Characterization of the complete chloroplast genome of<i>Veronica arvensis</i>and its phylogenomic inference in plantaginaceae

Liu, Huabing; He, Wei; Zhang, Xiaobing; Jiang, Zhimin; Li, Qi; Xia, Chen; Wang, Hui

doi:10.1080/23802359.2022.2139162

Cited by 5 publications

(4 citation statements)

References 17 publications

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“…S2 ) methods using the cp genomes. The four phylogenetic trees showed the same evolutionary relationships, of which the genetic relationship between Veronica and Neopicrorhiza is the closest, followed by Lagotis and Veronicastrum , this is consistent with previous research results 41 – 43 . While that with related genus species under Scrophulariaceae is the farthest.…”

Section: Discussionsupporting

confidence: 91%

“…Recent taxonomy studies have utilized cp genomes to assess the genetic relationship between related species [37][38][39][40] . The basic groups of nine species in this genus range in size variations from 149,386 to 152,319 bp, indicating that each of these species has significantly different cp gene sizes 13,[41][42][43] . A comparative analysis of the cp genomes in V. anagallis-aquatica and V. undulata showed that they contain highly conserved structures and genes as well as the same protein-coding genes, tRNA, and rRNA.…”

Section: Discussionmentioning

confidence: 99%

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The chloroplast genomes of two medicinal species (Veronica anagallis-aquatica L. and Veronica undulata Wall.) and its comparative analysis with related Veronica species

Hai,

Qian,

Yang

et al. 2024

Sci Rep

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Veronica anagallis-aquatica L. and Veronica undulata Wall. are widely used ethnomedicinal plants in China. The two species have different clinical efficacies, while their extremely similar morphology and unclear interspecific relationship make it difficult to accurately identify them, leading to increased instances of mixed usage. This article reports on the complete chloroplast genomes sequence of these two species and their related Veronica species to conduct a comparative genomics analysis and phylogenetic construction. The results showed that the chloroplast (cp) genomes of Veronica exhibited typical circular quadripartite structures, with total lengths of 149,386 to 152,319 base pairs (bp), and GC content of 37.9 to 38.1%, and the number of genes was between 129–134. The total number of simple sequence repeats (SSRs) in V. anagallis-aquatica and V. undulata is 37 and 36, while V. arvensis had the highest total number of 56, predominantly characterized by A/T single bases. The vast majority of long repeat sequence types are forward repeats and palindromic repeats. Selective Ka/Ks values showed that three genes were under positive selection. Sequence differences often occur in the non-coding regions of the large single-copy region (LSC) and small single-copy region (SSC), with the lowest sequence variation in the inverted repeat regions (IR). Seven highly variable regions (trnT-GGU-psbD, rps8-rpl16, trnQ-UUG, trnN-GUU-ndhF, petL, ycf3, and ycf1) were detected, which may be potential molecular markers for identifying V. anagallis-aquatica and V. undulata. The phylogenetic tree indicates that there is a close genetic relationship between the genera Veronica and Neopicrorhiza, and V. anagallis-aquatica and V. undulata are sister groups. The molecular clock analysis results indicate that the divergence time of Veronica may occur at ∼ 9.09 Ma, and the divergence time of these two species occurs at ∼ 0.48 Ma. It is speculated that climate change may be the cause of Veronica species diversity and promote the radiation of the genus. The chloroplast genome data of nine Veronica specie provides important insights into the characteristics and evolution of the chloroplast genome of this genus, as well as the phylogenetic relationships of the genus Veronica.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 99%

The chloroplast genomes of two medicinal species (Veronica anagallis-aquatica L. and Veronica undulata Wall.) and its comparative analysis with related Veronica species

Hai,

Qian,

Yang

et al. 2024

Sci Rep

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“…attenuata shows a quadripartite structure similar to that in the majority of other angiosperms (Liu et al. 2022 ), consisting of a pair of inverted repeats (IRs), a small single-copy (SSC) region, and a large single-copy (LSC) region. The phylogeny reconstructed from complete plastomes revealed that E. rubiginosa var.…”

Section: Discussionmentioning

confidence: 97%

The complete chloroplast genome of Eurya rubiginosa var. attenuata H. T. Chang (Pentaphylacaceae)

Sun

et al. 2023

Mitochondrial DNA Part B

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Eurya rubiginosa var. attenuata is a valuable multiuse tree with a long history of use in China. It has great economic and ecological importance and is used for landscape and urban planting, soil improvement, and raw materials for food production. However, genomic studies of E. rubiginosa var. attenuata are limited. Meanwhile, the classification of this taxon is controversial. In this study, the complete plastome of E. rubiginosa var. attenuata was successfully sequenced and assembled. The chloroplast genome is 157,215 bp in length with a 37.3% GC content. The chloroplast genome structure includes a quadripartite structure comprising a pair of inverted repeat (IR) sequences of 25,872 bp, a small single-copy (SSC) region of 18,216 bp, and a large single-copy (LSC) region of 87,255 bp. The genome contains 128 genes, including 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic inference based on complete plastome analysis showed that E. rubiginosa var. attenuata is closely related to E. alata and belongs to the family Pentaphylacaceae, which differs from the results of the traditional Engler system. The chloroplast genome sequence assembly and phylogenetic analysis enrich the genetic resources of Pentaphylacaceae and provide a molecular basis for further studies on the phylogeny of the family.

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“…The genomic structure of P. hadiensis consists of a pair of IRs, an SSC region, and an LSC region similar to that in the majority of other angiosperms (Liu et al. 2022 ). The phylogenetic results indicated that P. hadiensis exhibited the closest relationship with Isodon in the subfamily Nepetoideae.…”

Section: Discussionmentioning

confidence: 99%

The complete chloroplast genome sequence of Plectranthus hadiensis (Lamiaceae) and phylogenetic analysis

Hao,

Lu,

Dang

et al. 2023

Mitochondrial DNA Part B

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Plants of the genus Plectranthus are used for the treatment of digestive problems, skin diseases, and allergies, with a wide variety of uses. Here, the complete chloroplast genome sequence of Plectranthus hadiensis (Benth. ex E.Mey) Codd. 1788 was assembled and characterized for the first time. The full length of the chloroplast genome is 152,484 bp, consisting of a small single-copy region of 17,686 bp, a large single-copy region of 83,380 bp, and a pair of inverted repeats of 51,418 bp. The overall GC content is 37.73%. The chloroplast genome contains 131 unique genes, including 87 protein-coding genes, 36 transfer RNA genes, and eight ribosomal RNA genes. Phylogenetic tree construction based on the complete chloroplast genome sequences of 25 species (23 Nepetoideae, two Ajugoideae) of the Lamiaceae family showed that P. hadiensis exhibited the closest relationship with Isodon .

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Characterization of the complete chloroplast genome ofVeronica arvensisand its phylogenomic inference in plantaginaceae

Cited by 5 publications

References 17 publications

The chloroplast genomes of two medicinal species (Veronica anagallis-aquatica L. and Veronica undulata Wall.) and its comparative analysis with related Veronica species

The chloroplast genomes of two medicinal species (Veronica anagallis-aquatica L. and Veronica undulata Wall.) and its comparative analysis with related Veronica species

The complete chloroplast genome of Eurya rubiginosa var. attenuata H. T. Chang (Pentaphylacaceae)

The complete chloroplast genome sequence of Plectranthus hadiensis (Lamiaceae) and phylogenetic analysis

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