Complete chloroplast genomes of Liliaceae (s.l.) species: comparative genomic and phylogenetic analyses

She, Ruixue; Zhao, Peng; Zhou, Huijuan; Yue, Ming; Yan, Feng; Hu, Guojia; Gao, Xiaoxiao; Zhang, Shuoxin

doi:10.1111/njb.02477

Cited by 10 publications

(5 citation statements)

References 74 publications

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“…The chloroplast genome of L. auriculata was deposited in GenBank (NCBI) with the accession number MW355498. Comparative chloroplast genomics can provide insights into the mechanism of chloroplast evolution of plant species, including the structural rearrangements and gene features [54][55][56][57]. In our results, all the 12 Litsea chloroplast genomes exhibited the typical and canonical quadripartite structure akin to the majority of angiosperms and other taxa in the Lauraceae [5,6,58].…”

Section: Conservation Of Litsea Chloroplast Genomessupporting

confidence: 50%

Comparative Chloroplast Genomics of Litsea Lam. (Lauraceae) and Its Phylogenetic Implications

Zhang

Tian

Tng³

et al. 2021

Forests

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Litsea Lam. is an ecological and economic important genus of the “core Lauraceae” group in the Lauraceae. The few studies to date on the comparative chloroplast genomics and phylogenomics of Litsea have been conducted as part of other studies on the Lauraceae. Here, we sequenced the whole chloroplast genome sequence of Litsea auriculata, an endangered tree endemic to eastern China, and compared this with previously published chloroplast genome sequences of 11 other Litsea species. The chloroplast genomes of the 12 Litsea species ranged from 152,132 (L. szemaois) to 154,011 bp (L. garrettii) and exhibited a typical quadripartite structure with conserved genome arrangement and content, with length variations in the inverted repeat regions (IRs). No codon usage preferences were detected within the 30 codons used in the chloroplast genomes, indicating a conserved evolution model for the genus. Ten intergenic spacers (psbE–petL, trnH–psbA, petA–psbJ, ndhF–rpl32, ycf4–cemA, rpl32–trnL, ndhG–ndhI, psbC–trnS, trnE–trnT, and psbM–trnD) and five protein coding genes (ndhD, matK, ccsA, ycf1, and ndhF) were identified as divergence hotspot regions and DNA barcodes of Litsea species. In total, 876 chloroplast microsatellites were located within the 12 chloroplast genomes. Phylogenetic analyses conducted using the 51 additional complete chloroplast genomes of “core Lauraceae” species demonstrated that the 12 Litsea species grouped into four sub-clades within the Laurus-Neolitsea clade, and that Litsea is polyphyletic and closely related to the genera Lindera and Laurus. Our phylogeny strongly supported the monophyly of the following three clades (Laurus–Neolitsea, Cinnamomum–Ocotea, and Machilus–Persea) among the above investigated “core Lauraceae” species. Overall, our study highlighted the taxonomic utility of chloroplast genomes in Litsea, and the genetic markers identified here will facilitate future studies on the evolution, conservation, population genetics, and phylogeography of L. auriculata and other Litsea species.

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Section: Conservation Of Litsea Chloroplast Genomessupporting

confidence: 50%

Comparative Chloroplast Genomics of Litsea Lam. (Lauraceae) and Its Phylogenetic Implications

Zhang

Tian

Tng³

et al. 2021

Forests

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“…2B-D). Consistent with the previous reports in Liliaceae species, mononucleotides are the most common SSRs and the largest amount of SSRs is located in the LSC region [41].…”

Section: Discussionsupporting

confidence: 92%

Comparative analyses of complete plastid genomes from seven representative species of Convallarioideae (Asparagaceae)

Chen,

Wu,

Nie

et al. 2023

Preprint

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Background Convallarioideae is a subfamily of Asparagaceae, a morphologically diverse group comprising 7 tribes (i.e., Eriospermeae, Rusceae, Dracaeneae, Nolineae, Convallarieae, Ophiopogoneae, and Polygonateae) and two unclassified genera. Methods and Results In this study, we conducted comparative chloroplast genomic and phylogenetic analyses on seven species, representing seven lineages of the tribe. The results showed that all genomes exhibited a conserved quadripartite structure with two inverted repeat regions (26,261 − 26,522 bp) separated by a large single-copy region (83,007–85,692 bp) and a small single-copy region (18,205 − 18,707 bp). Each genome contains 137 unique genes, including 87 protein-coding genes, 38 transfer RNA, and 8 ribosomal RNA genes. Furthermore, we detected 33–61 simple sequence repeats in six categories and 39–57 long repeats in four categories. We selected eleven divergent hotspots for potential molecular markers. Phylogenetic analysis revealed that all the tribes are strongly supported except for Polygonateae, but weak supports were observed among the main lineages within the subfamily. Conclusions The use of the complete chloroplast genomes provides useful implications for a better understanding on the chloroplast evolution on Convallarioideae.

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“…(Fan et al, 2020; Henriquez et al, 2020), while atpB was under positive selection in Urophysa Ulbr. and the Liliaceae (sensu lato) (Xie et al, 2018; She et al, 2020). These genes are highly correlated with physiological processes such as photosynthesis and disease resistance; thus, their positive selection may assist Aquilegia species in rapid adaptation to various environments and enable their wide global distribution.…”

Section: Discussionmentioning

confidence: 99%

Comparative chloroplast genomes and phylogenetic analysis of Aquilegia

et al. 2021

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Aquilegia is an ideal taxon for studying the evolution of adaptive radiation. Current phylogenies of Aquilegia based on different molecular markers are inconsistent, and therefore a clear and accurate phylogeny remains uncertain. Analyzing the chloroplast genome, with its simple structure and low recombination rate, may help solve this problem. METHODS: Next-generation sequencing data were generated or downloaded for Aquilegia species, enabling their chloroplast genomes to be assembled. The assemblies were used to estimate the genome characteristics and infer the phylogeny of Aquilegia. RESULTS: In this study, chloroplast genome sequences were assembled for Aquilegia species distributed across Asia, North America, and Europe. Three of the genes analyzed (petG, rpl36, and atpB) were shown to be under positive selection and may be related to adaptation. The phylogenetic tree of Aquilegia showed that its member species formed two clades with high support, North American and European species, with the Asian species being paraphyletic; A. parviflora and A. amurensis clustered with the North American species, while the remaining Asian species were found in the European clade. In addition, A. oxysepala var. kansuensis should be considered as a separate species rather than a variety. DISCUSSION: The complete chloroplast genomes of these Aquilegia species provide new insights into the reconstruction of the phylogeny of related species and contribute to the further study of this genus.

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Complete chloroplast genomes of Liliaceae (s.l.) species: comparative genomic and phylogenetic analyses

Cited by 10 publications

References 74 publications

Comparative Chloroplast Genomics of Litsea Lam. (Lauraceae) and Its Phylogenetic Implications

Comparative Chloroplast Genomics of Litsea Lam. (Lauraceae) and Its Phylogenetic Implications

Comparative analyses of complete plastid genomes from seven representative species of Convallarioideae (Asparagaceae)

Comparative chloroplast genomes and phylogenetic analysis of Aquilegia

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