The complete chloroplast genome sequences of three lilies: genome structure, comparative genomic and phylogenetic analyses

Li, Yuan; Zhang, Lina; Wang, TianXi; Zhang, ChaoChao; Wang, RuiJia; Zhang, Da; Xie, YuQi; Zhou, NingNing; Wang, Weizhen; Zhang, Huimin; Hu, Bin; Li, WenHan; Zhao, Qingqing; Wang, Lihua; Wu, XueWei

doi:10.1007/s10265-022-01417-5

Cited by 10 publications

(9 citation statements)

References 62 publications

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“… 2023 ), Lilium souliei (GenBank accession number: ON409199; Li et al. 2022 ), Pandanus amaryllifolius (GenBank accession number: ON920703; this study), Pandanus odorifer (GenBank accession number: OK648473; Darshetkar et al. 2022 ), Pandanus tectorius (GenBank accession number: MH748568, ON040650; Tan et al.…”

Section: Resultsmentioning

confidence: 62%

“… 2023 ) and Lilium souliei (Liliaceae, Liliales; GenBank accession number: ON409199; Li et al. 2022 ) included as outgroups. For the maximum likelihood, the GTR + G substitution model was employed, and branch supports were calculated under 1,000 bootstrap replicates; for the Bayesian inference, a 4-by-4 nucleotide model was applied, and MCMC was performed under 2,000,000 generations with sampling taken at every 100 cycles.…”

Section: Resultsmentioning

confidence: 99%

“… 2023 ) and Lilium souliei (Liliaceae, Liliales; GenBank accession number: ON409199; Li et al. 2022 ). The CDS genes were aligned prior to concatenation.…”

Section: Methodsmentioning

confidence: 99%

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The complete chloroplast genome of Pandanus amaryllifolius Roxb. ex Lindl. (Pandanaceae) and its phylogenetic relationship

Chin,

Wong,

Chong

et al. 2024

Mitochondrial DNA Part B

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Pandanus amaryllifolius of Pandanaceae, a plant native to Southeast Asia, has been domesticated for its health benefits and aromatic leaves. It is also used for phytoremediation and soil rehabilitation. However, genetic studies of this species are limited. This study aims to expand its genomic information by assembling and characterizing the complete chloroplast genome of P. amaryllifolius . The chloroplast genome, which was 157,839 bp long, contains a total of 133 genes, including 87 protein-coding (CDS), 38 tRNA, and eight rRNA genes. The overall G/C content was 37.7%. A phylogenetic analysis using 79 shared unique CDS revealed a monophyletic relationship in Pandanales. Based on the limited sampling size, Pandanus amaryllifolius was the first to diverge in Pandanaceae. The genomic data will be useful for future phylogenetic and evolutionary studies of Pandanaceae.

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Section: Resultsmentioning

confidence: 62%

Section: Resultsmentioning

confidence: 99%

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The complete chloroplast genome of Pandanus amaryllifolius Roxb. ex Lindl. (Pandanaceae) and its phylogenetic relationship

Chin,

Wong,

Chong

et al. 2024

Mitochondrial DNA Part B

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“…The 23 representative chloroplast genomes exhibited minimal variation in genome characteristics, such as length, the pattern of repeat sequences, gene content, and order, closely resembling those of other species within the Liliaceae family ( Du et al., 2017 ; Lu et al., 2017 ; Kim et al., 2019 ; Huang et al., 2020 ; Wu et al., 2021 ; Duan et al., 2022 ; Sheikh-Assadi et al., 2022 ; Li et al., 2022b ).…”

Section: Discussionmentioning

confidence: 89%

Lilium liangiae, a new species in the genus Lilium (Liliaceae) that reveals parallel evolution within morphology

Yuan,

Gao

2024

Front. Plant Sci.

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The former genus Nomocharis, which has been merged as a clade within the genus Lilium (Liliaceae), represents one of the most complicated and unclear groups included in the latter. Research on members of the Nomocharis clade has been quite limited due to the sampling difficulties caused by its selective environmental preferences. In this study, we propose a new species within this clade, Lilium liangiae, as a further bridge connecting the former genus Nomocharis with other members of the genus Lilium. We conducted morphological clustering, phylogenetic, and comparative genomics analyses of nuclear internal spacers and the newly generated complete chloroplast genome, in conjunction with previously published sequences, and performed ancestral state reconstruction to clarify the evolutionary pattern of important traits in Lilium. The clustering results of 38 morphological traits indicated that the new species is allied to Nomocharis, further increasing the morphological polymorphism in the latter. The phylogenetic results and morphological clustering both supported L. liangiae belonging to the subclade Ecristata in Nomocharis, its closest affinity being Lilium gongshanense. Inconsistencies in phylogenetic relationships were detected between nuclear and plastid datasets, possibly due to ancient hybridization and ongoing introgression. Comparative genomics revealed the conservation and similarity of their chloroplast genomes, with variations observed in the expansion and contraction of the IR regions. A/T and palindromic repeat sequences were the most abundant. Seven highly variable regions (Pi≥0.015) were identified as potential molecular markers based on the chloroplast genomes of 47 species within Lilium. Both nuclear and plastid genes exhibited very low variability within the Nomocharis clade, contrasting with their highly variable morphological appearance. The ancestral state reconstruction analysis suggests that the campanulate flower form, as in L. liangiae, arose at least three times within the genus Lilium, revealing parallel evolution in the latter. Overall, this study adds important genetic and morphological evidence for understanding the phylogenetic relationships and parallel evolution patterns of species within the genus Lilium.

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“…For several reasons, cp genomes are more commonly used to study plant molecular evolution and phylogeny than mitochondrial genomes. The researchers note that differences in chloroplast genome sequences and their highly differentiated regions between plant species and individual plants not only enable a more comprehensive study of the taxonomy and phylogeny of these species, but also facilitate the identification, breeding, and conservation of valuable biological genetic information among related species [3,4]. Here, we collected representative plants of alpine meadow, alpine steppe, desert steppe grassland types on the Qinghai-Tibet Plateau and determined their chloroplast genome sequences to understand their genome characteristics and phylogenetic evolution.…”

Section: Introductionmentioning

confidence: 99%

Chloroplast Genome Characteristics of Plants on the Tibetan Plateau

Liu,

Qin,

et al. 2024

Physiology

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Located in the interior of Asia, the Qinghai-Tibet Plateau is the largest plateau in China and the highest plateau in the world. It is also known as the “Roof of the world” and the “third pole”. The various nature reserves on the Qinghai-Tibet Plateau are a treasure house of natural resources with the strangest ecological environment and the richest biological resources on the roof of the world. They are of high scientific value. This chapter will describe the chloroplast genome characteristics of several plants on the Qinghai-Tibet Plateau, such as Aster, Asterothamnus centraliasiaticus, Aster altaicus, Corethrodendron multijugum, Clematis nannophylla, and so on.

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The complete chloroplast genome sequences of three lilies: genome structure, comparative genomic and phylogenetic analyses

Cited by 10 publications

References 62 publications

The complete chloroplast genome of Pandanus amaryllifolius Roxb. ex Lindl. (Pandanaceae) and its phylogenetic relationship

The complete chloroplast genome of Pandanus amaryllifolius Roxb. ex Lindl. (Pandanaceae) and its phylogenetic relationship

Lilium liangiae, a new species in the genus Lilium (Liliaceae) that reveals parallel evolution within morphology

Chloroplast Genome Characteristics of Plants on the Tibetan Plateau

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