Comparative chloroplast genomics and phylogenetics of Fagopyrum esculentum ssp. ancestrale – A wild ancestor of cultivated buckwheat

<p>Abstract</p> <p>Background</p> <p>Chloroplast genome sequences are extremely informative about species-interrelationships owing to its non-meiotic and often uniparental inheritance over generations. The subject of our study, <it>Fagopyrum esculentum</it>, is a member of the family Polygonaceae belonging to the order Caryophyllales. An uncertainty remains regarding the affinity of Caryophyllales and the asterids that could be due to undersampling of the taxa. With that background, having access to the complete chloroplast genome sequence for <it>Fagopyrum </it>becomes quite pertinent.</p> <p>Results</p> <p>We report the complete chloroplast genome sequence of a wild ancestor of cultivated buckwheat, <it>Fagopyrum esculentum </it>ssp. <it>ancestrale</it>. The sequence was rapidly determined using a previously described approach that utilized a PCR-based method and employed universal primers, designed on the scaffold of multiple sequence alignment of chloroplast genomes. The gene content and order in buckwheat chloroplast genome is similar to <it>Spinacia oleracea</it>. However, some unique structural differences exist: the presence of an intron in the <it>rpl2 </it>gene, a frameshift mutation in the <it>rpl23 </it>gene and extension of the inverted repeat region to include the <it>ycf1 </it>gene. Phylogenetic analysis of 61 protein-coding gene sequences from 44 complete plastid genomes provided strong support for the sister relationships of Caryophyllales (including Polygonaceae) to asterids. Further, our analysis also provided support for <it>Amborella </it>as sister to all other angiosperms, but interestingly, in the bayesian phylogeny inference based on first two codon positions <it>Amborella </it>united with Nymphaeales.</p> <p>Conclusion</p> <p>Comparative genomics analyses revealed that the <it>Fagopyrum </it>chloroplast genome harbors the characteristic gene content and organization as has been described for several other chloroplast genomes. However, it has some unique structural features distinct from previously reported complete chloroplast genome sequences. Phylogenetic analysis of the dataset, including this new sequence from non-core Caryophyllales supports the sister relationship between Caryophyllales and asterids.</p

Polygonum schischkinii is a member of Atraphaxis (Polygonaceae, Polygoneae): evidences from morphological and molecular analyses

The Chinese endemic Polygonum schischkinii was studied from both morphological and molecular points of view. On the basis of the structure of ocreas and ocreolas, P. schischkinii appears to be a member of the genus Atraphaxis. The results of Maximum Likelihood and Bayesian analyses of combined data of the plastid [rpl32-trnL(UAG) IGS, trnL(UAA) intron, trnL-trnF IGS] and nuclear rDNA ITS1-2 regions, carried out on 61 members of tribe Polygoneae, confirmed position of P. schischkinii in the Atraphaxis clade. A new combination-Atraphaxis glareosa-based on P. glareosum, which has nomenclatural priority over P. schischkinii, is proposed. Ecological notes and a detailed distributional map of the species are also provided. © 2021 Magnolia Press. All rights reserved

Phylogenetic position and plastid genome structure of Vietorchis, a mycoheterotrophic genus of Orchidaceae (subtribe Orchidinae) endemic to Vietnam

The orchid genus Vietorchis comprises three species, all discovered in the 21 century. Each of these species is achlorophyllous, mycoheterotrophic and is known to be endemic to Vietnam. The type species of the genus, V. aurea, occurs in a single location in northern Vietnam within a lowland limestone karstic area. Vietorchis furcata and V. proboscidea, in contrast, are confined to mountains of southern Vietnam, far away from any limestone formations. Taxonomic placement of Vietorchis remained uncertain for the reason of inconclusive morphological affinities. At the same time, the genus has never been included into molecular phylogenetic studies. We investigate the phylogenetic relationships of two species of Vietorchis (V. aurea and V. furcata) based on three DNA datasets: (1) a dataset comprising two nuclear regions, (2) a dataset comprising two plastid regions, and (3) a dataset employing data on the entire plastid genomes. Our phylogenetic reconstructions support the placement of Vietorchis into the subtribe Orchidinae (tribe Orchideae, subfamily Orchidoideae). This leads to a conclusion that the previously highlighted similarities in the rhizome morphology between Vietorchis and certain mycoheterotrophic genera of the subfamilies Epidendroideae and Vanilloideae are examples of a convergence. Vietorchis is deeply nested within Orchidinae, and therefore the subtribe Vietorchidinae is to be treated as a synonym of Orchidinae. In the obtained phylogenetic reconstructions, Vietorchis is sister to the photosynthetic genus Sirindhornia. Sirindhornia is restricted to limestone mountains, which allows to speculate that association with limestone karst is plesiomorphic for Vietorchis. Flower morphology is concordant with the molecular data in placing Vietorchis into Orchidinae and strongly supports the assignment of the genus to one of the two major clades within this subtribe. Within this clade, however, Vietorchis shows no close structural similarity with any of its genera; in particular, the proximity between Vietorchis and Sirindhornia has never been proposed. Finally, we assembled the plastid genome of V. furcata, which is 65969 bp long and contains 45 unique genes, being one of the most reduced plastomes in the subfamily Orchidoideae. The plastome of Vietorchis lacks any rearrangements in comparison with the closest studied autotrophic species, and possesses substantially contracted inverted repeats. No signs of positive selection acting on the protein-coding plastid sequences were detected

When Morphology and Biogeography Approximate Nuclear ITS but Conflict with Plastid Phylogeny: Phylogeography of the Lotus dorycnium Species Complex (Leguminosae)

Lotus dorycnium s.l. is a complex of taxa traditionally regarded as members of Dorycnium. It has a wide Mediterranean range, extending in the north to Central and Eastern Europe, and in the east to the Crimea, the Caucasus, and the Western Caspian region. Molecular phylogenetic data support placement of the L. dorycnium complex in the genus Lotus. The present study investigated the phylogeny, phylogeography and morphological variability of the L. dorycnium complex across its distribution range to reveal the main trends in genetic and morphological differentiation in this group. The results of the morphological analyses demonstrated some degree of differentiation, with L. d. ssp. herbaceus, ssp. gracilis, and ssp. anatolicus more or less well defined, whereas ssp. dorycnium, ssp. germanicus, and ssp. haussknechtii can be hardly distinguished from each other using morphology. Analyses of the L. dorycnium complex based on nrITS revealed a tendency towards a geographic differentiation into Western, Eastern, and Turkish groups. Phylogenetic and phylogeographic analyses of the same set of specimens using concatenated plastid markers trnL-F, rps16, and psbA-trnH demonstrated a low resolution between the L. dorycnium complex and L. hirsutus, as well as among the taxa within the L. dorycnium complex, which can be interpreted as evidence of an incomplete lineage sorting or hybridization. The evolutionary processes responsible for incongruence in phylogenetic signals between plastid and nuclear sequences of the morphologically well-defined species L. dorycnium and L. hirsutus were most likely localized in the Eastern Mediterranean. A possibility of rare gene exchange between the L. dorycnium complex and the group of L. graecus is revealed for the first time

Comparative chloroplast genomics and phylogenetics of ssp. – A wild ancestor of cultivated buckwheat-2

Naceae taxa compared to . 1, 2 – ssp. -and -fragments respectively, 3, 4 – SSC -and -, 5, 6 – -and -, 7, 8 – -and -, 9, 10 – -and -, 11, 12 – -and -, 13, 14 – -and -, 15, 16 – -and -(-– no amplification). M is the 0.25 – 10 Kb DNA ladder (SibEnzyme Ltd, Moscow, Russia), lowermost visible lane corresponds to 0.5 Kb.<p><b>Copyright information:</b></p><p>Taken from "Comparative chloroplast genomics and phylogenetics of ssp. – A wild ancestor of cultivated buckwheat"</p><p>http://www.biomedcentral.com/1471-2229/8/59</p><p>BMC Plant Biology 2008;8():59-59.</p><p>Published online 20 May 2008</p><p>PMCID:PMC2430205.</p><p></p

Comparative chloroplast genomics and phylogenetics of ssp. – A wild ancestor of cultivated buckwheat-5

To small (SSC) and large (LSC) single copy regions. Genes shown inside the circle are transcribed clockwise, those outside the circle are transcribed counterclockwise. Asterisk (*) indicates pseudogenes.<p><b>Copyright information:</b></p><p>Taken from "Comparative chloroplast genomics and phylogenetics of ssp. – A wild ancestor of cultivated buckwheat"</p><p>http://www.biomedcentral.com/1471-2229/8/59</p><p>BMC Plant Biology 2008;8():59-59.</p><p>Published online 20 May 2008</p><p>PMCID:PMC2430205.</p><p></p

Comparative chloroplast genomics and phylogenetics of ssp. – A wild ancestor of cultivated buckwheat-3

6, consistency index is 0.41 and retention index is 0.48. Numbers at nodes indicate bootstrap support values; first number is for nucleotide sequence data set, second is for amino acid sequence data set. Species which differ in position according to the analysis of these two types of data are underlined. Branch lengths are proportional to the number of expected nucleotide substitutions; scale bar corresponds to 1000 changes.<p><b>Copyright information:</b></p><p>Taken from "Comparative chloroplast genomics and phylogenetics of ssp. – A wild ancestor of cultivated buckwheat"</p><p>http://www.biomedcentral.com/1471-2229/8/59</p><p>BMC Plant Biology 2008;8():59-59.</p><p>Published online 20 May 2008</p><p>PMCID:PMC2430205.</p><p></p

Comparative chloroplast genomics and phylogenetics of ssp. – A wild ancestor of cultivated buckwheat-4

Ach gene represents separate partition. Numbers at nodes indicate posterior probability, first number is for posterior probabilities inferred from the analysis of all codon position, second is for posterior probabilities inferred from the analysis of first two codon positions. Branch lengths are proportional to the number of expected nucleotide substitutions; scale bar corresponds to one substitution per ten sites. Species which differ in position according to the analysis of all and first two codon positions are underlined.<p><b>Copyright information:</b></p><p>Taken from "Comparative chloroplast genomics and phylogenetics of ssp. – A wild ancestor of cultivated buckwheat"</p><p>http://www.biomedcentral.com/1471-2229/8/59</p><p>BMC Plant Biology 2008;8():59-59.</p><p>Published online 20 May 2008</p><p>PMCID:PMC2430205.</p><p></p

Comparative chloroplast genomics and phylogenetics of ssp. – A wild ancestor of cultivated buckwheat-0

To small (SSC) and large (LSC) single copy regions. Genes shown inside the circle are transcribed clockwise, those outside the circle are transcribed counterclockwise. Asterisk (*) indicates pseudogenes.<p><b>Copyright information:</b></p><p>Taken from "Comparative chloroplast genomics and phylogenetics of ssp. – A wild ancestor of cultivated buckwheat"</p><p>http://www.biomedcentral.com/1471-2229/8/59</p><p>BMC Plant Biology 2008;8():59-59.</p><p>Published online 20 May 2008</p><p>PMCID:PMC2430205.</p><p></p