Historical biogeography and evolutionary diversification of Lilium (Liliaceae): New insights from plastome phylogenomics

Zhou, Nian; Miao, Ke; Liu, Chang-Kun; Jia, Lin‐Bo; Hu, Jinjin; Huang, Yong‐Jiang; Ji, Yunheng

doi:10.1016/j.pld.2023.07.009

Cited by 7 publications

(5 citation statements)

References 109 publications

(178 reference statements)

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“…The morphological polymorphism of lilies was considered the result of parallel evolution during rapid adaptation to various environments, especially for species located in the H-D Mountains and QTP ( Liu et al., 2006 ; Sun et al., 2012 ; Zhang et al., 2014 ; Durán-Castillo et al., 2022 ; Barnbrook et al., 2023 ), where the Nomocharis clade was a typical example ( Patterson and Givnish, 2002 ; Liu et al., 2006 ; Gao et al., 2012 ; Sun et al., 2012 ; Gao et al., 2013 ; Zhang et al., 2014 ; Gao et al., 2015 ; Givnish et al., 2020 ; Zhou et al., 2023 ). The observed relationship between floral morphology and altitude gradients ( Figure 6 ) suggests a significant evolutionary response to environmental pressures.…”

Section: Discussionmentioning

confidence: 99%

“…The ITS phylogeny can correspond well with morphology, while complete chloroplast genome phylogeny exhibited geographic preference. Hybridization and introgression now appear to be the primary causes of Lilium nuclear-plastid conflict (Gao et al, 2013(Gao et al, , 2015(Gao et al, , 2020Zhou et al, 2023), the evidence consisted of the conspicuous geographical divisions observed in the plastid phylogeny corresponding to relatively distant species in the nuclear phylogeny, and it was not random (Gao et al, 2013(Gao et al, , 2015.…”

Section: Conflict In Nuclear-plastid Phylogenetic Relationshipsmentioning

confidence: 99%

“…Nomocharis Franchet ( Franchet, 1889 ) was initially established as an independent genus close to Lilium and Fritillaria in the late 19th century. After much debate about the status of Lilium and Nomocharis ( Balfour, 1918 ; Evans, 1925 ; Sealy, 1950 , 1983 ; Liang, 1984 ), the latter was eventually accommodated and nested in Lilium as a subgenus clade based upon molecular phylogenetics ( Nishikawa et al., 1999 ; Peruzzi et al., 2009 ; Gao et al., 2013 ; Du et al., 2014 ; Gao et al., 2015 ; Gao and Gao, 2016 ; Huang et al., 2018 ; Li et al., 2022a ; Zhou et al., 2023 ). As one of the most complicated and unclear subgroups in Lilium , previous studies have provided us with a superficial understanding of its position within the genus and the possible processes of speciation that were involved ( Gao et al., 2012 , 2013 , 2015 ; Zhou et al., 2023 ), but the detailed phylogenetic framework and evolutionary mechanisms are not clear due to limited sampling.…”

Section: Introductionmentioning

confidence: 99%

“…During the process of rapid diversification and adaptation to the environment, the Nomocharis clade exhibits the contradiction of high divergence in morphology but with low genetic distancing, which has resulted in significant morphological differences compared to typical lily species ( Gao et al., 2015 ; Zhou et al., 2023 ). Such rapid diversification had already been detected in other groups such as Ligularia – Cremanthodium – Parasenecio complex (Asteraceae), Rheum (Polygonaceae), and Rhodiola (Crassulaceae) ( Liu et al., 2006 ; Sun et al., 2012 ; Zhang et al., 2014 ) (for further groups displaying such a pattern, see Gao et al., 2015 , Table 1 ).…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Discussionmentioning

confidence: 99%

Section: Conflict In Nuclear-plastid Phylogenetic Relationshipsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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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“…Compared with mitochondrial or nuclear genomes, the cp genomes of land plants are relatively highly conserved in structure, sequence, gene content and order (Palmer, 1991;Wicke et al, 2011;Mower and Vickrey, 2018). Because of advantages of the cp genome such as characterized by usually uniparental inheritance, lack of genetic recombination, and a moderate nucleotide substitution rate (Palmer, 1985;Wolfe et al, 1987;Drouin et al, 2008;Ravi et al, 2008;Wicke et al, 2011;Mower and Vickrey, 2018), cp genomes have been the primary workhorse for researches of phylogenetics, taxonomy, evolution, and species identification in land plants (Zhang et al, 2017;Niu et al, 2018;Fu et al, 2019;Sousa et al, 2020;Daniell et al, 2021;Wu et al, 2021;Du et al, 2022;Wang et al, 2022;Zhang et al, 2022;Hu et al, 2023;Xu et al, 2023;Zhou et al, 2024).…”

Section: Introductionmentioning

confidence: 99%

Comparative chloroplast genomes of Argentina species: genome evolution and phylogenomic implications

Li,

Zhang,

Aogan

et al. 2024

Front. Plant Sci.

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The genus Argentina Hill belongs to the tribe Potentilleae Sweet and contains approximately 75 species predominantly distributed in the Sino-Himalayan region and the Malesian archipelago. So far we have less knowledge on the phylogenetic relationships within Argentina owing to limited sampling of Argentina taxa or gene fragments in previous studies. Moreover, to date there is no phylogenetic study on Argentina from the perspective of comparative chloroplast (cp) genomics. Here we performed comparative genomic analyses on the cp genomes of 39 accessions representing 18 taxa of Argentina. The Argentina cp genomes presented the typical quadripartite structure, with the sizes ranging from 155 096 bp to 157 166 bp. The 39 Argentina cp genomes contained a set of 112 unique genes, comprising four ribosomal RNA (rRNA) genes, 30 transfer RNA (tRNA) genes, as well as 78 protein-coding genes (PCGs). The cp genome organization, gene content and order in Argentina were highly conserved, but some visible divergences were present in IR/SC boundary regions. Ten regions (trnH-GUG-psbA, trnG-GCC-trnfM-CAU, trnD-GUC-trnY-GUA, rpl32-trnL-UAG, atpH-atpI, rps16-trnQ-UUG, trnS-GCU-trnG-UCC, ndhF-rpl32, trnR-UCU-atpA, and accD-psaI) were identified as excellent candidate DNA markers for future studies on species identification, population genetics and phylogeny of Argentina. Our results indicated that Argentina is monophyletic. In the current sampling, the A. smithiana - A. anserina clade was sister to the remainder of Argentina. Our results corroborated the previous taxonomic treatments to transfer A. phanerophlebia and A. micropetala from the genus Sibbaldia L. to Argentina. Our results showed close relationships among A. stenophylla, A. microphylla, A. taliensis, and A. tatsienluensis, congruent with previous studies based on the morphology of these species. Twenty-six genes (rps3, rps15, rps16, rps19, rpl16, rpl20, rpl22, rpoA, rpoB, rpoC1, rpoC2, atpA, atpF, psbB, psbF, ndhA, ndhB, ndhC, ndhD, ndhF, rbcL, accD, ccsA, matK, ycf1, ycf2) were with sites under positive selection, and adaptive evolution of these genes might have played crucial roles in Argentina species adaptation to the harsh mountain environment. This study will facilitate future work on taxonomy, phylogenetics, and adaptive evolution of Argentina.

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Rampant intraspecific variation of plastid genomes in Gentiana section Chondrophyllae

Sun,

Pan,

et al. 2024

Ecology and Evolution

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Exploring the level of intraspecific diversity in taxa experienced radiation is helpful to understanding speciation and biodiversity assembly. Gentiana section Chondrophyllae sensu lato encompasses more than 180 species and occupies more a half of species in the genus. In this study, we collected samples across the range of three species (Gentiana aristata, G. crassuloides and G. haynaldii) in section Chondrophyllae s.l., and recovered the intra‐species variation by comparing with closely related taxon. Using 25 newly sequenced plastid genomes together with previously published data, we compared structural differences, quantified the variations in plastome size, and measured nucleotide diversity in various regions. Our results showed that the plastome size variation in the three Chondrophyllae species ranged from 285 to 628 bp, and the size variation in LSC, IR and SSC ranged from 236 to 898 bp, 52 to 393 bp and 135 to 356 bp, respectively. Nucleotide diversity of plastome or any of the four regions was much higher than the control species. The average nucleotide diversity in plastomes of the three species ranged from 0.0010 to 0.0023 in protein coding genes, and from 0.0023 to 0.0061 in intergenic regions. More repeat sequence variations were detected within the three Chondrophyllae species than the control species. Various plastid sequence matrixes resulted in different backbone topology in two target species, showed uncertainty in phylogenetic relationship based inference. In conclusion, our results recovered that species of G. section Chondrophyllae s.l. has high intraspecific plastome variation, and provided insights into the radiation in this speciose lineage.

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Historical biogeography and evolutionary diversification of Lilium (Liliaceae): New insights from plastome phylogenomics

Cited by 7 publications

References 109 publications

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

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

Comparative chloroplast genomes of Argentina species: genome evolution and phylogenomic implications

Rampant intraspecific variation of plastid genomes in Gentiana section Chondrophyllae

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