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

On generic rank and phylogenetic relationships of Dorycnopsis Boiss. (Leguminosae, Loteae)

Nuclear ribosomal ITS sequence data as well as morphological data show that Dorycnopsis gerardii (L.) Boiss. can not be placed in the genus Anthyllis L. The genus Dorycnopsis Boiss. includes two species, D. gerardii and D. abyssinica (A. Rich.) V.N. Tikhom. et D.D. Sokoloff (=Vermifrux abyssinica (A. Rich.) J.B. Gillett). Morphological similarity between Dorycnopsis gerardii and Anthyllis onobrychioides Cav. might be best explained by evolutionary parallelism. Anthyllis (including Hymenocarpos Savi but excluding Dorycnopsis and the monotypic Tripodion Medik.) is well-resolved as a highly supported monophyletic group in analyses of nrITS data set.Datos sobre la secuencia de ITS ribosómico nuclear así como datos morfológicos revelan que Dorycnopsis gerardii (L.) Boiss. no puede pertenecer al género Anthyllis L. El género Dorycnopsis Boiss. incluye dos especies, D. gerardii y D. abyssinica (A. Rich.) V.N. Tikhom. et D.D. Sokoloff (=Vermifrux abyssinica (A. Rich.) J.B. Gillett). La similitud morfológica entre Dorycnopsis gerardii y Anthyllis onobrychioides Cav. encuentra su explicación en un paralelismo evolutivo. Anthyllis (incluyendo a Hymenocarpos Savi, pero excluyendo a Dorycnopsis y al monotípico Tripodion Medik.) se considera, a partir del análisis del nrITS, un grupo monofílitico con un buen apoyo estadístico

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

On generic rank and phylogenetic relationships of Dorycnopsis Boiss. (Leguminosae, Loteae)

Nuclear ribosomal ITS sequence data as well as morphological data show that Dorycnopsis gerardii (L.) Boiss. can not be placed in the genus Anthyllis L. The genus Dorycnopsis Boiss. includes two species, D. gerardii and D. abyssinica (A. Rich.) V.N. Tikhom. et D.D. Sokoloff (=Vermifrux abyssinica (A. Rich.) J.B. Gillett). Morphological similarity between Dorycnopsis gerardii and Anthyllis onobrychioides Cav. might be best explained by evolutionary parallelism. Anthyllis (including Hymenocarpos Savi but excluding Dorycnopsis and the monotypic Tripodion Medik.) is well-resolved as a highly supported monophyletic group in analyses of nrITS data set.Datos sobre la secuencia de ITS ribosómico nuclear así como datos morfológicos revelan que Dorycnopsis gerardii (L.) Boiss. no puede pertenecer al género Anthyllis L. El género Dorycnopsis Boiss. incluye dos especies, D. gerardii y D. abyssinica (A. Rich.) V.N. Tikhom. et D.D. Sokoloff (=Vermifrux abyssinica (A. Rich.) J.B. Gillett). La similitud morfológica entre Dorycnopsis gerardii y Anthyllis onobrychioides Cav. encuentra su explicación en un paralelismo evolutivo. Anthyllis (incluyendo a Hymenocarpos Savi, pero excluyendo a Dorycnopsis y al monotípico Tripodion Medik.) se considera, a partir del análisis del nrITS, un grupo monofílitico con un buen apoyo estadístico

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

Plastid Phylogenomic Analysis of Tordylieae Tribe (Apiaceae, Apioideae)

Based on the nrDNA ITS sequence data, the Tordylieae tribe is recognized as monophyletic with three major lineages: the subtribe Tordyliinae, the Cymbocarpum clade, and the Lefebvrea clade. Recent phylogenomic investigations showed incongruence between the nuclear and plastid genome evolution in the tribe. To assess phylogenetic relations and structure evolution of plastomes in Tordylieae, we generated eleven complete plastome sequences using the genome skimming approach and compared them with the available data from this tribe and close relatives. Newly assembled plastomes had lengths ranging from 141,148 to 150,103 base pairs and contained 122&ndash;127 genes, including 79&ndash;82 protein-coding genes, 35&ndash;37 tRNAs, and 8 rRNAs. We observed substantial differences in the inverted repeat length and gene content, accompanied by a complex picture of multiple JLA and JLB shifts. In concatenated phylogenetic analyses, Tordylieae plastomes formed at least three not closely related lineages with plastomes of the Lefebvrea clade as a sister group to plastomes from the Selineae tribe. The newly obtained data have increased our knowledge on the range of plastome variability in Apiaceae

Seseli (sect. Libanotis) W. D. J. Koch 1824

Key to Turkish species of Seseli sect. Libanotis 1. Stems up to 200 cm, glabrous at base, bracts without membranous margin, stylopodium depressed; plant of salt marshes and salt steppes......................................................................................................................................................................... S. salsugineum – Stems up to 150 cm, pubescent at base, bracts with membranous margin, stylopodium conical; plant of forests, alpine meadows, and rocky slopes.................................................................................................................................................................................2 2. Terminal leaf segments 15–26 mm long; umbels up to 14 cm in diameter; bracts 8–19 mm long................................... S. libanotis – Terminal leaf segments 1–6 mm long; umbels at most 3–3.5 cm in diameter; bracts 4–7 mm long.................. S. transcaucasicumPublished as part of Duran, Ahmet, Samigullin, Tahir & Lyskov, Dmitry, 2021, Seseli salsugineum (Apiaceae), a new species from Central Anatolia, Turkey, pp. 27-42 in Phytotaxa 529 (1) on page 39, DOI: 10.11646/phytotaxa.529.1.2, http://zenodo.org/record/581425

FIGURE 4 in Aegokeras gazipashensis (Apiaceae), a new species from South Anatolia, Turkey

FIGURE 4. Aegokeras gazipashensis: a—rosette form leaves, b—unbranched stem, c—branched stems.Published as part of Duran, Ahmet, Samigullin, Tahir & Lyskov, Dmitry, 2023, Aegokeras gazipashensis (Apiaceae), a new species from South Anatolia, Turkey, pp. 234-248 in Phytotaxa 613 (3) on page 239, DOI: 10.11646/phytotaxa.613.3.3, http://zenodo.org/record/834600

Aegokeras gazipashensis A. Duran & Lyskov 2023, sp. nova

Aegokeras gazipashensis A.Duran & Lyskov sp. nova (Figs. 3–8). Type:— TURKEY. C4 Antalya: Gazipa&scedil;a, Çay&imath;ryaka Yaylas&imath;, 36°30′02′′N, 32°32′18′′E, 1730 m, mountain steppe, 12 June 2021, A.Duran 10795 (holotype: HUB, isotypes: ANK, GAZI, MW barcodes MW0595828 – MW0595831). Diagnosis: Aegokeras gazipashensis is similar to A. caespitosa. It mainly differs from A. caespitosa in non-caespitose habit (not caespitose habit), habitat semi-arid mountain steppe (not crevices of limestone cliffs), base of stem without remains of old leaf bases (not with remains of old leaf bases), leaves distinctly coriaceous and glaucous (not herbaceous and ±greenish), leaflets mostly overlapped, margin acute-laciniate to dentate, cartilaginous, broadly ovate to orbicular (not without overlapping, margin dentate to serrate, not cartilaginous, ovate or oblong), petiole with well-developed sheath, clearly flattened (not with a scarcely dilated sheath). Description: Polycarpic, perennial, hemicryptophytic herbaceous plants, (7–) 10–25 cm tall. Thickened rootstock cylindrical-oblong, vertical, 5–15 mm ⌀, without petiolar remains or with rarely remains a few papery old-leaf petioles at base of stem. Stem solitary or 2, unbranched or 2–4-branched, glabrous, terete, smooth, greenish, erect, slender, 1–2 mm ⌀ at base, slightly ribbed. Leaves completely basal, ±forming a rosette, oblong, 2.5–7 × 1–1.8 cm (incl. petiole), unipinnate or pinnatisect, distinctly glaucous and coriaceous, petiole and rachis mostly sparsely minutely puberulous; petiole with a well-developed sheath, 10–40 × 2–7 mm; petiole and rachis clearly flattened, whitish membranaceous margin, entire; lamina 1.7–4 cm long; leaflets 2–5-paired, 6–13 × 6–12 mm, mostly overlapped, often lower pairs distant, sessile, broadly ovate to orbicular, simple or 2–5-lobed to pinnatisect, sometimes sparsely puberulous; margin deeply acute-laciniate to dentate, cartilaginous. Stem leafless, only at base of lateral branches sheath-like form, and oblong, whitish-green ±membranaceous, 10–17 mm long (incl. lobes), 1–3(–5) linear-subulate lobes, lobes c. 3 mm long. Inflorescence with terminal umbel only or little-branched, compound umbel. Flowers hermaphroditic; umbels 3–11-rayed; rays 11–20 mm long, equal to subequal, glabrous, slightly striate. Bracts 1–10 or rarely absent, 3–5 × 0.3–0.6 mm, lanceolate to linear, unequal, margins membranous, persistent. Umbellules 6–13-flowered, when ripe 2–8; pedicels 1.5–2.5 mm long, glabrous. Bracteoles 2–7, 1–3 × 0.2–0.4 mm, narrowly linear-lanceolate to filiform. Sepals minute, inconspicuous, ± triangular. Petals white, 1 × 0.6–1 mm, obovate to oblong, strongly incurved at the apex, inflexed lobe slightly bifid, glabrous. Filaments ca. 2 mm long. Anthers oblong, ca. 0.5 mm long, yellowish. Stylopodium clearly conical, rim slightly undulate; styles c. 1.3 mm long, ascending at first, eventually horizontal to reflexed at the apex, gracefully conical; stigma capitate. Fruit narrowly oblong to ovate, glabrous, 4–5.5 × 1.5–2 mm, greenish-yellow when ripe; mericarps ± terete, smooth ridges inconspicuous, commissure narrow; dorsal vittae 1 per vallecula, commissural vittae 2–4, numerous inconspicuous vittae also present. Mesocarp consists of parenchymatous cells and several layers of sclerenchymatous cells in middle part. Paratypes:— TURKEY. C4 Antalya: Gazipa&scedil;a, Çay&imath;ryaka Yaylas&imath;, 36°30′02′′N, 32°32′18′′E, 1730 m, mountain steppe, 27 May 2021, A.Duran 10745 (HUB). Antalya: Gazipa&scedil;a, Çay&imath;ryaka Yayla, 1700 m, 14 July 1983, H.S¸mb¸l 2336 (HUB). Etymology: —The specific epithet refers to the type locality of the new species—the Gazipa&scedil;a district. The Turkish name of the new species was suggested as “gazipa&scedil;a aykeresi” (Menemen et al. 2016). Phenology: —Flowering in May-June, and fruiting in June-July. Distribution:— Aegokeras gazipashensis is a narrow endemic to Southern Anatolia (Antalya province), Turkey. This species is located in the East Mediterranean phytogeographical regions (Fig. 2). Ecology:— Ta&scedil;eli Plateau is located in the provinces of Antalya, Konya and &Idot;çel. It has a different geomorphological structure with its limestone rocky character and karst topographic features. Çay&imath;ryaka is one of the plateaus in Ta&scedil;eli Plateau where Aegokeras gazipashensis species grows. The altitude of the plateau varies between 1500–2500 meters. Water resources are insufficient in the entire plateau (Siler & &Scedil;engün 2014). Aegokeras gazipashensis species grows in semi-arid mountain steppes. Some of the plants that grow in the steppes in the Çay&imath;ryaka plateau are as follows; Polygala supina, Arabis androsacea, Aethionema spicatum, Gypsophila curvifolia, Helichrysum plicatum, Scorzonera longiana, S. violacea, Serratula lasiocephala, Ononis adenotricho, Thymus spyleus, Dorycnium pentaphyllum, Astragalus amoenus, Astragalus anthylloides, Daphne oleoides, Anthemis pestalozzae, Crepis willdenowii (Fig. 8). International Union for Conservation of Nature (IUCN) red list category:— Aegokeras gazipashensis is known only from the type locality, an area smaller than 5 km 2 (Criteria B1, B2a, b). The number of flowering individuals in population is less than 160 (Criteria C2a and D). The area has been subjected to systematic anthropogenic activities such as transhumance, construction of new roadways and settlements, expansion of agricultural areas, and overgrazing pressure (Fig. 8). The population of the new species is very limited, and adverse effects in area of occupancy are leading to the reduction in the number of plants. Because of all these factors the species should be considered Critically Endangered (CR) according to the IUCN Red List Criteria (IUCN 2022).Published as part of Duran, Ahmet, Samigullin, Tahir & Lyskov, Dmitry, 2023, Aegokeras gazipashensis (Apiaceae), a new species from South Anatolia, Turkey, pp. 234-248 in Phytotaxa 613 (3) on pages 237-241, DOI: 10.11646/phytotaxa.613.3.3, http://zenodo.org/record/834600

FIGURE 5 in Aegokeras gazipashensis (Apiaceae), a new species from South Anatolia, Turkey

FIGURE 5. Representative specimen of Aegokeras gazipashensis (isotype MW0595830). Courtesy of the National Depository Bank of Live Systems, Moscow State University.Published as part of Duran, Ahmet, Samigullin, Tahir & Lyskov, Dmitry, 2023, Aegokeras gazipashensis (Apiaceae), a new species from South Anatolia, Turkey, pp. 234-248 in Phytotaxa 613 (3) on page 240, DOI: 10.11646/phytotaxa.613.3.3, http://zenodo.org/record/834600