Plastid DNA Research Articles

Complete mitochondrial genome of Mentha spicata L. reveals multiple chromosomal configurations and RNA editing events

Mentha spicata L. is a valuable plant that yields spearmint oil, widely utilized in the pharmaceutical, chemical, and cosmetic industries. The mitochondrial genome (mitogenome) is an essential material for molecular breeding and evolution studies. Here, the mitogenome of M. spicata was assembled by combining Nanopore and Illumina reads. It consisted of a linear chromosome (Ch1) and two circular chromosomes (Ch2 and Ch3). Furthermore, we showed two pairs of repeats (R1 and R2) mediated recombinations resulting in multiple chromosomal configurations. The R1-mediated-recombination generated a large molecule formed by joining Ch2 and Ch1. Similarly, the R2-mediated-recombination generated a large molecule formed by joining Ch3 and Ch1. Then, we identified 17 mitochondrial plastid DNAs (MTPTs) by comparing the mitogenome and cpgenome. The MTPT14 was conserved in multiple species, which has undergone the same evolutionary process as the two organellar genomes among M. spicata, Hesperelaea palmeri and Castilleja paramensis. Based on the RNA-seq reads, 246 RNA editing sites were predicted, resulting in the conversion of cytosine to uracil bases. Furthermore, we successfully validated 40 out of 43 predicted sites. This project reported a complex structure of the M. spicata mitogenome resulting from repeat-mediated recombinations, which will provide valuable information for gene function study and the breeding of different varieties.

Ixeridiumsagittarioides (Asteraceae-Cichorieae) revisited: range extension and molecular evidence for its systematic position in the Lactuca alliance.

Our first record of the rare and scatteredly distributed Ixeridiumsagittarioides for Guizhou, China, triggered a study to assess its systematic position. The species was placed in four different genera in the course of its taxonomic history and was recently treated with doubts as a member of Ixeridium in the Flora of China. Comparative morphological investigation and phylogenetic analyses based on the nuclear ribosomal DNA internal transcribed spacer (nrITS) and five non-coding plastid DNA regions (petD region, psbA-trnH, trnL-trnF, rpl32-trnL (UAG) and 5´rps16-trnQ (UUG) spacers) provided evidence that the species is not a member of Ixeridium and the Crepidinae but has evolved by ancient hybridisation of members of the Lactuca alliance (Lactucinae). It is reinstated as Lactucasagittarioides and a comprehensive morphological description is provided, based on material from its entire range of distribution.

WHIRLY1-deficient chloroplasts display enhanced formation of cyclobutane pyrimidine dimers during exposure to UV-B radiation.

The single-stranded DNA/RNA binding protein WHIRLY1 is a major chloroplast nucleoid-associated protein required for the compactness of nucleoids. Most nucleoids in chloroplasts of WHIRLY1-knockdown barley plants are less compact compared to nucleoids in wild-type plants. The reduced compaction leads to an enhanced optical cross-section, which may cause the plastid DNA to be a better target for damaging UV-B radiation. To investigate this hypothesis, primary foliage leaves, chloroplasts, and nuclei from wild-type and WHIRLY1-knockdown plants were exposed to experimental UV-B radiation. Thereafter, total, genomic and plastid DNA were isolated, respectively, and analyzed for the occurrence of cyclobutane pyrimidine dimers (CPDs), which is a parameter for genome stability. The results of this study revealed that WHIRLY1-deficient chloroplasts had strongly enhanced DNA damages, whereas isolated nuclei from the same plant line were not more sensitive than nuclei from the wild-type, indicating that WHIRLY1 has different functions in chloroplasts and nucleus. This supports the hypothesis that the compaction of nucleoids may provide protection against UV-B radiation.

Phylogenetic, cytogenetic and morphological evidences are critical for recognizing a new genus: Valdesiana, an Iberian intergeneric allopolyploid between Schenkia and Exaculum

The present taxonomic status of Schenkia elegans, endemism recently described in the Iberian Peninsula, and its relationship with the sympatric and the nearest morphological species Schenkia spicata and Exaculum pusillum is revaluated. Different kinds of evidence based on plant morphology, ploidy estimation by flow cytometry, karyotype characterisation, and phylogenetic data have been analysed. Two maternally inherited plastid DNA regions (trnL intron and trnL-F spacer) and biparentally inherited nuclear ribosomal DNA sequence region (nrDNA ITS) have been used. Comparative multivariate analyses show an intermediate morphology of the S. elegans plants between the other two species studied. Flow cytometry and karyotype analyses in S. elegans point to an allopolyploid origin, with the latter constituted by a mixture of those of the diploids S. spicata and E. pusillum. Phylogenetic analyses based on plastid and nuclear DNA regions cluster S. elegans in two different clades, those of S. spicata and E. pusillum, suggesting a possible hybrid origin of S. elegans between both species, acting as maternal or paternal progenitors. In consequence, taking in consideration the taxonomic relationships among genera (Exaculum, Schenkia and the closely related genus Zeltnera found in America), a monotypic genus Valdesiana gen. nov. is proposed to accommodate the allopolyploid species, combined as V. elegans, for which immediate conservation measures must be evaluated.

Cymbidium × fugongense (Orchidaceae; Epidendroideae), a new natural hybrid from China: evidence from morphology and molecular analyses

This study illustrates and describes Cymbidium × fugongense, a natural hybrid of Cymbidium wenshanense and Cymbidium eburneum or Cymbidium maguanense, from Yunnan Province, China. Morphologically, it has white-pink sepals and petals; petals are mottled and contain purple-red patches at their centres. The midlobe of lip is purple-red, with occasionally purple-red mottling on the base and apex of side lobes. The column is purple-red and mottled ventrally. Molecular analysis of plastid DNA (matK and rbcL) sequence data confirmed the natural hybrid as related to C. wenshanense, whereas the nuclear (ITS) DNA clearly supported a relationship of this material to species of C. subgenus Cyperorchis.

Plastome evolution in the genus Sium (Apiaceae, Oenantheae) inferred from phylogenomic and comparative analyses

BackgroundSium L. (Apiaceae) is a small genus distributed primarily in Eurasia, with one species also occurring in North America. Recently, its circumscription has been revised to include 10 species, however, the phylogenetic relationships within its two inclusive clades were poorly supported or collapsed in previous studies based on nuclear ribosomal DNA ITS or cpDNA sequences. To identify molecular markers suitable for future intraspecific phylogeographic and population genetic studies, and to evaluate the efficacy of plastome in resolving the phylogenetic relationships of the genus, the complete chloroplast (cp) genomes of six Sium species were sequenced.ResultsThe Sium plastomes exhibited typical quadripartite structures of Apiaceae and most other higher plant plastid DNAs, and were relatively conserved in their size (153,029–155,006 bp), gene arrangement and content (with 114 unique genes). A total of 61–67 SSRs, along with 12 highly divergent regions (trnQ, trnG-atpA, trnE-trnT, rps4-trnT, accD-psbI, rpl16, ycf1-ndhF, ndhF-rpl32, rpl32-trnL, ndhE-ndhG, ycf1a and ycf1b) were discovered in the plastomes. No significant IR length variation was detected showing that plastome evolution was conserved within this genus. Phylogenomic analysis based on whole chloroplast genome sequences produced a highly resolved phylogenetic tree, in which the monophyly of Sium, as well as the sister relationship of its two inclusive clades were strongly supported.ConclusionsThe plastome sequences could greatly improve phylogenetic resolution, and will provide genomic resources and potential markers useful for future studies of the genus.

Dynamic hybridization between two spleenworts, Asplenium incisum and Asplenium ruprechtii in Korea.

Natural hybridization between Asplenium incisum and A. ruprechtii has been observed in Northeast Asia and its allotetraploid species, A. castaneoviride, was reported. However, the hybridization process between the parental species and the origin of the allotetraploid taxon remains obscure. Additionally, the systematic affinities of the recently described hybrid A. bimixtum, considered to have originated from the hybridization of A. ruprechtii, A. trichomanes, and A. incisum, is unresolved owing to its similarity to A. castaneoviride. The goals of this study were to (1) investigate the hybridization between A. ruprechtii and A. incisum; (2) verify the origin of A. castaneoviride occurring in Korea, whether it independently arose from 2x sterile hybrids; and (3) elucidate the reliability of identifying A. bimixtum. Three genotypes, A. incisum, A. ruprechtii, and their hybrid, were identified based on the nuclear gene pgiC sequence and finally divided them into six types by ploidy levels: diploid A. incisum, A. ruprechtii, and four hybrid types (diploid A. × castaneoviride, triploid A. × castaneoviride, allotetraploid A. castaneoviride, and A. bimixtum). In the analyses of plastid DNA, all hybrids had an A. ruprechtii-type rbcL gene. In addition, the four plastomes of A. ruprechtii and the hybrids had high pairwise sequence identities greater than 98.48%. They increased up to 99.88% when a large deletion of A. x castaneoriviride (2x) collected from Buramsan populations was ignored. Notably, this large deletion was also found in triploid A. × castaneoviride and allotetraploid A. castaneoviride in the same populations. Sequence data of the nuclear and plastid genes showed that hybridization is unidirectional, and A. ruprechtii is the maternal parent. The large deletion of rpoC2-rps2 commonly found in the different ploidy hybrids of the Buramsan population suggests that the allotetraploid A. castaneoviride can be created independently from sterile hybrids. We assume that both polyploidization driving allopolyploidy and minority cytotype exclusion took place independently in the population, since A castaenoviride co-occurs with A. ruprechtii in small populations. Furthermore, it was also observed that an enlarged noncoding region in fern organelle (ENRIFO) of the plastome was found in the genus Asplenium.

STUDY OF NON-CODING AREAS OF THE DNA GENOME OF DIFFERENT ANIMAL SPECIES

STUDY OF NON-CODING AREAS OF THE DNA GENOME OF DIFFERENT ANIMAL SPECIES

Phylogenetic relationships and diversification dynamics of Cerastium (Alsineae: Caryophyllaceae): implications for biogeographical patterns of herbs in the Northern Hemisphere

Abstract The evolutionary history of herbaceous species in the Northern Hemisphere remains poorly understood. The genus Cerastium is one of the most species-rich herbaceous genera in the Alsineae (Caryophyllaceae), and is mainly distributed in the Northern Hemisphere. Thus, it provides an ideal opportunity to explore the biogeographical history of herbs in the Northern Hemisphere. Here, we present a comprehensive phylogenetic tree for Cerastium with 75 species based on one nuclear and five plastid DNA markers. We then use an integrated phylogenetic, molecular dating, biogeographical, and diversification rate method to examine the spatiotemporal evolution of Cerastium. Cerastium is strongly supported as monophyletic and contains three major clades (Orthodon, Strephodon, and C. fragillimum). Cerastium originated from Europe in the middle Miocene (c. 13.45 million years ago), and subsequently colonized the New World, Africa, Asia, and Australasia through multiple intercontinental dispersal events. The dispersal of Cerastium from Europe (to both the East and West) and subsequent diversifications contributed to the formation of its contemporary Holarctic distribution pattern. The genus experienced rapid lineage accumulation during the late Miocene, possibly coinciding with a global decrease in temperature. These findings highlight the importance of the Northern Hemisphere in herbaceous species diversification in the late Miocene and Pliocene, and will deepen our understanding of the evolution of herbaceous plants.

Parallel anagenetic patterns in endemic Artemisia species from three Macaronesian archipelagos.

Anagenetic speciation is an important mode of evolution in oceanic islands, yet relatively understudied compared to adaptive radiation. In the Macaronesian region, three closely related species of Artemisia (i.e. A. argentea, A. thuscula and A. gorgonum) are each endemic from a single archipelago (i.e. Madeira, Canary Islands and Cape Verde, respectively), representing a perfect opportunity to study three similar but independent anagenetic speciation processes. By analysing plastid and nuclear DNA sequences, as well as nuclear DNA amount data, generated from a comprehensive sampling in all the islands and archipelagos where these species are currently distributed, we intend to find common evolutionary patterns that help us explain the limited taxonomic diversification experienced by endemic Macaronesian Artemisia. Our time-calibrated phylogenetic reconstruction suggested that divergence among the three lineages occurred in a coincidental short period of time during the Pleistocene. Haplotype and genetic differentiation analyses showed similar diversity values among A. argentea, A. thuscula and A. gorgonum. Clear phylogeographic patterns-showing comparable genetic structuring among groups of islands-were also found within the three archipelagos. Even from the cytogenetic point of view, the three species presented similarly lower genome size values compared to the mainland closely related species A. arborescens. We hypothesize that the limited speciation experienced by the endemic Artemisia in Madeira, Canary Islands and Cape Verde archipelagos could be related to their recent parallel evolutionary histories as independent lineages, combined with certain shared characteristics of seed dispersal, pollen transport and type of habitat.

A phylogenetic analysis of the Korean endemic species <i>Paraphlomis koreana</i> (Lamiaceae) inferred from nuclear and plastid DNA sequences

<i>Paraphlomis koreana</i> (Lamiaceae) was newly named and added to Korean flora in 2014. <i>Paraphlomis</i> belongs to the tribe Paraphlomideae, along with <i>Ajugoides</i> and <i>Matsumurella</i>. However, a recent study has suggested that <i>P. koreana</i> is morphologically similar to <i>Matsumurella chinensis</i>, making them difficult to distinguish from each other. Therefore, we aimed to examine the phylogenetic placement of <i>P. koreana</i> within the tribe and compare its genetic relationship with <i>M. chinensis</i>. We sequenced an additional complete plastid genome for an individual of <i>P. koreana</i> and generated sequences of nuclear ribosomal (nr) DNA regions of internal and external transcribed spacers (ITS and ETS) for two individuals of <i>P. koreana</i>. Maximum likelihood analyses based on two nrDNA regions (ITS and ETS) and four plastid DNA markers (<i>rpl16</i> intron, <i>rpl32</i>-trnL, <i>rps16</i> intron, and <i>trnL-F</i>) covering 13 <i>Paraphlomis</i> species and <i>M. chinensis</i> were conducted. Phylogenetic analyses concordantly supported that <i>P. koreana</i> forms a monophyletic group with <i>M. chinensis</i>. Moreover, our study revealed that <i>P. koreana</i> includes nrDNA sequences of <i>M. chinensis</i> as minor intraindividual variants, suggesting that the genetic divergence between the two taxa is incomplete and may represent intraspecific variation rather than distinct species. In conclusion, our findings suggest that the independent species status of <i>P. koreana</i> within <i>Paraphlomis</i> should be reconsidered.

The synergy of abiotic and biotic factors correlated with diversification of Fumarioideae (Papaveraceae) in the Cenozoic

Rapid diversification of a group is often associated with exploiting an ecological opportunity and/or the evolution of a key innovation. However, how the interplay of such abiotic and biotic factors correlates with organismal diversification has been rarely documented in empirical studies, especially for organisms inhabiting drylands. Fumarioideae is the largest subfamily in Papaveraceae and is mainly distributed in temperate regions of the Northern Hemisphere. Here, we used one nuclear (ITS) and six plastid (rbcL, atpB, matK, rps16, trnL-F, and trnG) DNA sequences to investigate the spatio-temporal patterns of diversification and potential related factors of this subfamily. We first present the most comprehensive phylogenetic analysis of Fumarioideae to date. The results of our integrated molecular dating and biogeographic analyses indicate that the most recent common ancestor of Fumarioideae started to diversify in Asia during the Upper Cretaceous, and then dispersed multiple times out of Asia in the Cenozoic. In particular, we discover two independent dispersal events from Eurasia to East Africa in the late Miocene, suggesting that the Arabian Peninsula might be an important exchange corridor between Eurasia and East Africa in the late Miocene. Within the Fumarioideae, increased speciation rates were detected in two groups, Corydalis and Fumariinae. Corydalis first experienced a burst of diversification in its crown group at ∼ 42 Ma, and further accelerated diversification from the mid-Miocene onwards. During these two periods, Corydalis had evolved diverse life history types, which could have facilitated the colonization of diverse habitats originating from extensive orogenesis in the Northern Hemisphere as well as Asian interior desertification. Fumariinae underwent a burst of diversification at ∼ 15 Ma, which temporally coincides with the increasing aridification in central Eurasia, but is markedly posterior to the shifts in habitat (from moist to arid) and in life history (from perennial to annual) and to range expansion from Asia to Europe, suggesting that Fumariinae species may have been pre-adapted to invade European arid habitats by the acquisition of annual life history. Our study provides an empirical case that documents the importance of pre-adaptation on organismal diversification in drylands and highlights the significant roles of the synergy of abiotic and biotic factors in promoting plant diversification.

Spergularia hanoverensis (Caryophyllaceae): Validation and Recircumscription of a Misinterpreted Species from South Africa.

The name "Spergularia hanoverensis Simon" has been misapplied to an endemic taxon confined to inland semidesert ecosystems in central-western South Africa. It is commonly accepted as a small annual species occurring in saline habitats in a wide elevation range, but its identity still remains obscure. In the context of taxonomic and phylogenetic research on the African species of Spergularia, we found that the name was never validly published. After revision of herbarium material housed in South African herbaria, a voucher collected from Hanover was found at PRE bearing some labels handwritten by E. Simon that suggest it might be an intended type for the name. Additional herbarium material and wild populations from the Karoo region were identified that matched the samples in that voucher, and taxonomic research was conducted to clarify their identity. Among other characters, those Karoo plants show a woody dense compact habit, woody perennial at base; stems prostrate to ascendent; leaves entirely glabrous, somewhat glaucous; large white-hyaline conspicuous stipules; inflorescence glanduliferous, many-flowered subdichasial cyme, with minute bracts; flowers small, with white petals approximately equalling sepals in length, stamens 7-8, and styles free from base; capsule small, with seeds dimorphic, unwinged to broadly winged, with testa always densely tuberculate. Molecular analyses of plastid (trnL-trnF region) and nuclear ribosomal (5.8S-ITS2 region) DNA sequence data support morphological differentiation of the Karoo plants, for which the name S. hanoverensis is here effectively published. A full morphological description and data on ecology, habitat, distribution, and taxonomic and phylogenetic relationships of S. hanoverensis are compared to other members of the "South African group", namely S. glandulosa, S. namaquensis, and S. quartzicola, from which the new species considerably differs. The adaptative significance of dimorphic seeds of S. hanoverensis is briefly commented on in the context of the species habitat preference. An identification key is presented for the South African related taxa.

An updated classification for the hyper-diverse genus Corydalis (Papaveraceae: Fumarioideae) based on phylogenomic and morphological evidence.

The genus Corydalis, with ca. 530 species, has long been considered taxonomically challenging because of its great variability. Previous molecular analyses, based on a few molecular markers and incomplete taxonomic sampling, were clearly inadequate to delimit sections and subgenera. We have performed phylogenetic analyses of Corydalis and related taxa, using 65 shared protein-coding plastid genes from 313 accessions (including 280 samples of ca. 226 species of Corydalis) and 152 universal low-copy nuclear genes from 296 accessions (including 271 samples of Corydalis) covering all 42 previously recognized sections and five independent "series". Phylogenetic trees were inferred using Bayesian Inference and Maximum Likelihood. Eight selected morphological characters were estimated using ancestral state reconstructions. Results include: (i) of the three subgenera of Corydalis, two are fully supported by both the plastid and nuclear data; the third, subg. Cremnocapnos, is weakly supported by plastid DNA only, whereas in the nuclear data the two included sections form successive outgroups to the rest of the genus; (ii) among all 42 sections and five "series", 25 sections and one "series" are resolved as monophyletic in both data sets; (iii) the common ancestor of Corydalis is likely to be a perennial plant with a taproot, yellow flowers with a short saccate spur, linear fruits with recurved fruiting pedicels, and seeds with elaiosomes; (iv) we provide a new classification of Corydalis with four subgenera (of which subg. Bipapillatae is here newly described), 39 sections, 16 of which are consistent with the previous classification, 16 sections have been recircumscribed, one section has been reinstated and six new sections are established. Characters associated with lifespan, underground structures, floral spur, fruit and elaiosomes are important for the recognition of subgenera and sections. These new phylogenetic analyses combined with ancestral character reconstructions uncovered previously unrecognized relationships, and greatly improved our understanding of the evolution of the genus.

Studies of Vietnamese Pteridophyte Flora 2

Abstract— We reported nine fern species: Amblovenatum opulentum, Athyrium erythropodum, Haplopteris angustifolia, Hymenophyllum acanthoides, Hymenophyllum pachydermicum, Huperzia liangshanica, Microlepia smithii, Selaginella bisulcata, and Selaginella reticulata as indigenous to Vietnam based on our new collections and study of type materials and relevant references. We also described one new species, Dryopteris huongii, to accommodate its morphological distinctiveness from its congeneric species. We further investigated the phylogenetic relationships of the new species using three plastid DNA markers, and the result shows it belongs to Acrorumohra clade, sister of D. gymnophylla.

Paraphlomis caloneura (Lamiaceae), A New Species From Guangxi, China

Abstract— Paraphlomis caloneura, a new species from Guangxi Zhuang Autonomous Region, China, is described and illustrated. Molecular phylogenetic analyses based on two nuclear ribosomal DNA regions (ITS and ETS) and three plastid DNA markers (rpl32-trnL, rps16, and trnL-trnF) revealed that the new species is sister to P. hirsutissima. Both species are found in the limestone forests and are geographically close to each other, but P. caloneura can be easily distinguished from P. hirsutissima by its oblong or ovate-oblong and adaxially densely hispid laminas with broadly cuneate to cordate bases, densely hispid petioles, and slightly 2-lobed margins of upper corolla lips.

Thyrocarpus fujianensis (Boraginaceae; Cynoglosseae), a new species from China: evidence from morphological and molecular analyses

We here describe and illustrate a new species, Thyrocarpus fujianensis (Boraginaceae), from Fujian Province in southern China. Morphological comparisons indicated that T. fujianensis is similar to T. sampsonii and T. glochidiatus but displays distinct differences in habitat, leaves, pedicel, calyx, corolla and fruit. Phylogenetic analysis based on the nuclear (ITS) and two plastid DNA sequences (rps16 and trnL–trnF) showed that T. fujianensis is nested within Thyrocarpus with relatively strong supporting values but only weak support as sister to T. sampsonii. The morphological and molecular evidence both support the status of T. fujianensis as a new species.

The complete mitochondrial genome of Amorphophallus albus and development of molecular markers for five Amorphophallus species based on mitochondrial DNA.

Amorphophallus albus is an herbaceous, cormous, perennial plant used as a food source and traditional medicine in Asia. In this study, we assembled and annotated the complete mitochondrial genome (mitogenome) of A. albus. Then we analyzed the repeated elements and mitochondrial plastid sequences (MTPTs), predicted RNA editing sites in mitochondrial protein-coding genes (PCGs). Lastly, we inferred the phylogenetic relationships of A. albus and other angiosperms based on mitochondrial PCGs, and designed two molecular markers based on mitochondrial DNA. The complete mitogenome of A. albus consists of 19 circular chromosomes. And the total length of A. albus mitogenome is 537,044 bp, with the longest chromosome measuring 56,458 bp and the shortest measuring 12,040 bp. We identified and annotated a total of 36 protein-coding genes (PCGs), 21 tRNA genes, and 3 rRNA genes in the mitogenome. Additionally, we analyzed mitochondrial plastid DNAs (MTPTs) and identified 20 MTPTs between the two organelle genomes, with a combined length of 22,421 bp, accounting for 12.76% of the plastome. Besides, we predicted a total of 676 C to U RNA editing sites on 36 protein-coding genes of high confidence using Deepred-mt. Furthermore, extensive genomic rearrangement was observed between A. albus and the related mitogenomes. We conducted phylogenetic analyses based on mitochondrial PCGs to determine the evolutionary relationships between A. albus and other angiosperms. Finally, we developed and validated two molecular markers, Ai156 and Ai976, based on two intron regions (nad2i156 and nad4i976) respectively. The discrimination success rate was 100 % in validation experiments for five widely grown konjac species. Our results reveal the multi-chromosome mitogenome of A. albus, and the developed markers will facilitate molecular identification of this genus.

Systematics and biogeography of Oleaceae subtribe Schreberinae, with recircumscription and revision of the Malagasy members

Abstract Clarifying generic circumscriptions in Oleaceae improves its complicated infrafamilial classification. Focusing on the small and disjunctly distributed subtribe Schreberinae, we use phylogenomic data from plastid and nuclear DNA from an extensive sampling to assess its phylogenetic patterns and biogeographic history. Results show paraphyly in the subtribe, with Comoranthus nested in Schrebera, leading us to synonymize these genera. Schrebera s.l. occurs in four major regions of the world, but its centre of origin remains uncertain, with three possible ancestral ranges identified. However, the diversification of this genus is estimated to have started in the Early Oligocene (c. 34 Mya), and its current distribution pattern is best explained by dispersal between landmasses rather than continental vicariance. Madagascar is the centre of diversity of Schrebera s.l., where ten endemic species, of which five are new, were recovered from analyses of morphological, molecular and ecoclimatic data. Therefore, a taxonomic treatment of the species from Madagascar and the Comoro Islands is presented. As currently circumscribed, Schrebera s.l., and thus the monogeneric subtribe, includes 16 species (one in South America, two in Southeast Asia, three in Africa, of which one is shared with Madagascar, and 11 in Madagascar and the Comoro Islands).

Assembly and Analysis of Plastomes for 15 Potato Cultivars Grown in Russia

Chloroplasts are important organelles in a plant cell, having their own DNA (cpDNA), transmitted only through the female line, and performing the function of photosynthesis. The determination of chloroplast DNA is of interest in the study of the genetic diversity and phylogeny of potatoes, and of cytoplasmic sterility, as well as for applications in biotechnology and genetic engineering. Here, we reconstructed the complete plastomes of 15 S. tuberosum potato cultivars grown in Russia. Our analysis allowed us to determine the composition and location of genes for these plastid DNAs. It was shown that the plastid genome contains both highly and low-variable regions. The region at position 63,001–68,000 nt has the highest variability. We determined the types of cpDNA based on in silico approaches: 10 cultivars have cpDNA of the W-type and 5 cultivars have cpDNA of the T-type. The genetic diversity of the plastid DNA for these potato cultivars was analyzed alongside the previously reconstructed plastomes of South American accessions, European/North American commercial cultivars and potato cultivars bred in the Ural region. The results show that plastid DNAs of the same type form clusters by sequence similarity, in agreement with previous studies.