Plastome sequencing of Myripnois dioica and comparison within Asteraceae

Lin, Nan; Zhang, Xu; Deng, Tao; Zhang, Jianwen; Meng, Anming; Wang, Hengchang; Sun, Hang; Sun, Yanxia

doi:10.1016/j.pld.2019.07.003

Cited by 11 publications

(7 citation statements)

References 55 publications

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“…This shows that the reported genomes have certain errors in annotations as stated previously in a detailed study of the family Solanaceae (Amiryousefi et al, 2018a) and the comparative genomics of the two species of Malvaceae . The gene content was found to be the same in all the species of Asteroideae after correction of annotations, which is also in agreement with gene features in the previously reported plastome of other subfamilies such as Cichorioideae, Pertyoideae, and Carduoideae (Jung et al, 2021;Kim et al, 2019;Lin et al, 2019).…”

Section: Plastome Comparison Of Blumea and Asteroideaesupporting

confidence: 89%

“…Hence, the plastomes of Asteroideae avoid the rearrangements by a certain mechanism. The GC content of the plastomes was also similar to previous Asteraceae genomes and of other plant lineages, and high GC content was observed in IRs, which might be due to the presence of rRNAs, as they have a GC content of up to 55% (Amiryousefi et al, 2018a;Jung et al, 2021;Kim et al, 2019;Lin et al, 2019;Poczai & Hyvönen, 2017).…”

Section: Plastome Comparison Of Blumea and Asteroideaesupporting

confidence: 78%

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Comparative plastome analysis of Blumea, with implications for genome evolution and phylogeny of Asteroideae

Abdullah

Mehmood

Rahim

et al. 2021

Ecology and Evolution

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Section: Plastome Comparison Of Blumea and Asteroideaesupporting

confidence: 89%

Section: Plastome Comparison Of Blumea and Asteroideaesupporting

confidence: 78%

Comparative plastome analysis of Blumea, with implications for genome evolution and phylogeny of Asteroideae

Abdullah

Mehmood

Rahim

et al. 2021

Ecology and Evolution

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“…The chloroplast genome of Asteraceae, except for the Barnadesieae lineage, is characterized by two inversions: the previously mentioned 22.8 kb inversion in the LSC region and a second, 3.3 kb inversion, nested within the larger one ( Kim, Choi & Jansen, 2005 ; Timme et al, 2007 ). The plastome size in the family varies from 149,5 to 153,7 kb ( Choi & Park, 2015 ; Lu et al, 2016 ) and the gene content is relatively conserved: from 111 to 115 different genes, including 79 to 83 protein-coding genes, four rRNAs genes, and 29–30 distinct tRNAs ( Wang et al, 2015 ; Salih et al, 2017 ; Lin et al, 2019 ; Wang et al, 2020 ). Some variations have been found in the gene structure and tRNA abundance, and in some regions the nucleotide diversity is higher than 5% ( Wang et al, 2015 ).…”

Section: Introductionmentioning

confidence: 99%

Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences fromAldama(Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera

Loeuille

Thode

Siniscalchi

et al. 2021

PeerJ

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Aldama (Heliantheae, Asteraceae) is a diverse genus in the sunflower family. To date, nearly 200 Asteraceae chloroplast genomes have been sequenced, but the plastomes of Aldama remain undescribed. Plastomes in Asteraceae usually show little sequence divergence, consequently, our hypothesis is that species of Aldama will be overall conserved. In this study, we newly sequenced 36 plastomes of Aldama and of five species belonging to other Heliantheae genera selected as outgroups (i.e., Dimerostemma asperatum, Helianthus tuberosus, Iostephane heterophylla, Pappobolus lanatus var. lanatus, and Tithonia diversifolia). We analyzed the structure and gene content of the assembled plastomes and performed comparative analyses within Aldama and with other closely related genera. As expected, Aldama plastomes are very conserved, with the overall gene content and orientation being similar in all studied species. The length of the plastome is also consistent and the junction between regions usually contain the same genes and have similar lengths. A large ∼20 kb and a small ∼3 kb inversion were detected in the Large Single Copy (LSC) regions of all assembled plastomes, similarly to other Asteraceae species. The nucleotide diversity is very low, with only 1,509 variable sites in 127,466 bp (i.e., 1.18% of the sites in the alignment of 36 Aldama plastomes, with one of the IRs removed, is variable). Only one gene, rbcL, shows signatures of positive selection. The plastomes of the selected outgroups feature a similar gene content and structure compared to Aldama and also present the two inversions in the LSC region. Deletions of different lengths were observed in the gene ycf2. Multiple SSRs were identified for the sequenced Aldama and outgroups. The phylogenetic analysis shows that Aldama is not monophyletic due to the position of the Mexican species A. dentata. All Brazilian species form a strongly supported clade. Our results bring new understandings into the evolution and diversity of plastomes at the species level.

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“…Up to now, more than 150 Asteraceae plastomes have been sequenced, a total of four subfamilies (Asteroideae, Cichorioideae, Carduoideae, and Pertyoideae) of the thirteen subfamilies were covered (Lin et al. 2019 ). However, no complete chloroplast genome of any Soroseris species have been recorded.…”

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confidence: 99%

The complete chloroplast genome of Soroseris umbrella (Asteraceae)

Zhang

Chen

et al. 2020

Mitochondrial DNA Part B

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Soroseris umbrella is an alpine medical plant that is distributed in the alpine screes of China, Bhutan, and India. Here, we identified the complete chloroplast genome of S. umbrella . The complete genome size is 152,462 bp, which consists of a large single-copy (LSC) region of 84,125 bp, a small single-copy (SSC) region of 18,561 bp, a pair of inverted repeat (IR) regions of 24,888 bp each. The overall GC content of genome is 37.7%. A total of 114 unique genes were identified, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis based on whole chloroplast genome result shows that S. umbrella is most closely related to Taraxacum .

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Plastome sequencing of Myripnois dioica and comparison within Asteraceae

Cited by 11 publications

References 55 publications

Comparative plastome analysis of Blumea, with implications for genome evolution and phylogeny of Asteroideae

Comparative plastome analysis of Blumea, with implications for genome evolution and phylogeny of Asteroideae

Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences fromAldama(Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera

The complete chloroplast genome of Soroseris umbrella (Asteraceae)

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