De Novo Genome Assembly at Chromosome-Scale of <i>Hermetia illucens</i> (Diptera Stratiomyidae) via PacBio and Omni-C Proximity Ligation Technology
<i>Hermetia illucens</i> is a species of great interest for numerous industrial applications. A high-quality reference genome is already available for <i>H. illucens</i>. However, the worldwide maintenance of numerous captive populations of <i>H. illucens</i>, eac...
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MDPI AG
2024-02-01
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| Series: | Insects |
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| Online Access: | https://www.mdpi.com/2075-4450/15/2/133 |
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| author | Simone Costagli Linda Abenaim Giulia Rosini Barbara Conti Roberto Giovannoni |
| author_facet | Simone Costagli Linda Abenaim Giulia Rosini Barbara Conti Roberto Giovannoni |
| author_sort | Simone Costagli |
| collection | DOAJ |
| description | <i>Hermetia illucens</i> is a species of great interest for numerous industrial applications. A high-quality reference genome is already available for <i>H. illucens</i>. However, the worldwide maintenance of numerous captive populations of <i>H. illucens</i>, each with its own genotypic and phenotypic characteristics, made it of interest to perform a de novo genome assembly on one population of <i>H. illucens</i> to define a chromosome-scale genome assembly. By combining the PacBio and the Omni-C proximity ligation technologies, a new <i>H. illucens</i> chromosome-scale genome of 888.59 Mb, with a scaffold N50 value of 162.19 Mb, was assembled. The final chromosome-scale assembly obtained a BUSCO completeness of 89.1%. By exploiting the Omni-C proximity ligation technology, topologically associated domains and other topological features that play a key role in the regulation of gene expression were identified. Further, 65.62% of genomic sequences were masked as repeated sequences, and 32,516 genes were annotated using the MAKER pipeline. The <i>H. illucens</i> Lsp-2 genes that were annotated were further characterized, and the three-dimensional organization of the encoded proteins was predicted. A new chromosome-scale genome assembly of good quality for <i>H. illucens</i> was assembled, and the genomic annotation phase was initiated. The availability of this new chromosome-scale genome assembly enables the further characterization, both genotypically and phenotypically, of a species of interest for several biotechnological applications. |
| first_indexed | 2024-03-07T22:27:59Z |
| format | Article |
| id | doaj.art-c968b084c3624a6c9890db3b55199916 |
| institution | Directory Open Access Journal |
| issn | 2075-4450 |
| language | English |
| last_indexed | 2024-03-07T22:27:59Z |
| publishDate | 2024-02-01 |
| publisher | MDPI AG |
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| series | Insects |
| spelling | doaj.art-c968b084c3624a6c9890db3b551999162024-02-23T15:21:35ZengMDPI AGInsects2075-44502024-02-0115213310.3390/insects15020133De Novo Genome Assembly at Chromosome-Scale of <i>Hermetia illucens</i> (Diptera Stratiomyidae) via PacBio and Omni-C Proximity Ligation TechnologySimone Costagli0Linda Abenaim1Giulia Rosini2Barbara Conti3Roberto Giovannoni4Department of Biology, University of Pisa, Via Derna 1, 56126 Pisa, ItalyDepartment of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, ItalyDepartment of Biology, University of Pisa, Via Derna 1, 56126 Pisa, ItalyDepartment of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, ItalyDepartment of Biology, University of Pisa, Via Derna 1, 56126 Pisa, Italy<i>Hermetia illucens</i> is a species of great interest for numerous industrial applications. A high-quality reference genome is already available for <i>H. illucens</i>. However, the worldwide maintenance of numerous captive populations of <i>H. illucens</i>, each with its own genotypic and phenotypic characteristics, made it of interest to perform a de novo genome assembly on one population of <i>H. illucens</i> to define a chromosome-scale genome assembly. By combining the PacBio and the Omni-C proximity ligation technologies, a new <i>H. illucens</i> chromosome-scale genome of 888.59 Mb, with a scaffold N50 value of 162.19 Mb, was assembled. The final chromosome-scale assembly obtained a BUSCO completeness of 89.1%. By exploiting the Omni-C proximity ligation technology, topologically associated domains and other topological features that play a key role in the regulation of gene expression were identified. Further, 65.62% of genomic sequences were masked as repeated sequences, and 32,516 genes were annotated using the MAKER pipeline. The <i>H. illucens</i> Lsp-2 genes that were annotated were further characterized, and the three-dimensional organization of the encoded proteins was predicted. A new chromosome-scale genome assembly of good quality for <i>H. illucens</i> was assembled, and the genomic annotation phase was initiated. The availability of this new chromosome-scale genome assembly enables the further characterization, both genotypically and phenotypically, of a species of interest for several biotechnological applications.https://www.mdpi.com/2075-4450/15/2/133<i>Hermetia illucens</i>de novo genome assemblytopology associated domainsgene annotation<i>Larval serum protein-2</i> |
| spellingShingle | Simone Costagli Linda Abenaim Giulia Rosini Barbara Conti Roberto Giovannoni De Novo Genome Assembly at Chromosome-Scale of <i>Hermetia illucens</i> (Diptera Stratiomyidae) via PacBio and Omni-C Proximity Ligation Technology Insects <i>Hermetia illucens</i> de novo genome assembly topology associated domains gene annotation <i>Larval serum protein-2</i> |
| title | De Novo Genome Assembly at Chromosome-Scale of <i>Hermetia illucens</i> (Diptera Stratiomyidae) via PacBio and Omni-C Proximity Ligation Technology |
| title_full | De Novo Genome Assembly at Chromosome-Scale of <i>Hermetia illucens</i> (Diptera Stratiomyidae) via PacBio and Omni-C Proximity Ligation Technology |
| title_fullStr | De Novo Genome Assembly at Chromosome-Scale of <i>Hermetia illucens</i> (Diptera Stratiomyidae) via PacBio and Omni-C Proximity Ligation Technology |
| title_full_unstemmed | De Novo Genome Assembly at Chromosome-Scale of <i>Hermetia illucens</i> (Diptera Stratiomyidae) via PacBio and Omni-C Proximity Ligation Technology |
| title_short | De Novo Genome Assembly at Chromosome-Scale of <i>Hermetia illucens</i> (Diptera Stratiomyidae) via PacBio and Omni-C Proximity Ligation Technology |
| title_sort | de novo genome assembly at chromosome scale of i hermetia illucens i diptera stratiomyidae via pacbio and omni c proximity ligation technology |
| topic | <i>Hermetia illucens</i> de novo genome assembly topology associated domains gene annotation <i>Larval serum protein-2</i> |
| url | https://www.mdpi.com/2075-4450/15/2/133 |
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