The complete chloroplast genome sequence of a threatened perennial herb species Taibai sweetvetch (<i>Hedysarum taipeicum</i> K.T. Fu)

She, Ruixue; Li, Wenqing; Xie, Xiaoman; Gao, Xiaoxiao; Wang, Lei; Liu, Peiliang; Yan, Feng; Khan, Hanif; Ullah, Irfan; Zhao, Peng

doi:10.1080/23802359.2019.1598817

Cited by 4 publications

(5 citation statements)

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“…Our phylogenetic analysis based on complete cp genomes and protein-coding genes confirmed previous studies on cp genome data of IRLC clade species, determining the phylogenetic position of Hedysarum as a sister to Onobrychis (She et al, 2019;Jin et al, 2021;Moghaddam et al, 2022;Tian et al, 2021). Our study also confirms the monophyly of Hedysarum based on plastid DNA genes, which is consistent with previous studies by Duan et al (2015); Liu et al (2017), andNafisi et al (2019).…”

Section: B a Figuresupporting

confidence: 91%

“…The cp genomes of six Hedysarum species showed high similarity with regard to genome size (except for H. taipeicum which was 126,738 bp), gene sequences, gene classes, and the lacking IR region. All selected Hedysarum species were found to have lost one copy of the IR region, which was first identified in H. taipeicum by She et al (2019). This loss of the IR region is common in most species belonging to the subfamily Papilionoideae in the family Fabaceae, forming a clade named the IR-lacking clade (IRLC) (Wojciechowski et al, 2004).…”

Section: Discussionmentioning

confidence: 99%

“…Most complete cp genomes harbor a typical quadripartite structure including a long single copy (LSC) region, a small single copy (SSC) region, and two copies of inverted repeat (IR) regions (Bock, 2007). Hedysarum belonging to the IRLC (Inverted Repeat Lacking Clade) clade is described by the lack of one copy of the inverted repeat (IR) region in the whole cp genome (Wojciechowski et al, 2004;She et al, 2019). Species belonging to the IRLC clade are characterized by having a cp genome size of around 121,000-133,000 bp (Moghaddam et al, 2022;Yuan et al, 2022;Tian et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

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First comparative analysis of complete chloroplast genomes among six Hedysarum (Fabaceae) species

Juramurodov,

Makhmudjanov,

Yusupov

et al. 2023

Front. Plant Sci.

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Hedysarum is one of the largest genera in the Fabaceae family, mainly distributed in the Northern Hemisphere. Despite numerous molecular studies on the genus Hedysarum, there is still a lack of research aimed at defining the specific characteristics of the chloroplast genome (cp genome) of the genus. Furthermore, the interrelationships between sections in the genus based on the cp genome have not yet been studied. In this study, comprehensive analyses of the complete cp genomes of six Hedysarum species, corresponding to sections Multicaulia, Hedysarum, and Stracheya were conducted. The complete cp genomes of H. drobovii, H. flavescens, and H. lehmannianum were sequenced for this study. The cp genomes of six Hedysarum species showed high similarity with regard to genome size (except for H. taipeicum), gene sequences, and gene classes, as well as the lacking IR region. The whole cp genomes of the six species were found to contain 110 genes ranging from 121,176 bp to 126,738 bp in length, including 76 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. In addition, chloroplast SSRs and repetitive sequence regions were reported for each species. The six Hedysarum species shared 7 common SSRs and exhibited 14 unique SSRs. As well, three highly variable genes (clpP, accD, and atpF) with high Pi values were detected among protein-coding genes. Furthermore, we conducted phylogenetic analyses using the complete cp genomes and 76 protein-coding genes of 14 legume species, including the seven Hedysarum species. The results showed that the Hedysarum species form a monophyletic clade closely related to the genera Onobrychis and Alhagi. Furthermore, both of our phylogenetic reconstructions showed that section Stracheya is more closely related to section Hedysarum than to section Multicaulia. This study is the first comprehensive work to investigate the genome characteristics of the genus Hedysarum, which provides useful genetic information for further research on the genus, including evolutionary studies, phylogenetic relationships, population genetics, and species identification.

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Section: B a Figuresupporting

confidence: 91%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

First comparative analysis of complete chloroplast genomes among six Hedysarum (Fabaceae) species

Juramurodov,

Makhmudjanov,

Yusupov

et al. 2023

Front. Plant Sci.

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“…We found that the codons in the C. fruticosum chloroplast genome exhibited a preference for A/T bases, which is often found in higher plants [ 47 , 48 , 49 ]. Accordingly, the GC content in C. fruticosum , as with C. multijugum and four Hedysarum species, was low [ 30 , 31 , 32 ].…”

Section: Discussionmentioning

confidence: 99%

“…In fact, 11,946 chloroplast genomes from 19,388 species, including 604 Leguminosae, have been integrated and curated in the chloroplast genome information resource (CGIR, https://ngdc.cncb.ac.cn/cgir accessed on 25 May 2023) [28,29]. In particular, the chloroplast genomes of C. multijugum and four Hedysarum species (Hedysarum semenovii, Hedysarum polybotrys, Hedysarum petrovii, and Hedysarum taipeicum) have been sequenced and annotated, thereby revealing that all five species have lost the IR regions [30][31][32].…”

Section: Introductionmentioning

confidence: 99%

Complete Chloroplast Genome of Corethrodendron fruticosum (Papilionoideae: Fabaceae): Comparative and Phylogenetic Analysis

Niu

Tian

Yang

et al. 2023

Genes

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Corethrodendron fruticosum is an endemic forage grasses in China with high ecological value. In this study, the complete chloroplast genome of C. fruticosum was sequenced using Illumina paired-end sequencing. The C. fruticosum chloroplast genome was 123,100 bp and comprised 105 genes, including 74 protein-coding genes, 4 rRNA-coding genes, and 27 tRNA-coding genes. The genome had a GC content of 34.53%, with 50 repetitive sequences and 63 simple repeat repetitive sequences that did not contain reverse repeats. The simple repeats included 45 single-nucleotide repeats, which accounted for the highest proportion and primarily comprised A/T repeats. A comparative analysis of C. fruticosum, C. multijugum, and four Hedysarum species revealed that the six genomes were highly conserved, with differentials primarily located in the conserved non-coding regions. Moreover, the accD and clpP genes in the coding regions exhibited high nucleotide variability. Accordingly, these genes may serve as molecular markers for the classification and phylogenetic analysis of Corethrodendron species. Phylogenetic analysis further revealed that C. fruticosum and C. multijugum appeared in different clades than the four Hedysarum species. The newly sequenced chloroplast genome provides further insights into the phylogenetic position of C. fruticosum, which is useful for the classification and identification of Corethrodendron.

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Characterization of the complete plastid genome of the perennial herb Astragalus complanatus Bunge (Fabales: Fabaceae)

Yang

2021

Mitochondrial DNA Part B

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The complete chloroplast genome sequence of a threatened perennial herb species Taibai sweetvetch (Hedysarum taipeicum K.T. Fu)

Cited by 4 publications

References 10 publications

First comparative analysis of complete chloroplast genomes among six Hedysarum (Fabaceae) species

First comparative analysis of complete chloroplast genomes among six Hedysarum (Fabaceae) species

Complete Chloroplast Genome of Corethrodendron fruticosum (Papilionoideae: Fabaceae): Comparative and Phylogenetic Analysis

Characterization of the complete plastid genome of the perennial herb Astragalus complanatus Bunge (Fabales: Fabaceae)

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