Cargando…
Draft genome and transcriptome of Nepenthes mirabilis, a carnivorous plant in China
OBJECTIVES: Nepenthes belongs to the monotypic family Nepenthaceae, one of the largest carnivorous plant families. Nepenthes species show impressive adaptive radiation and suffer from being overexploited in nature. Nepenthes mirabilis is the most widely distributed species and the only Nepenthes spe...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2023
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10103442/ https://www.ncbi.nlm.nih.gov/pubmed/37060047 http://dx.doi.org/10.1186/s12863-023-01126-5 |
_version_ | 1785025853251387392 |
---|---|
author | Gao, Yuan Liao, Hao-Bin Liu, Ting-Hong Wu, Jia-Ming Wang, Zheng-Feng Cao, Hong-Lin |
author_facet | Gao, Yuan Liao, Hao-Bin Liu, Ting-Hong Wu, Jia-Ming Wang, Zheng-Feng Cao, Hong-Lin |
author_sort | Gao, Yuan |
collection | PubMed |
description | OBJECTIVES: Nepenthes belongs to the monotypic family Nepenthaceae, one of the largest carnivorous plant families. Nepenthes species show impressive adaptive radiation and suffer from being overexploited in nature. Nepenthes mirabilis is the most widely distributed species and the only Nepenthes species that is naturally distributed within China. Herein, we reported the genome and transcriptome assemblies of N. mirabilis. The assemblies will be useful resources for comparative genomics, to understand the adaptation and conservation of carnivorous species. DATA DESCRIPTION: This work produced ~ 139.5 Gb N. mirabilis whole genome sequencing reads using leaf tissues, and ~ 21.7 Gb and ~ 27.9 Gb of raw RNA-seq reads for its leaves and flowers, respectively. Transcriptome assembly obtained 339,802 transcripts, in which 79,758 open reading frames (ORFs) were identified. Function analysis indicated that these ORFs were mainly associated with proteolysis and DNA integration. The assembled genome was 691,409,685 bp with 159,555 contigs/scaffolds and an N50 of 10,307 bp. The BUSCO assessment of the assembled genome and transcriptome indicated 91.1% and 93.7% completeness, respectively. A total of 42,961 genes were predicted in the genome identified, coding for 45,461 proteins. The predicted genes were annotated using multiple databases, facilitating future functional analyses of them. This is the first genome report on the Nepenthaceae family. |
format | Online Article Text |
id | pubmed-10103442 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-101034422023-04-15 Draft genome and transcriptome of Nepenthes mirabilis, a carnivorous plant in China Gao, Yuan Liao, Hao-Bin Liu, Ting-Hong Wu, Jia-Ming Wang, Zheng-Feng Cao, Hong-Lin BMC Genom Data Data Note OBJECTIVES: Nepenthes belongs to the monotypic family Nepenthaceae, one of the largest carnivorous plant families. Nepenthes species show impressive adaptive radiation and suffer from being overexploited in nature. Nepenthes mirabilis is the most widely distributed species and the only Nepenthes species that is naturally distributed within China. Herein, we reported the genome and transcriptome assemblies of N. mirabilis. The assemblies will be useful resources for comparative genomics, to understand the adaptation and conservation of carnivorous species. DATA DESCRIPTION: This work produced ~ 139.5 Gb N. mirabilis whole genome sequencing reads using leaf tissues, and ~ 21.7 Gb and ~ 27.9 Gb of raw RNA-seq reads for its leaves and flowers, respectively. Transcriptome assembly obtained 339,802 transcripts, in which 79,758 open reading frames (ORFs) were identified. Function analysis indicated that these ORFs were mainly associated with proteolysis and DNA integration. The assembled genome was 691,409,685 bp with 159,555 contigs/scaffolds and an N50 of 10,307 bp. The BUSCO assessment of the assembled genome and transcriptome indicated 91.1% and 93.7% completeness, respectively. A total of 42,961 genes were predicted in the genome identified, coding for 45,461 proteins. The predicted genes were annotated using multiple databases, facilitating future functional analyses of them. This is the first genome report on the Nepenthaceae family. BioMed Central 2023-04-14 /pmc/articles/PMC10103442/ /pubmed/37060047 http://dx.doi.org/10.1186/s12863-023-01126-5 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Data Note Gao, Yuan Liao, Hao-Bin Liu, Ting-Hong Wu, Jia-Ming Wang, Zheng-Feng Cao, Hong-Lin Draft genome and transcriptome of Nepenthes mirabilis, a carnivorous plant in China |
title | Draft genome and transcriptome of Nepenthes mirabilis, a carnivorous plant in China |
title_full | Draft genome and transcriptome of Nepenthes mirabilis, a carnivorous plant in China |
title_fullStr | Draft genome and transcriptome of Nepenthes mirabilis, a carnivorous plant in China |
title_full_unstemmed | Draft genome and transcriptome of Nepenthes mirabilis, a carnivorous plant in China |
title_short | Draft genome and transcriptome of Nepenthes mirabilis, a carnivorous plant in China |
title_sort | draft genome and transcriptome of nepenthes mirabilis, a carnivorous plant in china |
topic | Data Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10103442/ https://www.ncbi.nlm.nih.gov/pubmed/37060047 http://dx.doi.org/10.1186/s12863-023-01126-5 |
work_keys_str_mv | AT gaoyuan draftgenomeandtranscriptomeofnepenthesmirabilisacarnivorousplantinchina AT liaohaobin draftgenomeandtranscriptomeofnepenthesmirabilisacarnivorousplantinchina AT liutinghong draftgenomeandtranscriptomeofnepenthesmirabilisacarnivorousplantinchina AT wujiaming draftgenomeandtranscriptomeofnepenthesmirabilisacarnivorousplantinchina AT wangzhengfeng draftgenomeandtranscriptomeofnepenthesmirabilisacarnivorousplantinchina AT caohonglin draftgenomeandtranscriptomeofnepenthesmirabilisacarnivorousplantinchina |