Comparative Chloroplast Genomics at Low Taxonomic Levels: A Case Study Using Amphilophium (Bignonieae, Bignoniaceae)

Thode, Verônica A.; Lohmann, Lúcia G.

doi:10.3389/fpls.2019.00796

Cited by 59 publications

(53 citation statements)

References 94 publications

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“…2017 ), Solanaceae ( Amiryousefi et al. 2018 ), and Bignoniaceae ( Thode and Lohmann 2019 ). Decaloba species harbor larger variations, but P. capsularis lacks one of the IRs; P. suberosa exhibits a large expansion of the IRa/LSC up to the psaI gene.…”

Section: Discussionmentioning

confidence: 99%

A Repertory of Rearrangements and the Loss of an Inverted Repeat Region in Passiflora Chloroplast Genomes

Cauz-Santos

Costa

Callot

et al. 2020

Genome Biology and Evolution

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Chloroplast genomes (cpDNA) in angiosperms are usually highly conserved. Although rearrangements have been observed in some lineages, such as Passiflora, the mechanisms that lead to rearrangements are still poorly elucidated. In the present study, we obtained 20 new chloroplast genomes (18 species from the genus Passiflora, and Dilkea retusa and Mitostemma brevifilis from the family Passifloraceae) in order to investigate cpDNA evolutionary history in this group. Passiflora cpDNAs vary in size considerably, with ∼50 kb between shortest and longest. Large inverted repeat (IR) expansions were identified, and at the extreme opposite, the loss of an IR was detected for the first time in Passiflora, a rare event in angiosperms. The loss of an IR region was detected in P. capsularis and P. costaricensis, a species in which occasional biparental chloroplast inheritance has previously been reported. A repertory of rearrangements, such as inversions and gene losses were detected, making Passiflora one of the few groups with complex chloroplast genome evolution. We also performed a phylogenomic study based on all the available cp genomes and our analysis implies that there is a need to reconsider the taxonomic classifications of some species in the group.

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Section: Discussionmentioning

confidence: 99%

A Repertory of Rearrangements and the Loss of an Inverted Repeat Region in Passiflora Chloroplast Genomes

Cauz-Santos

Costa

Callot

et al. 2020

Genome Biology and Evolution

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“…Interestingly, accD genes in several angiosperm lineages, such as Campanulaceae and Poaceae, were lost or relocated to the nuclear genome, presumably due to endosymbiotic evolution [56]. Because the highly variable nucleotide sequences of accD and ycf1 in a range of land plants are likely to be the result of environmental adaptation during evolution [57][58][59], they may be useful markers for plastid evolution. In this study, the conserved coding sequences flanking variable regions of accD and ycf1 in Artemisia enabled the design of PCR primers for crossspecies amplification with clear sequence polymorphisms, yielding novel Artemisia barcode markers with sufficient resolution to distinguish 18 (ycf1b), 19 (accD-1 k), and 21 (accD-1 k + ycf1b) plastome haplotypes from 21 Artemisia taxa ( Table 5).…”

Section: Discussionmentioning

confidence: 99%

Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East Asia: insights into evolutionary divergence and phylogenomic implications

et al. 2020

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Background: Artemisia in East Asia includes a number of economically important taxa that are widely used for food, medicinal, and ornamental purposes. The identification of taxa, however, has been hampered by insufficient diagnostic morphological characteristics and frequent natural hybridization. Development of novel DNA markers or barcodes with sufficient resolution to resolve taxonomic issues of Artemisia in East Asia is significant challenge. Results: To establish a molecular basis for taxonomic identification and comparative phylogenomic analysis of Artemisia, we newly determined 19 chloroplast genome (plastome) sequences of 18 Artemisia taxa in East Asia, de novo-assembled and annotated the plastomes of two taxa using publicly available Illumina reads, and compared them with 11 Artemisia plastomes reported previously. The plastomes of Artemisia were 150,858-151,318 base pairs (bp) in length and harbored 87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNA genes in conserved order and orientation. Evolutionary analyses of whole plastomes and 80 non-redundant protein-coding genes revealed that the noncoding trnH-psbA spacer was highly variable in size and nucleotide sequence both between and within taxa, whereas the coding sequences of accD and ycf1 were under weak positive selection and relaxed selective constraints, respectively. Phylogenetic analysis of the whole plastomes based on maximum likelihood and Bayesian inference analyses yielded five groups of Artemisia plastomes clustered in the monophyletic subgenus Dracunculus and paraphyletic subgenus Artemisia, suggesting that the whole plastomes can be used as molecular markers to infer the chloroplast haplotypes of Artemisia taxa. Additionally, analysis of accD and ycf1 hotspots enabled the development of novel markers potentially applicable across the family Asteraceae with high discriminatory power. Conclusions: The complete sequences of the Artemisia plastomes are sufficiently polymorphic to be used as superbarcodes for this genus. It will facilitate the development of new molecular markers and study of the phylogenomic relationships of Artemisia species in the family Asteraceae.

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“…Several regions highlighted as hyper or moderately variable regarding the nucleotide diversity values across Opuntioideae chloroplast sequences (i.e., accD, ycf1, clpP, petD, rpl32 and ccsA) have been reported to be putatively under positive selection in some lineages, such as Brassicaceae, Bignoniaceae, Rutaceae, Orchidaceae, Geraniaceae and Poaceae (Hu et al 2015;Weng et al 2016;Dong et al 2018;Carbonell-Caballero et al 2015;Ruhlman and Jansen 2018;Thode & Lohmann 2019;Park et al 2017;Piot et al 2018). Positive selection may come into play in response to environmental changes (Piot et al 2018).…”

Section: Insights From Chloroplast Genome Assemblies In Opuntioideae mentioning

confidence: 99%

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

Köhler

Reginato

et al. 2020

Preprint

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Chloroplast genomes (plastomes) are frequently treated as highly conserved among land plants. However, many lineages of vascular plants have experienced extensive structural rearrangements, including inversions and modifications to the size and content of genes. Cacti are one of these lineages, containing the smallest plastome known for an obligately photosynthetic angiosperm, including the loss of one copy of the inverted repeat (~25 kb) and the ndh genes suite, but only a few cacti from the subfamily Cactoideae have been sufficiently characterized. Here, we investigated the variation of plastome sequences across the second-major lineage of the Cactaceae, the subfamily Opuntioideae, to address 1) how variable is the content and arrangement of chloroplast genome sequences across the subfamily, and 2) how phylogenetically informative are the plastome sequences for resolving major relationships among the clades of Opuntioideae. Our de novo assembly of the Opuntia quimilo plastome recovered an organelle of 150,347 bp in length with both copies of the inverted repeats and the presence of all the ndh genes suite. An expansion of the large single copy unit and a reduction of the small single copy was observed, including translocations and inversion of genes as well as the putative pseudogenization of numerous loci. Comparative analyses among all clades within Opuntioideae suggested that plastome structure and content vary across taxa of this subfamily, with putative independent losses of the ndh gene suite and pseudogenization of genes across disparate lineages, further demonstrating the dynamic nature of plastomes in Cactaceae. Our plastome dataset was robust in determining relationships among major clades and subclades within Opuntioideae, resolving three tribes with high support: Cylindropuntieae, Tephrocacteae and Opuntieae. A plastome-wide survey for highly informative phylogenetic markers revealed previously unused regions for future use in Sanger-based studies, presenting a valuable dataset with primers designed for continued evolutionary studies across Cactaceae. These results bring new insights into the evolution of plastomes in cacti, suggesting that further analyses should be carried out to address how ecological drivers, physiological constraints and morphological traits of cacti may be related with the common rearrangements in plastomes that have been reported across the family.

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Comparative Chloroplast Genomics at Low Taxonomic Levels: A Case Study Using Amphilophium (Bignonieae, Bignoniaceae)

Cited by 59 publications

References 94 publications

A Repertory of Rearrangements and the Loss of an Inverted Repeat Region in Passiflora Chloroplast Genomes

A Repertory of Rearrangements and the Loss of an Inverted Repeat Region in Passiflora Chloroplast Genomes

Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East Asia: insights into evolutionary divergence and phylogenomic implications

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

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