Comparative plastid genomics of four Pilea (Urticaceae) species: insight into interspecific plastid genome diversity in Pilea.

China Evolution, Molecular Gene Transfer, Horizontal Genetic Variation Genome, Plant Genome, Plastid Phylogeny Plants, Medicinal / genetics Sequence Analysis, DNA Urticaceae / genetics
Hypervariable region Interspecific diversity Phylogenetic relationship Pilea Plastid genome

Journal

BMC plant biology
ISSN: 1471-2229
Titre abrégé: BMC Plant Biol
Pays: England
ID NLM: 100967807

Informations de publication

Date de publication:
07 Jan 2021
Historique:
received: 25 07 2020
accepted: 09 12 2020
entrez: 8 1 2021
pubmed: 9 1 2021
medline: 8 9 2021
Statut: epublish

Résumé

Pilea is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of Pilea, which limits our understanding of this genus. Here, we report 4 plastid genomes of Pilea taxa (Pilea mollis, Pilea glauca 'Greizy', Pilea peperomioides and Pilea serpyllacea 'Globosa') and performed comprehensive comparative analysis. The four plastid genomes all have a typical quartile structure. The lengths of the plastid genomes ranged from 150,398 bp to 152,327 bp, and each genome contained 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Comparative analysis showed a rather high level of sequence divergence in the four genomes. Moreover, eight hypervariable regions were identified (petN-psbM, psbZ-trnG-GCC, trnT-UGU-trnL-UAA, accD-psbI, ndhF-rpl32, rpl32-trnL-UAG, ndhA-intron and ycf1), which are proposed for use as DNA barcode regions. Phylogenetic relationships based on the plastid genomes of 23 species of 14 genera of Urticaceae resulted in the placement of Pilea in the middle and lower part of the phylogenetic tree, with 100% bootstrap support within Urticaceae. Our results enrich the resources concerning plastid genomes. Comparative plastome analysis provides insight into the interspecific diversity of the plastid genome of Pilea. The identified hypervariable regions could be used for developing molecular markers applicable in various research areas.

Sections du résumé

BACKGROUND BACKGROUND
Pilea is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of Pilea, which limits our understanding of this genus. Here, we report 4 plastid genomes of Pilea taxa (Pilea mollis, Pilea glauca 'Greizy', Pilea peperomioides and Pilea serpyllacea 'Globosa') and performed comprehensive comparative analysis.
RESULTS RESULTS
The four plastid genomes all have a typical quartile structure. The lengths of the plastid genomes ranged from 150,398 bp to 152,327 bp, and each genome contained 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Comparative analysis showed a rather high level of sequence divergence in the four genomes. Moreover, eight hypervariable regions were identified (petN-psbM, psbZ-trnG-GCC, trnT-UGU-trnL-UAA, accD-psbI, ndhF-rpl32, rpl32-trnL-UAG, ndhA-intron and ycf1), which are proposed for use as DNA barcode regions. Phylogenetic relationships based on the plastid genomes of 23 species of 14 genera of Urticaceae resulted in the placement of Pilea in the middle and lower part of the phylogenetic tree, with 100% bootstrap support within Urticaceae.
CONCLUSION CONCLUSIONS
Our results enrich the resources concerning plastid genomes. Comparative plastome analysis provides insight into the interspecific diversity of the plastid genome of Pilea. The identified hypervariable regions could be used for developing molecular markers applicable in various research areas.

Identifiants

DOI: 10.1186/s12870-020-02793-7 PMID: 33413130 PMC: PMC7792329
pubmed: 33413130
doi: 10.1186/s12870-020-02793-7
pii: 10.1186/s12870-020-02793-7
pmc: PMC7792329
doi:

Types de publication

Comparative Study Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

25

Subventions

Organisme : National Natural Science Foundation of China
ID : 31772260
Organisme : Chongqing Study Abroad Innovation Project
ID : cx2019052

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Auteurs

Jingling Li (J)

College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China.

Jianmin Tang (J)

College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402160, China.

Siyuan Zeng (S)

College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China.

Fang Han (F)

College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China.

Jing Yuan (J)

College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China.

Jie Yu (J)

College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China. yujie1982@swu.edu.cn.
Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, 400716, China. yujie1982@swu.edu.cn.

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Classifications MeSH

questionsmedicales.fr › Régions géographiques › Asie › Extrême-Orient › Chine › Comparative plastid genomics of four Pilea...
questionsmedicales.fr › Phénomènes biologiques › Évolution biologique › Évolution moléculaire › Comparative plastid genomics of four Pilea...
questionsmedicales.fr › Phénomènes génétiques › Recombinaison génétique › Transfert horizontal de gène › Comparative plastid genomics of four Pilea...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Comparative plastid genomics of four Pilea...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome végétal › Comparative plastid genomics of four Pilea...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome plastidique › Comparative plastid genomics of four Pilea...
questionsmedicales.fr › Sciences de l'information › Phylogenèse › Comparative plastid genomics of four Pilea...
questionsmedicales.fr › Eucaryotes › Plantes › Plantes médicinales › Comparative plastid genomics of four Pilea...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › Comparative plastid genomics of four Pilea...
questionsmedicales.fr › Eucaryotes › Viridiplantae › Streptophyta › Embryophyta › Tracheobionta › Magnoliopsida › Rosanae › Rosales › Urticaceae › Comparative plastid genomics of four Pilea...