A chromosome-scale reference genome of Lobularia maritima, an ornamental plant with high stress tolerance

Lobularia maritima (L.) Desv. is an ornamental plant cultivated across the world. It belongs to the family Brassicaceae and can tolerate dry, poor and contaminated habitats. Here, we present a chromosome-scale, high-quality genome assembly of L. maritima based on integrated approaches combining Illu...

Descripción completa

Detalles Bibliográficos
Autores principales: Huang, Li, Ma, Yazhen, Jiang, Jiebei, Li, Ting, Yang, Wenjie, Zhang, Lei, Wu, Lei, Feng, Landi, Xi, Zhenxiang, Xu, Xiaoting, Liu, Jianquan, Hu, Quanjun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7705659/
https://www.ncbi.nlm.nih.gov/pubmed/33328471
http://dx.doi.org/10.1038/s41438-020-00422-w
_version_ 1783616988597190656
author Huang, Li
Ma, Yazhen
Jiang, Jiebei
Li, Ting
Yang, Wenjie
Zhang, Lei
Wu, Lei
Feng, Landi
Xi, Zhenxiang
Xu, Xiaoting
Liu, Jianquan
Hu, Quanjun
author_facet Huang, Li
Ma, Yazhen
Jiang, Jiebei
Li, Ting
Yang, Wenjie
Zhang, Lei
Wu, Lei
Feng, Landi
Xi, Zhenxiang
Xu, Xiaoting
Liu, Jianquan
Hu, Quanjun
author_sort Huang, Li
collection PubMed
description Lobularia maritima (L.) Desv. is an ornamental plant cultivated across the world. It belongs to the family Brassicaceae and can tolerate dry, poor and contaminated habitats. Here, we present a chromosome-scale, high-quality genome assembly of L. maritima based on integrated approaches combining Illumina short reads and Hi–C chromosome conformation data. The genome was assembled into 12 pseudochromosomes with a 197.70 Mb length, and it includes 25,813 protein-coding genes. Approximately 41.94% of the genome consists of repetitive sequences, with abundant long terminal repeat transposable elements. Comparative genomic analysis confirmed that L. maritima underwent a species-specific whole-genome duplication (WGD) event ~22.99 million years ago. We identified ~1900 species-specific genes, 25 expanded gene families, and 50 positively selected genes in L. maritima. Functional annotations of these genes indicated that they are mainly related to stress tolerance. These results provide new insights into the stress tolerance of L. maritima, and this genomic resource will be valuable for further genetic improvement of this important ornamental plant.
format Online
Article
Text
id pubmed-7705659
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher Nature Publishing Group UK
record_format MEDLINE/PubMed
spelling pubmed-77056592020-12-03 A chromosome-scale reference genome of Lobularia maritima, an ornamental plant with high stress tolerance Huang, Li Ma, Yazhen Jiang, Jiebei Li, Ting Yang, Wenjie Zhang, Lei Wu, Lei Feng, Landi Xi, Zhenxiang Xu, Xiaoting Liu, Jianquan Hu, Quanjun Hortic Res Article Lobularia maritima (L.) Desv. is an ornamental plant cultivated across the world. It belongs to the family Brassicaceae and can tolerate dry, poor and contaminated habitats. Here, we present a chromosome-scale, high-quality genome assembly of L. maritima based on integrated approaches combining Illumina short reads and Hi–C chromosome conformation data. The genome was assembled into 12 pseudochromosomes with a 197.70 Mb length, and it includes 25,813 protein-coding genes. Approximately 41.94% of the genome consists of repetitive sequences, with abundant long terminal repeat transposable elements. Comparative genomic analysis confirmed that L. maritima underwent a species-specific whole-genome duplication (WGD) event ~22.99 million years ago. We identified ~1900 species-specific genes, 25 expanded gene families, and 50 positively selected genes in L. maritima. Functional annotations of these genes indicated that they are mainly related to stress tolerance. These results provide new insights into the stress tolerance of L. maritima, and this genomic resource will be valuable for further genetic improvement of this important ornamental plant. Nature Publishing Group UK 2020-12-01 /pmc/articles/PMC7705659/ /pubmed/33328471 http://dx.doi.org/10.1038/s41438-020-00422-w Text en © The Author(s) 2020 Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Huang, Li
Ma, Yazhen
Jiang, Jiebei
Li, Ting
Yang, Wenjie
Zhang, Lei
Wu, Lei
Feng, Landi
Xi, Zhenxiang
Xu, Xiaoting
Liu, Jianquan
Hu, Quanjun
A chromosome-scale reference genome of Lobularia maritima, an ornamental plant with high stress tolerance
title A chromosome-scale reference genome of Lobularia maritima, an ornamental plant with high stress tolerance
title_full A chromosome-scale reference genome of Lobularia maritima, an ornamental plant with high stress tolerance
title_fullStr A chromosome-scale reference genome of Lobularia maritima, an ornamental plant with high stress tolerance
title_full_unstemmed A chromosome-scale reference genome of Lobularia maritima, an ornamental plant with high stress tolerance
title_short A chromosome-scale reference genome of Lobularia maritima, an ornamental plant with high stress tolerance
title_sort chromosome-scale reference genome of lobularia maritima, an ornamental plant with high stress tolerance
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7705659/
https://www.ncbi.nlm.nih.gov/pubmed/33328471
http://dx.doi.org/10.1038/s41438-020-00422-w
work_keys_str_mv AT huangli achromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance
AT mayazhen achromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance
AT jiangjiebei achromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance
AT liting achromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance
AT yangwenjie achromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance
AT zhanglei achromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance
AT wulei achromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance
AT fenglandi achromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance
AT xizhenxiang achromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance
AT xuxiaoting achromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance
AT liujianquan achromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance
AT huquanjun achromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance
AT huangli chromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance
AT mayazhen chromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance
AT jiangjiebei chromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance
AT liting chromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance
AT yangwenjie chromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance
AT zhanglei chromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance
AT wulei chromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance
AT fenglandi chromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance
AT xizhenxiang chromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance
AT xuxiaoting chromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance
AT liujianquan chromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance
AT huquanjun chromosomescalereferencegenomeoflobulariamaritimaanornamentalplantwithhighstresstolerance

Ejemplares similares