Dataset of de novo assembly and functional annotation of the transcriptome of certain developmental stages of coconut rhinoceros beetle, Oryctes rhinoceros L.

Arvind, Kumar; Rajesh, M. K.; Josephrajkumar, A.; Grace, Tony

doi:10.1016/j.dib.2019.105036

Cited by 6 publications

(10 citation statements)

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“…3 J) which enables an automated training of the gene prediction tools (GeneMark-EX and AUGUSTUS) with the extrinsic evidence from the RNA-Seq experiments [ 40 – 46 ]. We used the publicly-available RNA-seq data that cover different life stages of O. rhinoceros , from early instar larva, late instar larva, pupa, and the adult stage (NCBI accession: PRJNA486419; [ 47 ]), which is expected to maximize the probability of capturing the sequences of the entire set of expressed genes in this organism. To check data quality from these RNA-seq samples, we first aligned the reads against our genome assembly with the splice-aware aligner HISAT2 [ 48 ], and used these alignments to produce a genome-guided transcriptome with Trinity [ 49 ].…”

Section: Resultsmentioning

confidence: 99%

A high-quality de novo genome assembly based on nanopore sequencing of a wild-caught coconut rhinoceros beetle (Oryctes rhinoceros)

et al. 2022

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Background An optimal starting point for relating genome function to organismal biology is a high-quality nuclear genome assembly, and long-read sequencing is revolutionizing the production of this genomic resource in insects. Despite this, nuclear genome assemblies have been under-represented for agricultural insect pests, particularly from the order Coleoptera. Here we present a de novo genome assembly and structural annotation for the coconut rhinoceros beetle, Oryctes rhinoceros (Coleoptera: Scarabaeidae), based on Oxford Nanopore Technologies (ONT) long-read data generated from a wild-caught female, as well as the assembly process that also led to the recovery of the complete circular genome assemblies of the beetle’s mitochondrial genome and that of the biocontrol agent, Oryctes rhinoceros nudivirus (OrNV). As an invasive pest of palm trees, O. rhinoceros is undergoing an expansion in its range across the Pacific Islands, requiring new approaches to management that may include strategies facilitated by genome assembly and annotation. Results High-quality DNA isolated from an adult female was used to create four ONT libraries that were sequenced using four MinION flow cells, producing a total of 27.2 Gb of high-quality long-read sequences. We employed an iterative assembly process and polishing with one lane of high-accuracy Illumina reads, obtaining a final size of the assembly of 377.36 Mb that had high contiguity (fragment N50 length = 12 Mb) and accuracy, as evidenced by the exceptionally high completeness of the benchmarked set of conserved single-copy orthologous genes (BUSCO completeness = 99.1%). These quality metrics place our assembly ahead of the published Coleopteran genomes, including that of an insect model, the red flour beetle (Tribolium castaneum). The structural annotation of the nuclear genome assembly contained a highly-accurate set of 16,371 protein-coding genes, with only 2.8% missing BUSCOs, and the expected number of non-coding RNAs. The number and structure of paralogous genes in a gene family like Sigma GST is lower than in another scarab beetle (Onthophagus taurus), but higher than in the red flour beetle (Tribolium castaneum), which suggests expansion of this GST class in Scarabaeidae. The quality of our gene models was also confirmed with the correct placement of O. rhinoceros among other members of the rhinoceros beetles (subfamily Dynastinae) in a phylogeny based on the sequences of 95 protein-coding genes in 373 beetle species from all major lineages of Coleoptera. Finally, we provide a list of 30 candidate dsRNA targets whose orthologs have been experimentally validated as highly effective targets for RNAi-based control of several beetles. Conclusions The genomic resources produced in this study form a foundation for further functional genetic research and management programs that may inform the control and surveillance of O. rhinoceros populations, and we demonstrate the efficacy of de novo genome assembly using long-read ONT data from a single field-caught insect.

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Section: Resultsmentioning

confidence: 99%

A high-quality de novo genome assembly based on nanopore sequencing of a wild-caught coconut rhinoceros beetle (Oryctes rhinoceros)

et al. 2022

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“…To delineate protein-coding genes, we used the BRAKER pipeline (Figure 3J) which enables an automated training of the gene prediction tools (GeneMark-EX and AUGUSTUS) with the extrinsic evidence from the RNA-Seq experiments [39]–[45]. We used the publicly-available RNA-seq data that cover different life stages of O. rhinoceros , from early instar larva, late instar larva, pupa, and the adult stage (NCBI accession: PRJNA486419; [46]), which is expected to maximize the probability of capturing the sequences of the entire set of expressed genes in this organism. To check data quality from these RNA-seq samples, we first aligned the reads against our genome assembly with the splice-aware aligner HISAT2 [47], and used these alignments to produce a genome-guided transcriptome with Trinity [48].…”

Section: Resultsmentioning

confidence: 99%

“…The completeness of the initial genome assembly (S4-i-v3) was evaluated using: (a) alignment of DNA-seq data, (b) alignment of RNA-seq data, and (c) the recovery of the benchmarked universal single copy orthologs (BUSCOs) [33]. We used the BWA-MEM aligner with default settings and recorded the percentage of mapped Illumina reads from the whole-genome sequencing dataset (Illumina DNA library described above) and four independently-generated RNA-seq datasets from the beetle’s four life stages [46](NCBI SRA Accession: PRJNA486419) that were combined prior to alignment with the beetle genome assembly. The number of recovered universal singlecopy orthologs (SCOs) was obtained using the “genome autolineage” mode in BUSCO version 4.0.6, that first searched the databases ‘eucariota_odb10’ (7 species, 255 SCOs), and ‘endopterigota_odb10’ (56 species, 2,124 SCOs).…”

Section: Methodsmentioning

confidence: 99%

“…rhinoceros, from early instar larva, late instar larva, pupa, and the adult stage (NCBI accession: PRJNA486419; [46]), which is expected to maximize the probability of capturing the sequences of the entire set of expressed genes in this organism. To check data quality from these RNA-seq samples, we first aligned the reads against our genome assembly with the splice-aware aligner HISAT2 [47], and used these alignments to produce a genome-guided transcriptome with Trinity [48].…”

Section: Structural Annotation and Quality Assessment Of The Assemblymentioning

confidence: 99%

“…To perform the structural annotation of the final genome assembly, we used the independently-generated RNA-seq datasets from the beetle's four different life stages (NCBI SRA Accession: PRJNA486419) [46]. The RNA-seq reads were pruned of the Illumina adapters and aligned against our genome assembly with the splice-aware aligner HISAT2 (Figure 3I).…”

Section: Structural Annotationmentioning

confidence: 99%

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A high-quality de novo genome assembly based on nanopore sequencing of a wild-caught coconut rhinoceros beetle (Oryctes rhinoceros)

Filipović

Rašić

Hereward

et al. 2021

Preprint

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Background: An optimal starting point for relating genome function to organismal biology is a high-quality nuclear genome assembly, and long-read sequencing is revolutionizing the production of this genomic resource in insects. Despite this, nuclear genome assemblies have been under-represented for agricultural insect pests, particularly from the order Coleoptera. Here we present a de novo genome assembly and structural annotation for the coconut rhinoceros beetle, Oryctes rhinoceros (Coleoptera: Scarabaeidae), based on Oxford Nanopore Technologies (ONT) long-read data generated from a wild-caught female, as well as the assembly process that also led to the recovery of the complete circular genome assemblies of the beetle's mitochondrial genome and that of the biocontrol agent, Oryctes rhinoceros nudivirus (OrNV). As an invasive pest of palm trees, O. rhinoceros is undergoing an expansion in its range across the Pacific Islands, requiring new approaches to management that may include strategies facilitated by genome assembly and annotation. Results: High-quality DNA isolated from an adult female was used to create four ONT libraries that were sequenced using four MinION flow cells, producing a total of 27.2 Gb of high-quality long-read sequences. We employed an iterative assembly process and polishing with one lane of high-accuracy Illumina reads, obtaining a final size of the assembly of 377.36 Mb that had high contiguity (fragment N50 length = 12 Mb) and accuracy, as evidenced by the exceptionally high completeness of the benchmarked set of conserved single-copy orthologous genes (BUSCO completeness = 99.11%). These quality metrics place our assembly as the most complete of the published Coleopteran genomes. The structural annotation of the nuclear genome assembly contained a highly-accurate set of 16,371 protein-coding genes showing BUSCO completeness of 92.09%, as well as the expected number of non-coding RNAs and the number and structure of paralogous genes in a gene family like Sigma GST. Conclusions: The genomic resources produced in this study form a foundation for further functional genetic research and management programs that may inform the control and surveillance of O. rhinoceros populations, and we demonstrate the efficacy of de novo genome assembly using long-read ONT data from a single field-caught insect.

show abstract

Reference genes for expression studies in different developmental stages of Oryctes rhinoceros, the coconut rhinoceros beetle

Arvind

Antony

Rajesh

et al. 2023

Journal of Asia-Pacific Entomology

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Dataset of de novo assembly and functional annotation of the transcriptome of certain developmental stages of coconut rhinoceros beetle, Oryctes rhinoceros L.

Cited by 6 publications

References 4 publications

A high-quality de novo genome assembly based on nanopore sequencing of a wild-caught coconut rhinoceros beetle (Oryctes rhinoceros)

A high-quality de novo genome assembly based on nanopore sequencing of a wild-caught coconut rhinoceros beetle (Oryctes rhinoceros)

A high-quality de novo genome assembly based on nanopore sequencing of a wild-caught coconut rhinoceros beetle (Oryctes rhinoceros)

Reference genes for expression studies in different developmental stages of Oryctes rhinoceros, the coconut rhinoceros beetle

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