Analysis of complete chloroplast genome sequences and insight into the phylogenetic relationships of Ferula L.

Ferula / genetics Genome, Chloroplast Microsatellite Repeats Phylogeny
Chloroplast genome Comparative analysis Ferula Phylogenetic relationships

Journal

BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258

Informations de publication

Date de publication:
08 Sep 2022
Historique:
received: 30 05 2022
accepted: 30 08 2022
entrez: 8 9 2022
pubmed: 9 9 2022
medline: 14 9 2022
Statut: epublish

Résumé

Ferula L. is one of the largest and most taxonomically complicated genera as well as being an important medicinal plant resource in the family Apiaceae. To investigate the plastome features and phylogenetic relationships of Ferula and its neighboring genera Soranthus Ledeb., Schumannia Kuntze., and Talassia Korovin, we sequenced 14 complete plastomes of 12 species.  RESULTS: The size of the 14 complete chloroplast genomes ranged from 165,607 to 167,013 base pairs (bp) encoding 132 distinct genes (87 protein-coding, 37 tRNA, and 8 rRNA genes), and showed a typical quadripartite structure with a pair of inverted repeats (IR) regions. Based on comparative analysis, we found that the 14 plastomes were similar in codon usage, repeat sequence, simple sequence repeats (SSRs), and IR borders, and had significant collinearity. Based on our phylogenetic analyses, Soranthus, Schumannia, and Talassia should be considered synonymous with Ferula. Six highly divergent regions (rps16/trnQ-UUG, trnS-UGA/psbZ, psbH/petB, ycf1/ndhF, rpl32, and ycf1) were also detected, which may represent potential molecular markers, and combined with selective pressure analysis, the weak positive selection gene ccsA may be a discriminating DNA barcode for Ferula species. Plastids contain abundant informative sites for resolving phylogenetic relationships. Combined with previous studies, we suggest that there is still much room for improvement in the classification of Ferula. Overall, our study provides new insights into the plastome evolution, phylogeny, and taxonomy of this genus.

Sections du résumé

BACKGROUND BACKGROUND
Ferula L. is one of the largest and most taxonomically complicated genera as well as being an important medicinal plant resource in the family Apiaceae. To investigate the plastome features and phylogenetic relationships of Ferula and its neighboring genera Soranthus Ledeb., Schumannia Kuntze., and Talassia Korovin, we sequenced 14 complete plastomes of 12 species.  RESULTS: The size of the 14 complete chloroplast genomes ranged from 165,607 to 167,013 base pairs (bp) encoding 132 distinct genes (87 protein-coding, 37 tRNA, and 8 rRNA genes), and showed a typical quadripartite structure with a pair of inverted repeats (IR) regions. Based on comparative analysis, we found that the 14 plastomes were similar in codon usage, repeat sequence, simple sequence repeats (SSRs), and IR borders, and had significant collinearity. Based on our phylogenetic analyses, Soranthus, Schumannia, and Talassia should be considered synonymous with Ferula. Six highly divergent regions (rps16/trnQ-UUG, trnS-UGA/psbZ, psbH/petB, ycf1/ndhF, rpl32, and ycf1) were also detected, which may represent potential molecular markers, and combined with selective pressure analysis, the weak positive selection gene ccsA may be a discriminating DNA barcode for Ferula species.
CONCLUSION CONCLUSIONS
Plastids contain abundant informative sites for resolving phylogenetic relationships. Combined with previous studies, we suggest that there is still much room for improvement in the classification of Ferula. Overall, our study provides new insights into the plastome evolution, phylogeny, and taxonomy of this genus.

Identifiants

DOI: 10.1186/s12864-022-08868-z PMID: 36076164 PMC: PMC9461113
pubmed: 36076164
doi: 10.1186/s12864-022-08868-z
pii: 10.1186/s12864-022-08868-z
pmc: PMC9461113
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

643

Subventions

Organisme : Taxonomic revision of polymorphic plant families of the flora of Uzbekistan
ID : FZ-20200929321
Organisme : The work was supported by the Third Xinjiang Scientific Expedition Program
ID : Grant No.2021xjkk0600
Organisme : the National Science and Technology Basic Program of China
ID : 2019FY100204
Organisme : the Shanghai cooperation organization partnership and international technology cooperation plan of science and technology projects
ID : 2021E01020
Organisme : Youth Innovation Promotion Association Foundation of the Chinese Academy of Sciences, China
ID : No. 2019429

Informations de copyright

© 2022. The Author(s).

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Auteurs

Lei Yang (L)

State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, No.818 South Beijing Road, Urumqi, 830011, China.
Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, No.818 South Beijing Road, Urumqi, 830011, China.
College of Resources and Environment, University of Chinese Academy of Sciences, Shijingshan District, No.19(A) Yuquan Road, Beijing, 100049, China.

Ozodbek Abduraimov (O)

Institute of Botany, Uzbekistan Academy of Sciences, No.32 Durmon Yuli Street, Tashkent, Uzbekistan, 100125.

Komiljon Tojibaev (K)

Institute of Botany, Uzbekistan Academy of Sciences, No.32 Durmon Yuli Street, Tashkent, Uzbekistan, 100125.

Khabibullo Shomurodov (K)

Institute of Botany, Uzbekistan Academy of Sciences, No.32 Durmon Yuli Street, Tashkent, Uzbekistan, 100125.

Yuan-Ming Zhang (YM)

State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, No.818 South Beijing Road, Urumqi, 830011, China.
College of Resources and Environment, University of Chinese Academy of Sciences, Shijingshan District, No.19(A) Yuquan Road, Beijing, 100049, China.
Sino-Tajikistan Joint Laboratory for Conservation and Utilization of Biological Resources, No.818 South Beijing Road, Urumqi, 830011, China.

Wen-Jun Li (WJ)

State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, No.818 South Beijing Road, Urumqi, 830011, China. liwenjunao@ms.xjb.ac.cn.
College of Resources and Environment, University of Chinese Academy of Sciences, Shijingshan District, No.19(A) Yuquan Road, Beijing, 100049, China. liwenjunao@ms.xjb.ac.cn.
Sino-Tajikistan Joint Laboratory for Conservation and Utilization of Biological Resources, No.818 South Beijing Road, Urumqi, 830011, China. liwenjunao@ms.xjb.ac.cn.
The Specimen Museum of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China. liwenjunao@ms.xjb.ac.cn.

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Viridiplantae › Streptophyta › Embryophyta › Tracheobionta › Magnoliopsida › Apiaceae › Ferula › Analysis of complete chloroplast genome...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome plastidique › Génome de chloroplaste › Analysis of complete chloroplast genome...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Séquences répétées en tandem › Répétitions microsatellites › Analysis of complete chloroplast genome...
questionsmedicales.fr › Sciences de l'information › Phylogenèse › Analysis of complete chloroplast genome...