Plastome sequences help to improve the systematic position of trinerved <i>Lindera</i> species in the family Lauraceae

Tian, Xiangyu; Ye, Junwei; Song, Yu

doi:10.7717/peerj.7662

Cited by 23 publications

(34 citation statements)

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“…Subclade III was sister to subclade I and II in our study, consistent with previous analyses ( Zhao et al, 2018 ; Song et al, 2019 ; Tian, Ye & Song, 2019 ). The three Lindera species in subclade I share common morphological traits, such as alternate and pinninerved leaves, a persistent involucre, vegetative terminal buds in inflorescences and 3-merous flowers ( Li et al, 2008a ).…”

Section: Discussionsupporting

confidence: 93%

“…In subclade III, the trinerved or triplinerved species of Lindera ( Lindera aggregata , L. chunii , L. fragrans , L. limprichtii , L. pulcherrima , L. supracostata , L. thomsonii and L. thomsonii var. vernayana ) formed a well-supported clade in both our study and that of Tian, Ye & Song (2019) . However, triplinerved leaves also exist in most species of Neolitsea ( Li et al, 2008b ; Li et al, 2008a ).…”

Section: Discussionsupporting

confidence: 69%

“…When combined, such biological processes may make accurate inference of evolutionary relationships in Laureae difficult. Unfortunately, previous phylogenomic studies of Laureae have ignored potential conflicts among different plastid loci and the underlying processes that may have generated them ( Zhao et al, 2018 ; Song et al, 2019 ; Tian, Ye & Song, 2019 ). These characteristics make Laureae an ideal group in which to explore intra-plastome conflict and its influence on phylogenetic inference.…”

Section: Introductionmentioning

confidence: 99%

“…Despite these efforts, phylogenetic relationships among and within these genera have been poorly resolved based on molecular markers like the ITS, the external transcribed spacer (ETS), matK , trnL - F and trnH - psbA . Compared with these molecular markers, complete plastomes have better performance at the species level within Laureae, although generic delimitation still remains unclear due to limited taxon sampling ( Zhao et al, 2018 ; Song et al, 2019 ; Tian, Ye & Song, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

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Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae)

Xiao

Jin

et al. 2020

PeerJ

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Background Gene tree discordance is common in phylogenetic analyses. Many phylogenetic studies have excluded non-coding regions of the plastome without evaluating their impact on tree topology. In general, plastid loci have often been treated as a single unit, and tree discordance among these loci has seldom been examined. Using samples of Laureae (Lauraceae) plastomes, we explored plastome variation among the tribe, examined the influence of non-coding regions on tree topology, and quantified intra-plastome conflict. Results We found that the plastomes of Laureae have low inter-specific variation and are highly similar in structure, size, and gene content. Laureae was divided into three groups, subclades I, II and III. The inclusion of non-coding regions changed the phylogenetic relationship among the three subclades. Topologies based on coding and non-coding regions were largely congruent except for the relationship among subclades I, II and III. By measuring the distribution of phylogenetic signal across loci that supported different topologies, we found that nine loci (two coding regions, two introns and five intergenic spacers) played a critical role at the contentious node. Conclusions Our results suggest that subclade III and subclade II are successively sister to subclade I. Conflicting phylogenetic signals exist between coding and non-coding regions of Laureae plastomes. Our study highlights the importance of evaluating the influence of non-coding regions on tree topology and emphasizes the necessity of examining discordance among different plastid loci in phylogenetic studies.

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Section: Discussionsupporting

confidence: 93%

Section: Discussionsupporting

confidence: 69%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae)

Xiao

Jin

et al. 2020

PeerJ

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“…Its quality wood is widely used in furniture and architecture. Though phylogenic studies on Lauraceae were conducted, some taxonomic controversies on intra-generic relationship of the genus Lindera as well as the inter-generic relationship with allied genera were still unsolved (Tian et al 2019).…”

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confidence: 99%

The complete chloroplast genome ofLindera pulcherrimavar.hemsleyana(Lauraceae)

Qian

Zhang

2020

Mitochondrial DNA Part B

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Lindera pulcherrima var. hemsleyana is an evergreen tree of the genus Lindera with important medicinal value. The complete chloroplast genome of L. pulcherrima var. hemsleyana is 152,710 bp in length, containing a LSC region of 93,751 bp, a SSC region of 18,813 bp, and a pair of inverted repeats (IRA and IRB) of 20,073 bp each. The genome encoded 128 genes, including 83 protein-coding genes, 8 ribosomal RNA genes, 36 transfer RNA genes, and one pseudogene (ycf1). Most of these genes occurred in a single copy, whereas 15 genes occurred in double copies, including all rRNA, 6 tRNA, and 5 protein-coding genes. The GC content of the whole genome, LSC, SSC, and IR regions is 39.2%, 38.0%, 33.9%, and 44.4%, respectively. A total of 90 SSRs were discovered, the numbers of mono-, di-, tri-, tetra-, penta-, and hexa-nucleotides SSRs were 66, 10, 4, 8, 1, and 1, respectively. Phylogenetic analysis of cp genomes from 24 species of Lauraceae revealed that cp genomes of L. pulcherrima var. hemsleyana, L. pulcherrima var. attenuata, and L. pulcherrima formed a monophyletic clade with 100% bootstrap value.

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Intraspecific differentiation of Lindera obtusiloba as revealed by comparative plastomic and evolutionary analyses

Tian,

Guo,

Song

et al. 2024

Ecology and Evolution

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Lindera obtusiloba Blume is the northernmost tree species in the family Lauraceae, and it is a key species in understanding the evolutionary history of this family. The species of L. obtusiloba in East Asia has diverged into the Northern and Southern populations, which are geographically separated by an arid belt. Though the morphological differences between populations have been observed and well documented, intraspecific variations at the plastomic level have not been systematically investigated to date. Here, ten chloroplast genomes of L. obtusiloba individuals were sequenced and analyzed along with three publicly available plastomes. Comparative plastomic analysis suggests that both the Northern and the Southern populations share similar overall structure, gene order, and GC content in their plastomes although the size of the plasome and the level of intraspecific variability do vary between the two populations. The Northern have relatively larger plastomes while the Southern population possesses higher intraspecific variability, which could be attributed to the complexity of the geological environments in the South. Phylogenomic analyses also support the split of the Northern and Southern clades among L. obtusiloba individuals. However, there is no obvious species boundary between var. obtusiloba and var. heterophylla in the Southern population, indicating that gene flow could still occur between these two varieties, and this could be used as a good example of reticulate evolution. It is also found that a few photosynthesis‐related genes are under positive selection, which is mainly related to the geological and environmental differences between the Northern and the Southern regions. Our results provide a reference for phylogenetic analysis within species and suggest that phylogenomic analyses with a sufficient number of nuclear and chloroplast genomic target loci from widely distributed individuals could provide a deeper understanding of the population evolution of the widespread species.

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Plastome sequences help to improve the systematic position of trinerved Lindera species in the family Lauraceae

Cited by 23 publications

References 50 publications

Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae)

Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae)

The complete chloroplast genome ofLindera pulcherrimavar.hemsleyana(Lauraceae)

Intraspecific differentiation of Lindera obtusiloba as revealed by comparative plastomic and evolutionary analyses

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