Complete chloroplast genome of Anathallis obovata (Orchidaceae: Pleurothallidinae)

Mauad, Anna Victoria Silvério Righetto; Vieira, Leila do Nascimento; Bolson, Mônica; Baura, Valter A.; Balsanelli, Eduardo; Souza, Emanuel Maltempi de; Brito, A. L. V. Toscano de; Smidt, Eric de Camargo

doi:10.1007/s40415-019-00524-3

Cited by 3 publications

(7 citation statements)

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“…Eurystyles and Lankesterella are the only genera of the epiphytic clade in Spiranthinae (sensu [17]), and their ndh gene loss should probably be considered an apomorphic character in the relation to the other two Spiranthinae plastomes sequenced. [54,55] suggested that there is a clear relationship between the loss of ndh genes and instability in IR/SSC boundaries, and [24] also reported length variation in ycf1. In our study, both conditions are related to differences in these boundaries (Fig 2).…”

Section: Plastome Description and Hotspot Characterizationmentioning

confidence: 99%

“…The ndh gene complex comprises 11 genes that act in electron transport in photosystem I [53]. However, in Orchidaceae plastomes, there is a great variation in retention/ deletion of the ndh genes among different clades, suggesting independent losses [24,[54][55][56][57].…”

Section: Plastome Description and Hotspot Characterizationmentioning

confidence: 99%

“…The plastome is circular and usually ranges from 107 to 218 kbp in length with about 120 genes [20]. In the orchid family, the length of the plastome is usually within this range [23,24], except for holomycotrophic species in which some plastomes have shrunk to 19 kbp [25,26].…”

Section: Introductionmentioning

confidence: 99%

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Characterization of sequence variability hotspots in Cranichideae plastomes (Orchidaceae, Orchidoideae)

et al. 2020

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This study reports complete plastome sequences for six species of Neotropical Cranichideae and focuses on identification of the most variable regions (hotspots) in this group of orchids. These structure of these six plastomes is relatively conserved, exhibiting lengths ranging between 142,599 to 154,562 bp with 36.7% GC on average and exhibiting typical quadripartite arrangement (LSC, SSC and two IRs). Variation detected in the LSC/IR and SSC/IR junctions is explained by the loss of ndhF and ycf1 length variation. For the two genera of epiphytic clade in Spiranthinae, almost whole sets of the ndh-gene family were missing. Eight mutation hotspots were identified based on nucleotide diversity, sequence variability and parsimony-informative sites. Three of them (rps16-trnQ, trnT-trnL, rpl32-trnL) seem to be universal hotspots in the family, and the other five (trnG-trnR, trnR-atpA, trnP-psaJ, rpl32-infA, and rps15-ycf1) are described for the first time as orchid molecular hotspots. These regions have much more variation than all those used previously in phylogenetics of the group and offer useful plastid markers for phylogenetic, barcoding and population genetic studies. The use of whole plastomes or exclusive no-gap matrices also positioned with high support the holomycotrophic Rhizanthella among Orchidoideae plastomes in model-based analyses, showing the utility of plastomes for phylogenetic placement of this unusual genus.

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Section: Plastome Description and Hotspot Characterizationmentioning

confidence: 99%

Section: Plastome Description and Hotspot Characterizationmentioning

confidence: 99%

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Characterization of sequence variability hotspots in Cranichideae plastomes (Orchidaceae, Orchidoideae)

et al. 2020

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“…We also used the plastome sequence of Anathallis obovata (Lindl.) Pridgeon & MW.Chase (MH979332), which was previously published by us [30], and obtained from GenBank the plastome sequence of Masdevallia picturata Rchb.f. (KJ566305), totaling ten species from subtribe Pleurothallidinae, representing seven of the nine generic affinity groups proposed by Karremans [18].…”

Section: Species Samplingmentioning

confidence: 99%

“…Hence, comparative analyses of complete plastome sequences of Pleurothallidinae can indicate better molecular markers, but thus far only three plastomes of the subtribe are publicly available. Only the overall structure of these plastomes was analyzed and compared so far [30], with no analysis of which regions were more variable.…”

Section: Introductionmentioning

confidence: 99%

Plastid phylogenomics of Pleurothallidinae (Orchidaceae): Conservative plastomes, new variable markers, and comparative analyses of plastid, nuclear, and mitochondrial data

et al. 2021

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We present the first comparative plastome study of Pleurothallidinae with analyses of structural and molecular characteristics and identification of the ten most-variable regions to be incorporated in future phylogenetic studies. We sequenced complete plastomes of eight species in the subtribe and compared phylogenetic results of these to parallel analyses of their nuclear ribosomal DNA operon (26S, 18S, and 5.8S plus associated spacers) and partial mitochondrial genome sequences (29–38 genes and partial introns). These plastomes have the typical quadripartite structure for which gene content is similar to those of other orchids, with variation only in the composition of the ndh genes. The independent loss of ndh genes had an impact on which genes border the inverted repeats and thus the size of the small single-copy region, leading to variation in overall plastome length. Analyses of 68 coding sequences indicated the same pattern of codon usage as in other orchids, and 13 protein-coding genes under positive selection were detected. Also, we identified 62 polymorphic microsatellite loci and ten highly variable regions, for which we designed primers. Phylogenomic analyses showed that the top ten mutational hotspots represent well the phylogenetic relationships found with whole plastome sequences. However, strongly supported incongruence was observed among plastid, nuclear ribosomal DNA operon, and mitochondrial DNA trees, indicating possible occurrence of incomplete lineage sorting and/or introgressive hybridization. Despite the incongruence, the mtDNA tree retrieved some clades found in other analyses. These results, together with performance in recent studies, support a future role for mitochondrial markers in Pleurothallidinae phylogenetics.

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Phylogenomics and plastomics offer new evolutionary perspectives on Kalanchoideae (Crassulaceae)

Han,

Zhang,

et al. 2024

Annals of Botany

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Background and Aims Kalanchoideae is one of three subfamilies within Crassulaceae and contains four genera. Despite previous efforts, the phylogeny of Kalanchoideae remains inadequately resolved with persistent issues including low support, unstructured topologies and polytomies. This study aimed to address two central objectives: (1) resolving the pending phylogenetic questions within Kalanchoideae by using organelle-scale ‘barcodes’ (plastomes) and nuclear data; and (2) investigating interspecific diversity patterns among Kalanchoideae plastomes. Methods To explore the plastome evolution in Kalanchoideae, we newly sequenced 38 plastomes representing all four constituent genera (Adromischus, Cotyledon, Kalanchoe and Tylecodon). We performed comparative analyses of plastomic features, including GC and gene contents, gene distributions at the IR (inverted repeat) boundaries, nucleotide divergence, plastomic tRNA (pttRNA) structures and codon aversions. Additionally, phylogenetic inferences were inferred using both the plastomic dataset (79 genes) and nuclear dataset (1054 genes). Key Results Significant heterogeneities were observed in plastome lengths among Kalanchoideae, strongly correlated with LSC (large single copy) lengths. Informative diversities existed in the gene content at SSC/IRa (small single copy/inverted repeat a), with unique patterns individually identified in Adromischus leucophyllus and one major Kalanchoe clade. The ycf1 gene was assessed as a shared hypervariable region among all four genera, containing nine lineage-specific indels. Three pttRNAs exhibited unique structures specific to Kalanchoideae and the genera Adromischus and Kalanchoe. Moreover, 24 coding sequences revealed a total of 41 lineage-specific unused codons across all four constituent genera. The phyloplastomic inferences clearly depicted internal branching patterns in Kalanchoideae. Most notably, by both plastid- and nuclear-based phylogenies, our research offers the first evidence that Kalanchoe section Eukalanchoe is not monophyletic. Conclusions This study conducted comprehensive analyses on 38 newly reported Kalanchoideae plastomes. Importantly, our results not only reconstructed well-resolved phylogenies within Kalanchoideae, but also identified highly informative unique markers at the subfamily, genus and species levels. These findings significantly enhance our understanding of the evolutionary history of Kalanchoideae.

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Complete chloroplast genome of Anathallis obovata (Orchidaceae: Pleurothallidinae)

Cited by 3 publications

References 45 publications

Characterization of sequence variability hotspots in Cranichideae plastomes (Orchidaceae, Orchidoideae)

Characterization of sequence variability hotspots in Cranichideae plastomes (Orchidaceae, Orchidoideae)

Plastid phylogenomics of Pleurothallidinae (Orchidaceae): Conservative plastomes, new variable markers, and comparative analyses of plastid, nuclear, and mitochondrial data

Phylogenomics and plastomics offer new evolutionary perspectives on Kalanchoideae (Crassulaceae)

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