Comparative analyses of the complete chloroplast genomes of four Caragana species, a specific genus distributed in arid and semi-arid area.

Wenyan Chen, Xue Zhang, Qin Li, Liqiong Jiang, Miaomiao Jiang, Xiaohong Bai, Lei Wang

Abstract readComparative Study

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Article in Planta, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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7 authors.

Wenyan ChenNorthwest National Key Laboratory Breeding Base for Land Degradation and Ecological Restoration, Ningxia University, Yinchuan, 750000, China.

Xue ZhangNorthwest National Key Laboratory Breeding Base for Land Degradation and Ecological Restoration, Ningxia University, Yinchuan, 750000, China. zhxue@nxu.edu.cn.ORCID http://orcid.org/0000-0002-7738-9873

Qin LiNorthwest National Key Laboratory Breeding Base for Land Degradation and Ecological Restoration, Ningxia University, Yinchuan, 750000, China.

Liqiong JiangCollege of Life Sciences, Henan Normal University, Xinxiang, 453007, China.

Miaomiao JiangNorthwest National Key Laboratory Breeding Base for Land Degradation and Ecological Restoration, Ningxia University, Yinchuan, 750000, China.

Xiaohong BaiNorthwest National Key Laboratory Breeding Base for Land Degradation and Ecological Restoration, Ningxia University, Yinchuan, 750000, China.

Lei WangNorthwest National Key Laboratory Breeding Base for Land Degradation and Ecological Restoration, Ningxia University, Yinchuan, 750000, China.

Funding

National Natural Science Foundation of China 32100307

6 · The paper itself

Abstract

Caragana species, perennial deciduous shrubs of Leguminosae, are significant to illustrate the synchronous evolution of floristics, vegetation, and climate change in arid Central Asia, cold arid alpine Qinghai-Tibetan plateau (QTP), and mesophytic East Asia. The objective of this study was to assemble and annotate the complete cp genome of four Caragana species, including C. opulens, C. roborovskyi, C. stenophylla, C. tibetica, and to compare their various characteristics with previously published data of Caragana species. High-quality DNA was paired-end sequenced utilizing the Illumina NovaSeq platform, followed by de novo assembly with the NOVOPlasty. The four cp genomes of Caragana lacked the IR region and ranged in length from 129,303 to 132,895 bp. The cp genome encoded 112-113 genes, consisting of 77 protein coding genes, 31-32 tRNA genes and four rRNA genes. Similar to other IRLC species, the genes rpl22 and rps16, as well as the intron of rpl2 and rps12 were found to be absent. A total of 77-94 simple sequence repeats (SSRs) were identified with the proportion of SSRs ≥ 10 bp ranging from 55.32 to 66.23%. Comparative analyses indicated that five genes (clpP, matK, rbcL, rpoC and ycf1) underwent positive selection during evolution, and 13 hypervariable regions were recommended as potential molecular markers for distinguishing Caragana species. Phylogenetic analyses showed that the Caragana species were classified into two distinct clades and exhibited a close relationship with Hedysareae. These findings will greatly facilitate the further exploration of the phylogenetic development and adaptive evolution of Caragana species and also IRLC at the genomic scale.

Indexed as

CaraganaGenome, ChloroplastMicrosatellite RepeatsPhylogenySpecies SpecificityCaragana speciesComparative analysesGenome structureGenomic divergencePhylogenetic analysis

Identifiers

PMID40471310

DOI10.1007/s00425-025-04729-7

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