Sequence Analysis of the Internal Transcribed Spacer (ITS) Region of the Nuclear Ribosomal DNA (nrDNA), and trnL Intron of Chloroplast DNA (cpDNA) of the Chrysochamela (Fenzl) Boiss. (Brassicaceae) In Turkey

Brassicaceae family is an important one since it includes many economic and significant industrial oilseeds, spices, vegetables and some forage plants. In this study, sequences analysis among Chrysochamela (Brassicaceae) species distributed in Turkey were conducted nrDNA ITS and cpDNA trnL intron sequences. Chrysochamela species were collected and brought to the laboratory. ITS and trnL intron sequences were corrected with BioEdit and FinchTV programs. As a result of the study, ITS nucleotide compound compositions were determined as 22.7% T, 29.1 C, 21.5% A and 26.7% G. The lowest distance was 0.000 and the highest distance was 0.037. The phylogenetic tree obtained using the MEGA 6.0 program consists of two large groups. According to trnL intron sequences 37.9% T, 18.4 C, 28.3% A and 15.5% G. Nucleotide compound compositions were determined. The genetic distance between species was determined between 0.000 and 0.022. Maximum likelihood phylogenetic tree consists of two large groups. As a result, phylogenetic analyzes using ITS and trnL intron sequences were compatible with each other. It was also in past studies found to be supported by morphological, anatomical and RAPD data.

A revised infrageneric classification of Bellevalia Lapeyr. (Asparagaceae: Scilloideae) based on molecular analysis

Within the genus Bellevalia (Asparagaceae: Scilloideae: Hyacintheae), flower shape and colour, the ratio of leaf to scape length, and the orientation of the pedicels were traditionally used to delimit sections, subsections and species. We conducted a phylogenetic analysis of representative species from sections Bellevalia, Conicae, Nutantes and Oxydontae, representing four out of the six sections that are currently recognised, using the four chloroplast regions rbcL, matK, trnL intron, and trnL-F spacer. Our results indicate that the sections are not monophyletic as currently circumscribed. Our analyses retrieve two major, well-supported clades. The first clade (sect. Conicae) includes only species with ciliate leaves and green-veined perianth lobes, and the second clade (sect. Bellevalia) includes the species lacking these characteristics. Within the second clade, the species with yellow anthers are separated from those with violet anthers. Our molecular analysis does not support the traditional subdivisions of the genus but establishes the value of cilia on the leaf margin, green veins in the perianths lobes, and the colour of the anthers as indicators of relationships among the species. We recommend that the current four sections and six subsections of Bellevalia be reduced to two sections without subsections and we provide an updated and corrected nomenclature for these sections and subsections, designating lectotypes where necessary.

XÁC ĐỊNH MÃ VẠCH DNA CHO HAI LOÀI THUỘC CHI HOMALOMENA (HỌ ARACEAE) Ở VIỆT NAM

Homalomena là chi thực vật thuộc họ Araceae với nhiều loài có giá trị dược liệu và được sử dụng trong y học cổ truyền ở Việt Nam. Trong một số nghiên cứu đã công bố, một vài loài trong chi này có sự không thống nhất về danh pháp khoa học cũng như vị trí phân bố. Nghiên cứu hiện tại được thực hiện nhằm mô tả chi tiết hình thái và xác định chính xác danh pháp hai đối tượng nghiên cứu là loài Homalomena occulta và Homalomena pierreana thuộc chi Homalomena. Kết quả giải trình tự gen đã lần đầu cung cấp dữ liệu phân tử của vùng trình tự trnL intron và trnL-trnF IGS) cho 2 loài H. occulta và H. pierreana. Bằng việc so sánh trình tự trnL intron và trnL-trnF IGS giữa 2 loài nghiên cứu với các loài hiện có trên GenBank, đặc biệt là loài H. aromatica, một loài có đặc điểm hình thái tương tự với loài H. occulta. Nghiên cứu này đã xác định H. occulta và H. aromatica là 2 loài riêng biệt. Kết quả nghiên cứu đã cung cấp dữ liệu khoa học để khẳng định chính xác vị trí phân loại của một số loài thuộc chi Homalomena.

Evidence of a Possible Double Hybrid Origin for Two Malagasy Species of Piper L. (Piperaceae)

two new species of genus Piper L. from Madagascar: Piper malgassicum and Piper tsarasotrae, were analyzed to investigate their phylogenetic position and evolutionary history. Both plastidial and nuclear markers were used for sequencing. The plastidial markers (ndhF and the trnL intron) showed a close relationship between the two species with respect to the other species of Piper. Both species appeared phylogenetically related to the African P. guineense and the Malagasian/Mascarenhas endemic P. borbonense. The nuclear marker (G3PDH) amplification produced two separate sets of sequences: “long” sequences, that could be easily translated into an amino acid chain, and “short” sequences, characterized by deletions that did not allowed to translate them correctly to an amino acid sequence. Analyzing together the nuclear sequences, we observed that the “long” sequence of P. tsarasotrae had a stricter relationship to the African accessions of P. guineense, while the accession of P. malgassicum was more strictly related to P. borbonense. On the contrary both “short” sequences of Piper malgassicum and Piper tsaratsotrae resulted phylogenetically related to Asian accessions and more distantly related to the formerly cited species. This unexpected result was tentatively explained with a more ancient hybridization event between an ancestor of P. malgassicum and P. tsarasotrae (and possibly P. borbonense) and an Asian species of Piper. The Asian contribution would have produced the ancestors of the “short” sequences that would eventually have lost functionality by deletions, becoming paralogs. A more recent hybridization event would have led to the separation of Piper malgassicum from Piper tsarasotrae with an African pollen-derived genome contribution from P. guineense or, more probably, an ancestor thereof, to an ancestor of P. tsarasotrae. The chromosome numbers of P. tsarasotrae (2n = about 38) and P. malgassicum (2n = about 46), were more like the Asian species than to the American species. Unfortunately, no chromosome number of the African species P. guineense is currently available, to analyze eventual chromosomal connections.

The non-monophyly of Dasymaschalon dasymaschalum (Annonaceae) revealed by a plastid DNA phylogeny, with D. halabalanum sp. nov. from Thailand and D. argenteum comb. nov.

An extended molecular phylogeny of the genus Dasymaschalon (Annonaceae) has been reconstructed using up to six plastid DNA regions (matK, ndhF, rbcL exons; trnL intron; psbA-trnH, trnL-trnF intergenic spacers). The results unraveled the non-monophyly of a widely distributed D. dasymaschalum. A lineage of D. dasymaschalum native to Java and cultivated at Bogor Botanical Garden represents the true D. dasymaschalum, whereas the name Pelticalyx argentea is applicable to a distantly related clade of D. dasymaschalum from mainland Asia. Dasymaschalon argenteum comb. nov. is accordingly made. Additionally, the true D. dasymaschalum has been retrieved as the sister group of D. halabalanum, a new species from Narathiwat Province, southern Thailand herein described. Pedicel length, petal size and color, and the number of stamens per flower principally distinguish the new species from its sister group.

Genetic Characterization of an Endangered Chilean Endemic Species, Prosopis burkartii Muñoz, Reveals its Hybrids Parentage

The hybridization of Prosopis burkartii, a critically endangered endemic species, and the identification of its paternal species has not been genetically studied before. In this study we aimed to genetically confirm the origin of this species. To resolve the parental status of P. burkartii, inter-simple sequence repeat (ISSR), simple sequence repeats (SSR) and intron trnL molecular markers were used, and compared with Chilean species from the Algarobia and Strombocarpa sections. Out of seven ISSRs, a total of 70 polymorphic bands were produced in four species of the Strombocarpa section. An Multi-dimensional scaling (MDS) and Bayasian (STRUCTURE) analysis showed signs of introgression of genetic material in P. burkartii. Unweighted pair group method with arithmetic average (UPGMA) cluster analysis showed three clusters, and placed the P. burkartii cluster nested within the P. tamarugo group. Sequencing of the trnL intron showed a fragment of 535 bp and 529 bp in the species of the Algarobia and Strombocarpa sections, respectively. Using maximum parsimony (MP) and maximum likelihood (ML) trees with the trnL intron, revealed four clusters. A species-specific diagnostic method was performed, using the trnL intron Single Nucleotide Polymorphism (SNP). This method identified if individuals of P. burkartii inherited their maternal DNA from P. tamarugo or from P. strombulifera. We deduced that P. tamarugo and P. strombulifera are involved in the formation of P. burkartii.

Generic status of Winitia (Annonaceae, Miliuseae) reaffirmed by molecular phylogenetic analysis, including a new species and a new combination from Thailand

The generic status of Winitia Chaowasku (Annonaceae Juss., Miliuseae Hook.f. & Thomson) is reaffirmed by an extensive phylogenetic reconstruction using seven plastome regions (matK, ndhF, rbcL, ycf1 exons; trnL intron; psbA-trnH, trnL-trnF intergenic spacers) and including, among others, seven accessions of Winitia plus two accessions of its sister group, Stelechocarpus Hook.f. & Thomson. The results disclosed a maximally supported clade of Winitia, as well as of Stelechocarpus. The sister relationship of the two genera is still rather poorly supported and the branch uniting them is very short, whereas the branches leading to Winitia and to Stelechocarpus are relatively long, corresponding to their considerable morphological differences. Additionally, in Miliuseae there is a particular indel of eight continuous base pairs in the trnL-trnF intergenic spacer potentially diagnostic for generic discrimination, i.e., members in the same genus possess the same indel structure (absence or presence of a gap), and this indel differentiates Winitia from Stelechocarpus. Winitia cauliflora (Scheff.) Chaowasku appears polyphyletic and Winitia longipes (Craib) Chaowasku & Aongyong comb. nov. based on Stelechocarpus longipes Craib is consequently proposed. Furthermore, our phylogenetic data support a new species, Winitia thailandana Chaowasku & Aongyong sp. nov. from southern Thailand, which is described and illustrated. A key to genera in the sageraeoid clade (Sageraea-Winitia-Stelechocarpus) and a key to the four species of Winitia are provided.

Peponium elgonense (Cucurbitaceae), a new species from Mount Elgon in Kenya

Peponium elgonense, a new species of Cucurbitaceae from Mount Elgon in Kenya, is described and illustrated here with photographs. This species is similar to P. cienkowskii and P. vogelii, but differs by being monoecious and having a longer ovary. A molecular phylogenetic analysis of Peponium based on ITS and five plastid markers (trnL–F, rpl20–rps12, matK, rbcL, and trnL intron) of four species of Peponium further shows that P. elgonense individuals cluster together supporting the argument to regard it as a separate species.

Ruehssia sumiderensis (Apocynaceae), a new species from Chiapas state, Mexico

It is herein presented Ruehssia sumiderensis as a new species known only in the Cañón del Sumidero National Park, in Chiapas, Mexico. It is illustrated with a line drawing, live images and SEM photographs of the gynostegium and pollinarium. Morphological and molecular evidence with plastid data (trnL intron and trnL-F intergenic spacer) confirms its position in Ruehssia, a recently proposed genus that includes American Marsdenieae species. It is similar to Marsdenia laxiflora and M. pinetorum due to the basally rounded or truncate leaves, rotate corolla without callous cushions in the sinuses. Two new combinations are also made in Ruehssia, for M. laxiflora and M. pinetorum.

Phylogenetics of Taxus Using the Internal Transcribed Spacers of Nuclear Ribosomal DNA and Plastid trnL-F Regions

Taxus is a genus of trees and shrubs with high value in horticulture and medicine as a source of the anticancer drug paclitaxel. The taxonomy of the group is complex due to the lack of diagnostic morphological characters and the high degree of similarity among species. Taxus has a wide global geographic distribution and some taxonomists recognize only a single species with geographically defined subgroups, whereas others have described several species. To address these differences in taxonomic circumscription, phylogenetic analyses were conducted on DNA sequences using Maximum Likelihood, Bayesian Inference and TCS haplotype networks on single and combined gene regions obtained for the nuclear ribosomal ITS region and the plastid trnL intron and trnL-F intergenic spacer. Evidence is presented for the sister group status of Pseudotaxus to Taxus and the inclusion of Amentotaxus, Austrotaxus, Cephalotaxus and Torreya within Taxaceae. Results are consistent with the taxonomic recognition of nine species: T. baccata, T. brevifolia, T. canadensis, T. cuspidata, T. floridana, T. fuana, T. globosa, T. sumatrana and T. wallichiana, but evidence is found for less species distinction and considerable reticulation within the T. baccata, T. canadensis and T. cuspidata group. We compare the results to known taxonomy, biogeography, present new leaf anatomical data and discuss the origins of the hybrids T. ×media and T. ×hunnewelliana.