Implications of plastome evolution in the true lilies (monocot order Liliales)

Khoa, Hoang Dang; Kim, Changkyun; Chase, Mark W.; Kim, Joo‐Hwan

doi:10.1016/j.ympev.2020.106818

Cited by 28 publications

(24 citation statements)

References 98 publications

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“…in the SSC-IR border (JSB) of Z. mesochloa the ndhF and ycf1 genes overlapped, whereas these two genes were separated by a gap in Z. phycelloides , H. rutilum and H. vittatum . This corresponds to previous studies in Allioideae species that found that the SSC-IR border (JSB) can be variable, showing either overlap or present a gap between ycf1 and ndhF ( Do et al, 2020 , Namgung et al, 2021 ). We did not find the rps19 gene within the IR-LSC borders (JLB and JLA) in any of the four Hippeastrinae species.…”

Section: Discussionsupporting

confidence: 91%

Characterization of the complete chloroplast genome of Zephyranthes phycelloides (Amaryllidaceae, tribe Hippeastreae) from Atacama region of Chile

Contreras-Díaz

Arias-Aburto

Brink

2022

Saudi Journal of Biological Sciences

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Sporadic rains in the Atacama Desert reveal a high biodiversity of plant species that only occur there. One of these rare species is the “Red añañuca” ( Zephyranthes phycelloides ), formerly known as Rhodophiala phycelloides . Many species of Zephyranthes in the Atacama Desert are dangerously threatened, due to massive extraction of bulbs and cutting of flowers. Therefore, studies of the biodiversity of these endemic species, which are essential for their conservation, should be conducted sooner rather than later. There are some chloroplast genomes available for Amaryllidaceae species, however there is no complete chloroplast genome available for any of the species of Zephyranthes subgenus Myostemma . The aim of the present work was to characterize and analyze the chloroplast of Z. phycelloides by NGS sequencing. The chloroplast genome of the Z. phycelloides consists of 158,107 bp, with typical quadripartite structures: a large single copy (LSC, 86,129 bp), a small single copy (SSC, 18,352 bp), and two inverted repeats (IR, 26,813 bp). One hundred thirty-seven genes were identified: 87 coding genes, 8 rRNA, 38 tRNA and 4 pseudogenes. The number of SSRs was 64 in Z. phycelloides and a total of 43 repeats were detected. The phylogenetic analysis of Z. phycelloides shows a distinct subclade with respect to Z. mesochloa . The average nucleotide variability ( Pi ) between Z. phycelloides and Z. mesochloa was of 0.02000, and seven loci with high variability were identified: psbA , trnS GCU -trnG UCC , trnD GUC -trnY GUA , trnL UAA -trnF GAA , rbcL, psbE-petL and ndhG-ndhI . The differences between the species are furthermore confirmed by the high amount of SNPs between these two species. Here, we report for the first time the complete cp genome of one species of the Zephyranthes subgenus Myostemma , which can be used for phylogenetic and population genomic studies.

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Section: Discussionsupporting

confidence: 91%

Characterization of the complete chloroplast genome of Zephyranthes phycelloides (Amaryllidaceae, tribe Hippeastreae) from Atacama region of Chile

Contreras-Díaz

Arias-Aburto

Brink

2022

Saudi Journal of Biological Sciences

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“…This is consistent with the phylogenetic tree constructed using both complete chloroplast genomes and marker gene sequences recently published (Do et al. 2020 ). The Melanthiaceae was a sister group to Liliaceae and Smilacaceae families.…”

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confidence: 92%

The complete chloroplast genome of a shrub species, Smilax glabra (Smilacaceae) from Guangdong, China

Zhang

Liu

et al. 2021

Mitochondrial DNA Part B

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Smilax glabra is a perennial woody scandent shrub, of which the dried aerial tuber has been used as Chinese medicine. Here, we sequenced S. glabra and assembled its complete chloroplast (cp) genome. The genome is 157,889 bp in length and has a typical quadripartite structure. We annotated 131 genes, of which 84 were protein-coding genes, 37 were tRNAs and 8 were rRNA genes. Phylogenetic analysis of this genome with 26 representatives Liliales fully resolved S. glabr a in a clade with S. china . The phylogenetic tree we constructed is largely consistent with recently published phylogenetic trees using both complete chloroplast genomes and marker gene sequences.

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“…As an alternative, genome skimming has been employed to generate complete chloroplast genomes (plastomes), an approach that has been dubbed as "super-barcoding" (Erickson et al, 2008;Yang et al, 2013;Li et al, 2015). The maternal inheritance and conservative genome structure of plastomes have rendered them essential markers in studying the evolutionary history of angiosperms (Gitzendanner et al, 2018;Do et al, 2020;Cai et al, 2021); noteworthy examples include the recent applications in Magnoliaceae (Wang et al, 2020), Rosaceae (Liu et al, 2019(Liu et al, , 2020a, and Vitaceae (Wen et al, 2018). However, the uniparental inheritance of plastomes limits their power to fully elucidate the evolutionary histories of lineages with reticulate evolution, which has been proved to be very common in Rosaceae (Liu et al, 2020a,b;Hodel et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

On the Species Delimitation of the Maddenia Group of Prunus (Rosaceae): Evidence From Plastome and Nuclear Sequences and Morphology

Liu

Wang

et al. 2021

Front. Plant Sci.

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The recognition, identification, and differentiation of closely related plant species present significant and notorious challenges to taxonomists. The Maddenia group of Prunus, which comprises four to seven species, is an example of a group in which species delimitation and phylogenetic reconstruction have been difficult, due to the lack of clear morphological distinctions, limited sampling, and low informativeness of molecular evidence. Thus, the precise number of species in the group and the relationships among them remain unclear. Here, we used genome skimming to generate the DNA sequence data for 22 samples, including 17 Maddenia individuals and five outgroups in Amygdaloideae of Rosaceae, from which we assembled the plastome and 446 single-copy nuclear (SCN) genes for each sample. The phylogenetic relationships of the Maddenia group were then reconstructed using both concatenated and coalescent-based methods. We also identified eight highly variable regions and detected simple sequence repeats (SSRs) and repeat sequences in the Maddenia species plastomes. The phylogenetic analysis based on the complete plastomes strongly supported three main subclades in the Maddenia group of Prunus, while five subclades were recognized based on the nuclear tree. The phylogenetic network analysis detected six hybridization events. Integrating the nuclear and morphological evidence, we proposed to recognize five species within the Maddenia group, i.e., Prunus fujianensis, P. himalayana, P. gongshanensis, P. hypoleuca, and P. hypoxantha. Within this group, the first three species are well-supported, while the gene flow occurring throughout the Maddenia group seems to be especially frequent between P. hypoleuca and P. hypoxantha, eroding the barrier between them. The phylogenetic trees based on eight concatenated hypervariable regions had a similar topology with the complete plastomes, showing their potential as molecular markers and effective barcodes for further phylogeographic studies on Maddenia.

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Implications of plastome evolution in the true lilies (monocot order Liliales)

Cited by 28 publications

References 98 publications

Characterization of the complete chloroplast genome of Zephyranthes phycelloides (Amaryllidaceae, tribe Hippeastreae) from Atacama region of Chile

Characterization of the complete chloroplast genome of Zephyranthes phycelloides (Amaryllidaceae, tribe Hippeastreae) from Atacama region of Chile

The complete chloroplast genome of a shrub species, Smilax glabra (Smilacaceae) from Guangdong, China

On the Species Delimitation of the Maddenia Group of Prunus (Rosaceae): Evidence From Plastome and Nuclear Sequences and Morphology

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