Plastome variations reveal the distinct evolutionary scenarios of plastomes in the subfamily Cereoideae (Cactaceae)

Li, Jingling; Zuo, Youwei; Qin, Qiulin; Zeng, Siyuan; Rennenberg, Heinz; Hongping, Deng

doi:10.1186/s12870-023-04148-4

Cited by 9 publications

(21 citation statements)

References 79 publications

(104 reference statements)

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“…We conducted a phylogenetic analysis using 59 shared genes across nine Mammillaria species and one Obregonia species (serving as an outgroup) (Yu et al., 2023 ). In the resulting phylogenetic topology, M. elongata and M. gracilis are distinctly clustered.…”

Section: Resultsmentioning

confidence: 99%

“…M. elongata (MW553058.1) is distinctively marked in red. The sequences incorporated in the tree are as follows: M. huitzilopochtli (MN517612.1) (Solórzano et al., 2019 ), M. supertexta (MN508963.1) (Solórzano et al., 2019 ), M. solisioides (MN518341.1) (Solórzano et al., 2019 ), M. pectinifera (MN519716.1) (Solórzano et al., 2019 ), M. gracilis (MW553059.1) (Yu et al., 2023 ), M. albiflora (MN517610.1) (Solórzano et al., 2019 ), M. zephyranthoides (MN517611.1) (Solórzano et al., 2019 ), and O. denegrii (MW553062.1) (Yu et al., 2023 ). the scale bar represents a genetic distance of 0.1 substitutions per site.…”

Section: Resultsmentioning

confidence: 99%

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Characterizing the chloroplast genome of Mammillaria elongata DC. 1828 in the Cactaceae family and unveiling its phylogenetic affinities within the genus Mammillaria

Ni,

Li,

et al. 2023

Mitochondrial DNA Part B

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With its nearly 200 species, the Mammillaria genus is the most species-rich within the Cactaceae family, yet surprisingly, few of its chloroplast genomes have been studied. We focused on the species Mammillaria elongata DC. 1828, a petite cactus native to Mexico and favored by horticulturists, yet whose phylogenetic relationships remain uncertain due to a lack of genomic data. We extracted the DNA from a sample obtained in China, sequenced it using the NovaSeq 6000 platform, and assembled the chloroplast genome using GetOrganelle software. Our assembly resulted in a chloroplast genome of 110,981 base pairs with an overall GC content of 36.28%, which included 100 genes (95 unique). Notably, several protein-coding genes were absent. Phylogenetic analysis using 59 shared genes across nine Mammillaria species and one Obregonia species revealed that M. elongata and M. gracilis are closely related, suggesting a recent common ancestor and possible shared evolutionary pressures or ecological niches. This study provides crucial genomic data for M. elongata and hints at intriguing phylogenetic relationships within the Mammillaria genus.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Characterizing the chloroplast genome of Mammillaria elongata DC. 1828 in the Cactaceae family and unveiling its phylogenetic affinities within the genus Mammillaria

Ni,

Li,

et al. 2023

Mitochondrial DNA Part B

Self Cite

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“…2022; Qin et al . 2022; Yu et al ., 2023). Cactaceae seem to have the smallest plastome for an obligately photosynthetic angiosperm (∼104-113 kb, Sanderson et al ., 2015; Solórzano et al ., 2019; Amaral et al ., 2021).…”

Section: Introductionmentioning

confidence: 99%

“…Nonetheless, beyond their morphological, physiological, and ecological aspects, molecular components also may reveal intriguing traits of cacti. The study of entire cactus plastomes was initiated recently (Sanderson et al, 2015), and since then, it has been revealed that plastomes across cacti have undergone significant changes in gene content, order, and structure compared to canonical angiosperm references (Majure et al, 2019;Solórzano et al, 2019;Köhler et al, 2020;Oulo et al 2020;Amaral et al, 2021;Silva et al, 2021;Almeida et al, 2021;Dalla Costa et al 2022;Qin et al 2022;Yu et al, 2023). Cactaceae seem to have the smallest plastome for an obligately photosynthetic angiosperm (~104-113 kb, Sanderson et al, 2015;Solórzano et al, 2019;Amaral et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

More than a prickly morphology: plastome variation in the prickly pear cacti (Opuntieae)

Köhler

Reginato

Jin

et al. 2023

Preprint

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Plastid genomes (plastomes) have long been recognized as highly conserved in their overall structure, size, gene arrangement and content among land plants. However, recent studies have shown that some lineages present unusual variations in some of these features. Members of the cactus family are one of these lineages, with distinct plastome structures reported across disparate lineages including gene losses, inversions, boundary movements, or loss of the canonical inverted repeat (IR) region. Here, we further investigated plastome features of the tribe Opuntieae, the remarkable prickly pear cacti, which represent a diverse and important lineage of Cactaceae. We assembled the plastome of 43 species, representing a comprehensive sampling of the tribe including all seven genera. Plastomes varied considerably in length from 121 kbp to 162 kbp, with striking differences in the content and size of the IR region (contraction and expansion events), including the lack of the canonical IR in some lineages, and the pseudogenization or loss of some genes. Overall, nine different types of plastomes were reported deviating in the presence of the IR region or the genes contained in the IR. Plastomes sequences resolved phylogenetic relationships within major clades of Opuntieae but presented some contentious nodes depending on the data set analyzed (e.g., whole plastome vs. genes only). Incongruence analyses revealed that few plastome regions are supporting the most likely topology, while disputing topologies are driven by a handful of plastome markers, which may be the result of hard recalcitrant nodes in the phylogeny or by the lack of phylogenetic signal in certain markers. Our study reveals a dynamic nature of plastome evolution across closely related lineages, shedding light on peculiar features of cactus plastomes. Variation of plastome types across Opuntieae is remarkable in size, structure, and content, and can be important for the recognition of species in some major clades. Unraveling connections between the causes of plastome variation and the consequences on species biology, ecology, diversification, and adaptation, is a promising endeavor.

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“…With the advancement of next-generation sequencing and bioinformatics technologies, obtaining plastid genome data is now more affordable and faster than ever before. As a result, plastid genome sequences have been widely and successfully utilized in plant phylogenetic analyses [ 46 , 47 , 48 , 49 , 50 ].…”

Section: Introductionmentioning

confidence: 99%

Phylogeny and Taxonomic Revision of the Genus Melanosciadium (Apiaceae), Based on Plastid Genomes and Morphological Evidence

Jiang,

Guo,

Zhao

et al. 2024

Plants

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Melanosciadium is considered a monotypic genus and is also endemic to the southwest of China. No detailed phylogenetic studies or plastid genomes have been identified in Melanosciadium. In this study, the plastid genome sequence and nrDNA sequence were used for the phylogenetic analysis of Melanosciadium and its related groups. Angelica tsinlingensis was previously considered a synonym of Hansenia forbesii. Similarly, Ligusticum angelicifolium was previously thought to be the genus Angelica or Ligusticopsis. Through field observations and morphological evidence, we believe that the two species are more similar to M. pimpinelloideum in leaves, umbel rays, and fruits. Meanwhile, we found a new species from Anhui Province (eastern China) that is similar to M. pimpinelloideum and have named it M. Jinzhaiensis. We sequenced and assembled the complete plastid genomes of these species and another three Angelica species. The genome comparison results show that M. pimpinelloideum, A. tsinlingensis, Ligusticum angelicifolium, and M. jinzhaiensis have similarities to each other in the plastid genome size, gene number, and length of the LSC and IR regions; the plastid genomes of these species are distinct from those of the Angelica species. In addition, we reconstruct the phylogenetic relationships using both plastid genome sequences and nrDNA sequences. The phylogenetic analysis revealed that A. tsinlingensis, M. pimpinelloideum, L. angelicifolium, and M. jinzhaiensis are closely related to each other and form a monophyletic group with strong support within the Selineae clade. Consequently, A. tsinlingensis and L. angelicifolium should be classified as members of the genus Melanosciadium, and suitable taxonomical treatments have been proposed. Meanwhile, a comprehensive description of the new species, M. jinzhaiensis, is presented, encompassing its habitat environment and detailed morphological traits.

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Plastome variations reveal the distinct evolutionary scenarios of plastomes in the subfamily Cereoideae (Cactaceae)

Cited by 9 publications

References 79 publications

Characterizing the chloroplast genome of Mammillaria elongata DC. 1828 in the Cactaceae family and unveiling its phylogenetic affinities within the genus Mammillaria

Characterizing the chloroplast genome of Mammillaria elongata DC. 1828 in the Cactaceae family and unveiling its phylogenetic affinities within the genus Mammillaria

More than a prickly morphology: plastome variation in the prickly pear cacti (Opuntieae)

Phylogeny and Taxonomic Revision of the Genus Melanosciadium (Apiaceae), Based on Plastid Genomes and Morphological Evidence

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