Characterization of the complete chloroplast genome of alfalfa ( Medicago sativa ) (Leguminosae)

Tao, Xiaoli; Ma, Lichao; Zhang, Zhengshe; Liu, Wenxian

doi:10.1016/j.genrep.2016.12.006

Cited by 24 publications

(21 citation statements)

References 44 publications

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“…According to the published data, the plastid genomes of most photosynthetic land plants are conserved in size (140-160 kb) and display the typical quadripartite structure by showing the LSC, LSC, and two IRs [14,19,20]. However, our results indicate that the R. pulchrum cp genome lacks the IRs, which has also been reported in Monotropeae [10], Medicago [43,44] and Erodium plants (Erodium carvifolium HQ713469.1).…”

Section: Discussionsupporting

confidence: 72%

The Complete Plastid Genome of Rhododendron pulchrum and Comparative Genetic Analysis of Ericaceae Species

Jia

Zhu

Huang

et al. 2020

Forests

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Background and Objectives: Rhododendron pulchrum Sweet (R. pulchrum) belongs to the genus Rhododendron (Ericaceae), a valuable horticultural and medicinal plant species widely used in Western Europe and the US. Despite its importance, this is the first member to have its cpGenome sequenced. Materials and Methods: In this study, the complete cp genome of R. pulchrum was sequenced with NGS Illumina HiSeq2500, analyzed, and compared to eight species in the Ericaceae family. Results: Our study reveals that the cp genome of R. pulchrum is 136,249 bp in length, with an overall GC content of 35.98% and no inverted repeat regions. The R. pulchrum chloroplast genome encodes 73 genes, including 42 protein-coding genes, 29 tRNA genes, and two rRNA genes. The synonymous (Ks) and nonsynonymous (Ka) substitution rates were estimated and the Ka/Ks ratio of R. pulchrum plastid genes were categorized; the results indicated that most of the genes have undergone purifying selection. A total of 382 forward and 259 inverted long repeats, as well as 221 simple-sequence repeat loci (SSR) were detected in the R. pulchrum cp genome. Comparison between different Ericaceae cp genomes revealed significant differences in genome size, structure, and GC content. Conclusions: The phylogenetic relationships among eight Ericaceae species suggested that R. pulchrum is closely related to Vaccinium oldhamii Miq. and Vaccinium macrocarpon Aiton. This study provides a theoretical basis for species identification and future biological research of Rhododendron resources.

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Section: Discussionsupporting

confidence: 72%

The Complete Plastid Genome of Rhododendron pulchrum and Comparative Genetic Analysis of Ericaceae Species

Jia

Zhu

Huang

et al. 2020

Forests

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“…RSCU indicates the relative probability of a particular codon encoding the synonymous codon of the corresponding amino acid. In this study, 93.5% of the codons were found prefer A/U in third position, similar to that of M. sativa [25] and Gossypium [32]. This phenomenon could be attributed to the fact that dicotyledon prefers to the A/U-end codons and manifests a potential force in molecular evolution of Trifolium species: mutation and natural selection.…”

Section: Relative Synonymous Codon Usage Analysis (Rscu)supporting

confidence: 76%

“…infA gene, which codes for translation initiation factor 1 (IF1), was defunct in all the listed fifteen Trifolium species. Considered as the most transferable gene in cp genome, infA was in existence in about 24 angiosperm lineages including Trifolium species, and related Medicago species [24,25]. It is worth noting that there are two rrn16 gene in each of Trifolium species sequenced in this study, and this phenomenon was also reported in cp genomes of T. strictum [13] and T. glanduliferum [13].…”

Section: Genome Feature Of T Alexandrinum and T Resupinatum And Comsupporting

confidence: 68%

“…4) and rps16 (ribosomal protein S16), which were found in most cp genomes of angiosperm and some relic plant like Amborella trichopoda [29], are not present in the two Trifolium species cp genomes sequenced in this study, and rps16 is not present in all the fifteen Trifolium species. The rps8 (ribosomal protein S8) gene was found without stop codons in Medicago truncatula and M. sativa [25], while it possesses a stop codon in the fifteen Trifolium cp genomes. In the gene ndhB, no internal stop codon was detected in the fourteen (except T. resupinatum) Trifolium cp genomes, which is inconsistent with many legume cp genomes whose ndhB gene contains an internal stop codon [25].…”

Section: Genome Feature Of T Alexandrinum and T Resupinatum And Commentioning

confidence: 99%

“…The rps8 (ribosomal protein S8) gene was found without stop codons in Medicago truncatula and M. sativa [25], while it possesses a stop codon in the fifteen Trifolium cp genomes. In the gene ndhB, no internal stop codon was detected in the fourteen (except T. resupinatum) Trifolium cp genomes, which is inconsistent with many legume cp genomes whose ndhB gene contains an internal stop codon [25].…”

Section: Genome Feature Of T Alexandrinum and T Resupinatum And Commentioning

confidence: 99%

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The Complete Chloroplast Genome of Two Important Annual Clover Species, Trifolium alexandrinum and T. resupinatum: Genome Structure, Comparative Analyses and Phylogenetic Relationships with Relatives in Leguminosae

Xiong

He²,

et al. 2020

Plants

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Trifolium L., which belongs to the IR lacking clade (IRLC), is one of the largest genera in the Leguminosae and contains several economically important fodder species. Here, we present whole chloroplast (cp) genome sequencing and annotation of two important annual grasses, Trifolium alexandrinum (Egyptian clover) and T. resupinatum (Persian clover). Abundant single nucleotide polymorphisms (SNPs) and insertions/deletions (In/Dels) were discovered between those two species. Global alignment of T. alexandrinum and T. resupinatum to a further thirteen Trifolium species revealed a large amount of rearrangement and repetitive events in these fifteen species. As hypothetical cp open reading frame (ORF) and RNA polymerase subunits, ycf1 and rpoC2 in the cp genomes both contain vast repetitive sequences and observed high Pi values (0.7008, 0.3982) between T. alexandrinum and T. resupinatum. Thus they could be considered as the candidate genes for phylogenetic analysis of Trifolium species. In addition, the divergence time of those IR lacking Trifolium species ranged from 84.8505 Mya to 4.7720 Mya. This study will provide insight into the evolution of Trifolium species.

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The complete sequence of Lens tomentosus chloroplast genome

Bozkurt,

Kaymaz,

Ateş

et al. 2023

Acta Physiol Plant

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Characterization of the complete chloroplast genome of alfalfa ( Medicago sativa ) (Leguminosae)

Cited by 24 publications

References 44 publications

The Complete Plastid Genome of Rhododendron pulchrum and Comparative Genetic Analysis of Ericaceae Species

The Complete Plastid Genome of Rhododendron pulchrum and Comparative Genetic Analysis of Ericaceae Species

The Complete Chloroplast Genome of Two Important Annual Clover Species, Trifolium alexandrinum and T. resupinatum: Genome Structure, Comparative Analyses and Phylogenetic Relationships with Relatives in Leguminosae

The complete sequence of Lens tomentosus chloroplast genome

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