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Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales

The genus Sedum, with about 470 recognized species, is classified in the family Crassulaceae of the order Saxifragales. Phylogenetic relationships within the Saxifragales are still unresolved and controversial. In this study, the plastome of S. plumbizincicola was firstly presented, with a focus on...

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Autores principales: Ding, Hengwu, Zhu, Ran, Dong, Jinxiu, Bi, De, Jiang, Lan, Zeng, Juhua, Huang, Qingyu, Liu, Huan, Xu, Wenzhong, Wu, Longhua, Kan, Xianzhao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6843225/
https://www.ncbi.nlm.nih.gov/pubmed/31569538
http://dx.doi.org/10.3390/plants8100386
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author Ding, Hengwu
Zhu, Ran
Dong, Jinxiu
Bi, De
Jiang, Lan
Zeng, Juhua
Huang, Qingyu
Liu, Huan
Xu, Wenzhong
Wu, Longhua
Kan, Xianzhao
author_facet Ding, Hengwu
Zhu, Ran
Dong, Jinxiu
Bi, De
Jiang, Lan
Zeng, Juhua
Huang, Qingyu
Liu, Huan
Xu, Wenzhong
Wu, Longhua
Kan, Xianzhao
author_sort Ding, Hengwu
collection PubMed
description The genus Sedum, with about 470 recognized species, is classified in the family Crassulaceae of the order Saxifragales. Phylogenetic relationships within the Saxifragales are still unresolved and controversial. In this study, the plastome of S. plumbizincicola was firstly presented, with a focus on the structural analysis of rrn operon and phylogenetic implications within the order Saxifragaceae. The assembled complete plastome of S. plumbizincicola is 149,397 bp in size, with a typical circular, double-stranded, and quadripartite structure of angiosperms. It contains 133 genes, including 85 protein-coding genes (PCGs), 36 tRNA genes, 8 rRNA genes, and four pseudogenes (one ycf1, one rps19, and two ycf15). The predicted secondary structure of S. plumbizincicola 16S rRNA includes three main domains organized in 74 helices. Further, our results confirm that 4.5S rRNA of higher plants is associated with fragmentation of 23S rRNA progenitor. Notably, we also found the sequence of putative rrn5 promoter has some evolutionary implications within the order Saxifragales. Moreover, our phylogenetic analyses suggested that S. plumbizincicola had a closer relationship with S. sarmentosum than S. oryzifolium, and supported the taxonomic revision of Phedimus. Our findings of the present study will be useful for further investigation of the evolution of plastid rRNA operon and phylogenetic relationships within Saxifragales.
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spelling pubmed-68432252019-11-25 Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales Ding, Hengwu Zhu, Ran Dong, Jinxiu Bi, De Jiang, Lan Zeng, Juhua Huang, Qingyu Liu, Huan Xu, Wenzhong Wu, Longhua Kan, Xianzhao Plants (Basel) Article The genus Sedum, with about 470 recognized species, is classified in the family Crassulaceae of the order Saxifragales. Phylogenetic relationships within the Saxifragales are still unresolved and controversial. In this study, the plastome of S. plumbizincicola was firstly presented, with a focus on the structural analysis of rrn operon and phylogenetic implications within the order Saxifragaceae. The assembled complete plastome of S. plumbizincicola is 149,397 bp in size, with a typical circular, double-stranded, and quadripartite structure of angiosperms. It contains 133 genes, including 85 protein-coding genes (PCGs), 36 tRNA genes, 8 rRNA genes, and four pseudogenes (one ycf1, one rps19, and two ycf15). The predicted secondary structure of S. plumbizincicola 16S rRNA includes three main domains organized in 74 helices. Further, our results confirm that 4.5S rRNA of higher plants is associated with fragmentation of 23S rRNA progenitor. Notably, we also found the sequence of putative rrn5 promoter has some evolutionary implications within the order Saxifragales. Moreover, our phylogenetic analyses suggested that S. plumbizincicola had a closer relationship with S. sarmentosum than S. oryzifolium, and supported the taxonomic revision of Phedimus. Our findings of the present study will be useful for further investigation of the evolution of plastid rRNA operon and phylogenetic relationships within Saxifragales. MDPI 2019-09-29 /pmc/articles/PMC6843225/ /pubmed/31569538 http://dx.doi.org/10.3390/plants8100386 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Ding, Hengwu
Zhu, Ran
Dong, Jinxiu
Bi, De
Jiang, Lan
Zeng, Juhua
Huang, Qingyu
Liu, Huan
Xu, Wenzhong
Wu, Longhua
Kan, Xianzhao
Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales
title Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales
title_full Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales
title_fullStr Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales
title_full_unstemmed Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales
title_short Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales
title_sort next-generation genome sequencing of sedum plumbizincicola sheds light on the structural evolution of plastid rrna operon and phylogenetic implications within saxifragales
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6843225/
https://www.ncbi.nlm.nih.gov/pubmed/31569538
http://dx.doi.org/10.3390/plants8100386
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