Chloroplast genome features of Moricandia arvensis (Brassicaceae), a C3-C4 intermediate photosynthetic species.

Moricandia arvensis, a plant species originating from the Mediterranean, has been classified as a rare C3-C4 intermediate species, and it is a possible bridge during the evolutionary process from C3 to C4 plant photosynthesis in the family Brassicaceae. Understanding the genomic structure, gene orde...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Bin Zhu, Lijuan Hu, Fang Qian, Zuomin Gao, Chenchen Gan, Zhaochao Liu, Xuye Du, Hongcheng Wang
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/68fd921f178b4116bea722d9a80f7022
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:68fd921f178b4116bea722d9a80f7022
record_format	dspace
spelling	oai:doaj.org-article:68fd921f178b4116bea722d9a80f70222021-12-02T20:09:37ZChloroplast genome features of Moricandia arvensis (Brassicaceae), a C3-C4 intermediate photosynthetic species.1932-620310.1371/journal.pone.0254109https://doaj.org/article/68fd921f178b4116bea722d9a80f70222021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0254109https://doaj.org/toc/1932-6203Moricandia arvensis, a plant species originating from the Mediterranean, has been classified as a rare C3-C4 intermediate species, and it is a possible bridge during the evolutionary process from C3 to C4 plant photosynthesis in the family Brassicaceae. Understanding the genomic structure, gene order, and gene content of chloroplasts (cp) of such species can provide a glimpse into the evolution of photosynthesis. In the present study, we obtained a well-annotated cp genome of M. arvensis using long PacBio and short Illumina reads with a de novo assembly strategy. The M. arvensis cp genome was a quadripartite circular molecule with the length of 153,312 bp, including two inverted repeats (IR) regions of 26,196 bp, divided by a small single copy (SSC) region of 17,786 bp and a large single copy (LSC) region of 83,134 bp. We detected 112 unigenes in this genome, comprising 79 protein-coding genes, 29 tRNAs, and four rRNAs. Forty-nine long repeat sequences and 51 simple sequence repeat (SSR) loci of 15 repeat types were identified. The analysis of Ks (synonymous) and Ka (non-synonymous) substitution rates indicated that the genes associated with "subunits of ATP synthase" (atpB), "subunits of NADH-dehydrogenase" (ndhG and ndhE), and "self-replication" (rps12 and rpl16) showed relatively higher Ka/Ks values than those of the other genes. The gene content, gene order, and LSC/IR/SSC boundaries and adjacent genes of the M. arvensis cp genome were highly conserved compared to those in related C3 species. Our phylogenetic analysis demonstrated that M. arvensis was clustered into a subclade with cultivated Brassica species and Raphanus sativus, indicating that M. arvensis was not involved in an independent evolutionary origin event. These results will open the way for further studies on the evolutionary process from C3 to C4 photosynthesis and hopefully provide guidance for utilizing M. arvensis as a resource for improvinng photosynthesis efficiency in cultivated Brassica species.Bin ZhuLijuan HuFang QianZuomin GaoChenchen GanZhaochao LiuXuye DuHongcheng WangPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 7, p e0254109 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Bin Zhu Lijuan Hu Fang Qian Zuomin Gao Chenchen Gan Zhaochao Liu Xuye Du Hongcheng Wang Chloroplast genome features of Moricandia arvensis (Brassicaceae), a C3-C4 intermediate photosynthetic species.
description	Moricandia arvensis, a plant species originating from the Mediterranean, has been classified as a rare C3-C4 intermediate species, and it is a possible bridge during the evolutionary process from C3 to C4 plant photosynthesis in the family Brassicaceae. Understanding the genomic structure, gene order, and gene content of chloroplasts (cp) of such species can provide a glimpse into the evolution of photosynthesis. In the present study, we obtained a well-annotated cp genome of M. arvensis using long PacBio and short Illumina reads with a de novo assembly strategy. The M. arvensis cp genome was a quadripartite circular molecule with the length of 153,312 bp, including two inverted repeats (IR) regions of 26,196 bp, divided by a small single copy (SSC) region of 17,786 bp and a large single copy (LSC) region of 83,134 bp. We detected 112 unigenes in this genome, comprising 79 protein-coding genes, 29 tRNAs, and four rRNAs. Forty-nine long repeat sequences and 51 simple sequence repeat (SSR) loci of 15 repeat types were identified. The analysis of Ks (synonymous) and Ka (non-synonymous) substitution rates indicated that the genes associated with "subunits of ATP synthase" (atpB), "subunits of NADH-dehydrogenase" (ndhG and ndhE), and "self-replication" (rps12 and rpl16) showed relatively higher Ka/Ks values than those of the other genes. The gene content, gene order, and LSC/IR/SSC boundaries and adjacent genes of the M. arvensis cp genome were highly conserved compared to those in related C3 species. Our phylogenetic analysis demonstrated that M. arvensis was clustered into a subclade with cultivated Brassica species and Raphanus sativus, indicating that M. arvensis was not involved in an independent evolutionary origin event. These results will open the way for further studies on the evolutionary process from C3 to C4 photosynthesis and hopefully provide guidance for utilizing M. arvensis as a resource for improvinng photosynthesis efficiency in cultivated Brassica species.
format	article
author	Bin Zhu Lijuan Hu Fang Qian Zuomin Gao Chenchen Gan Zhaochao Liu Xuye Du Hongcheng Wang
author_facet	Bin Zhu Lijuan Hu Fang Qian Zuomin Gao Chenchen Gan Zhaochao Liu Xuye Du Hongcheng Wang
author_sort	Bin Zhu
title	Chloroplast genome features of Moricandia arvensis (Brassicaceae), a C3-C4 intermediate photosynthetic species.
title_short	Chloroplast genome features of Moricandia arvensis (Brassicaceae), a C3-C4 intermediate photosynthetic species.
title_full	Chloroplast genome features of Moricandia arvensis (Brassicaceae), a C3-C4 intermediate photosynthetic species.
title_fullStr	Chloroplast genome features of Moricandia arvensis (Brassicaceae), a C3-C4 intermediate photosynthetic species.
title_full_unstemmed	Chloroplast genome features of Moricandia arvensis (Brassicaceae), a C3-C4 intermediate photosynthetic species.
title_sort	chloroplast genome features of moricandia arvensis (brassicaceae), a c3-c4 intermediate photosynthetic species.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/68fd921f178b4116bea722d9a80f7022
work_keys_str_mv	AT binzhu chloroplastgenomefeaturesofmoricandiaarvensisbrassicaceaeac3c4intermediatephotosyntheticspecies AT lijuanhu chloroplastgenomefeaturesofmoricandiaarvensisbrassicaceaeac3c4intermediatephotosyntheticspecies AT fangqian chloroplastgenomefeaturesofmoricandiaarvensisbrassicaceaeac3c4intermediatephotosyntheticspecies AT zuomingao chloroplastgenomefeaturesofmoricandiaarvensisbrassicaceaeac3c4intermediatephotosyntheticspecies AT chenchengan chloroplastgenomefeaturesofmoricandiaarvensisbrassicaceaeac3c4intermediatephotosyntheticspecies AT zhaochaoliu chloroplastgenomefeaturesofmoricandiaarvensisbrassicaceaeac3c4intermediatephotosyntheticspecies AT xuyedu chloroplastgenomefeaturesofmoricandiaarvensisbrassicaceaeac3c4intermediatephotosyntheticspecies AT hongchengwang chloroplastgenomefeaturesofmoricandiaarvensisbrassicaceaeac3c4intermediatephotosyntheticspecies
_version_	1718375065810108416

Chloroplast genome features of Moricandia arvensis (Brassicaceae), a C3-C4 intermediate photosynthetic species.

Ejemplares similares