Comparative analysis of chloroplast genomes in Vasconcellea pubescens A.DC. and Carica papaya L.

Lin, Zhicong; Zhou, Ping; Ma, Xinyi; Deng, Youjin; Liao, Zhenyang; Li, Ruoyu; Ming, Ray

doi:10.1038/s41598-020-72769-y

Cited by 12 publications

(9 citation statements)

References 82 publications

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“…Further, the cp genome was compared with 1). The size range of S. persica cp genome is found in the same range as the sizes of the previously reported cp genomes of A. tetracantha (153,415 bp) and other related species [29,[34][35][36]. Like typical angiosperms cp genomes (20 ± 28 kb), these species' IRs length ranges from 25 to 26 kb in length [34,37].…”

Section: Discussionsupporting

confidence: 77%

Decoding first complete chloroplast genome of toothbrush tree (Salvadora persica L.): insight into genome evolution, sequence divergence and phylogenetic relationship within Brassicales

et al. 2021

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Background Salvadora persica L. (Toothbrush tree – Miswak; family-Salvadoraceae) grows in the arid-land ecosystem and possesses economic and medicinal importance. The species, genus and the family have no genomic datasets available specifically on chloroplast (cp) genomics and taxonomic evolution. Herein, we have sequenced the complete chloroplast genome of S. persica for the first time and compared it with 11 related specie’s cp genomes from the order Brassicales. Results The S. persica cp genome was 153,379 bp in length containing a sizeable single-copy region (LSC) of 83,818 bp which separated from the small single-copy region (SSC) of 17,683 bp by two inverted repeats (IRs) each 25,939 bp. Among these genomes, the largest cp genome size (160,600 bp) was found in M. oleifera, while in S. persica it was the smallest (153,379 bp). The cp genome of S. persica encoded 131 genes, including 37 tRNA genes, eight rRNA genes and 86 protein-coding genes. Besides, S. persica contains 27 forward, 36 tandem and 19 palindromic repeats. The S. persica cp genome had 154 SSRs with the highest number in the LSC region. Complete cp genome comparisons showed an overall high degree of sequence resemblance between S. persica and related cp genomes. Some divergence was observed in the intergenic spaces of other species. Phylogenomic analyses of 60 shared genes indicated that S. persica formed a single clade with A. tetracantha with high bootstrap values. The family Salvadoraceae is closely related to Capparaceae and Petadiplandraceae rather than to Bataceae and Koberliniacaea. Conclusion The current genomic datasets provide pivotal genetic resources to determine the phylogenetic relationships, genome evolution and future genetic diversity-related studies of S. persica in complex angiosperm families.

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Section: Discussionsupporting

confidence: 77%

Decoding first complete chloroplast genome of toothbrush tree (Salvadora persica L.): insight into genome evolution, sequence divergence and phylogenetic relationship within Brassicales

et al. 2021

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“…Herein, four Cuscuta species (C. epithymum, C. europaea, C. approximata and C. pedicellata) lacked an IR region (Table 1). The loss of IR is common in the chloroplast genomes of higher plants [37]. These results further con rmed the structural plasticity of the chloroplast.…”

Section: Variation In Chloroplast Gene Structuresupporting

confidence: 65%

Complete Chloroplast genomes of five Cuscuta species and their evolutionary significance in the Cuscuta genus

Pan

Zagorchev

Chen

et al. 2023

Preprint

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Background Cuscuta, a parasitic plant species in the Convolvulaceae family, grows in many countries and regions. However, the relationship between some species is still unclear. Therefore, more studies are needed to assess the variation of the chloroplast genome in Cuscuta species and their relationship with subgenera or sections, thus, providing important information on the evolution of Cuscuta species. Results In the present study, we identified the whole chloroplast genomes of C. epithymum, C. europaea, C. gronovii, C. chinensis and C. japonica, and then constructed a phylogenetic tree of 23 Cuscuta species based on the genome sequences. We also compared the number of genes and the structure of chloroplast genome and the patterns of gene reduction. Most chloroplast genomes of Cuscuta spp. have tetragonal and circular structures except for C. epithymum, C. europaea, C. pedicellata and C. approximata. Moreover, a simple sequence repeat analysis showed that the Cuscuta chloroplast genome is species-specific. The inverted repeat boundaries of the four regions between different subgenera were similar. Gene rearrangement showed that different Cuscuta species in the same subgenus have similar chloroplast genome structures. Several chloroplast genes were lost. In addition, the numbers and types of the lost genes in the same subgenus were similar. Most of the lost genes were related to photosynthesis (ndh, rpo, psa, psb, pet, and rbcL). Thus, they could have gradually caused the plants to lose the ability to photosynthesize. Conclusion Our results enrich the data on cp genomes of genus Cuscuta. This study provides new insights into understanding the phylogenetic relationships and variations in the chloroplast genome of Cuscuta species.

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“…), and more commonly in Angiosperms, with 58 species across 16 other orders showing similar patterns [22]. Recent studies have also revealed the presence of two cp haplotypes in other orders, such as Asparagales ( Ophrys apifera orchid, [72]), Brassicales ( Carica papaya , Vasconcellea pubescens , [73]), Solanales ( Solanum tuberosum , [74]), and even in a new order, Laurales (Avocado Persea americana , [75]). Furthermore, Wanichthanarak et al .…”

Section: Discussionmentioning

confidence: 99%

Sequencing, de novo assembly ofLudwigiaplastomes, and comparative analysis within the Onagraceae family

Barloy-Hubler,

Le Gac,

Boury

et al. 2023

Preprint

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Background: The Onagraceae family, which belongs to the order Myrtales, consists of approximately 657 species and 17 genera, including the genus Ludwigia L., which is comprised of 82 species. There are few genomic resources for Onagraceae, which limits phylogenetic and population genetics, as well as genomic studies. In this study, new complete plastid genomes of Ludwigia grandiflora subps. hexapetala (Lgh) and Ludwigia peploides subsp montevidensis (Lpm) were generated using a combination of different sequencing technologies. These plastomes were then compared to the published Ludwigia octovalvis (Lo) plastid genome, which was re-annotated by the authors. Results: We initially sequenced and assembled the chloroplast (cp) genomes of Lpm and Lgh using a hybrid strategy. We observed the existence of two Lgh haplotypes and two potential Lpm haplotypes. Lgh, Lpm, and Lo plastomes were similar in terms of genome size, gene number, structure, and inverted repeat (IR) boundaries, comparable to other species in the Myrtales order. A total of 45 to 65 SSRs (simple sequence repeats), were detected, depending on the species, with the majority consisting solely of A and T, which is common among angiosperms. Four chloroplast genes (matK, accD, ycf2 and ccsA) were found under positive selection pressure, which is commonly associated with plant development, and especially in aquatic plants such as Lgh, and Lpm. Conclusion: Our hybrid sequencing approach revealed the presence of two Lgh plastome haplotypes which will help to advance phylogenetic and evolutionary studies, not only specifically for Ludwigia, but also the Onagraceae family and Myrtales order. To enhance the robustness of our findings, a larger dataset of chloroplast genomes would be beneficial.

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Comparative analysis of chloroplast genomes in Vasconcellea pubescens A.DC. and Carica papaya L.

Cited by 12 publications

References 82 publications

Decoding first complete chloroplast genome of toothbrush tree (Salvadora persica L.): insight into genome evolution, sequence divergence and phylogenetic relationship within Brassicales

Decoding first complete chloroplast genome of toothbrush tree (Salvadora persica L.): insight into genome evolution, sequence divergence and phylogenetic relationship within Brassicales

Complete Chloroplast genomes of five Cuscuta species and their evolutionary significance in the Cuscuta genus

Sequencing, de novo assembly ofLudwigiaplastomes, and comparative analysis within the Onagraceae family

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