazil
| | | | - Fernando C. A. Fonseca
- Embrapa Genetic Resources and Biotechnology, Brasília-DF, Brazil
- Department of Cellular Biology, University of Brasília, Brasília-DF, Brazil
| | | | | | | | | | - Carolina V. Morgante
- Embrapa Genetic Resources and Biotechnology, Brasília-DF, Brazil
- Embrapa Semi Arid, Petrolina-PE, Brazil
| | - Maria F. Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology, Brasília-DF, Brazil
- Catholic University of Brasília, Brasília-DF, Brazil
- National Institute of Science and Technology–INCT PlantStress Biotech–EMBRAPA, Brasilia-DF, Brazil
| |
Collapse
|
6
|
Brousseau L, Nidelet S, Streiff R. New WGS data and annotation of the heterosomal vs. autosomal localization of Ostrinia scapulalis (Lepidoptera, Crambidae) nuclear genomic scaffolds. Data Brief 2018; 20:644-648. [PMID: 30197923 PMCID: PMC6127984 DOI: 10.1016/j.dib.2018.08.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/09/2018] [Accepted: 08/03/2018] [Indexed: 11/17/2022] Open
Abstract
Here, we introduce new whole-genome shotgun sequencing and annotation data describing the autosomal vs. Z-heterosomal localization of nuclear genomic scaffolds of the moth species Ostrinia scapulalis. Four WGS libraries (corresponding to 2 males and 2 females) were sequenced with an Illumina HiSeq2500 sequencing technology, and the so-called ‘AD-ratio’ method was applied to distinguish between autosomal and Z-heterosomal scaffolds based on sequencing depth comparisons between homogametic (male) and heterogametic (female) libraries. A total of 25,760 scaffolds (corresponding to 341.69 Mb) were labelled as autosomal and 1273 scaffolds (15.29 Mb) were labelled as Z-heterosomal, totaling about 357 Mb. Besides, 4874 scaffolds (29.07 Mb) remain ambiguous because of a lack of AD-ratio reproducibility between the two replicates. The annotation method was evaluated a posteriori, by comparing depth-based annotation with the exact localization of known genes. Raw genomic data have been deposited and made accessible via the EMBL ENA BioProject id PRJEB26557. Comprehensive annotation is made accessible via the LepidoDB database (http://bipaa.genouest.org/sp/ostrinia_scapulalis/download/genome/v1.2/).
Collapse
Affiliation(s)
- Louise Brousseau
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France.,IRD, UMR DIADE Diversité - Adaptation - Développement, 911 Avenue Agropolis, BP64501, 34394 Montpellier, France
| | - Sabine Nidelet
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Réjane Streiff
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| |
Collapse
|