Genetic Diversity of Orobanche cumana Populations in Serbia

In this study, we report genetic characterization of Orobanche cumana, the causal agent of sunflower wilting in Serbia. The genetic diversity of this parasitic plant in Serbia was not studied before. Random amplified polymorphic DNA (RAPD) markers and partial rbcL gene sequences analysis were used to characterize the O. cumana populations at the molecular level. While phylogenetic analyses of RAPD-PCR amplicons were performed using unweighted pair-group Method analyses, rbcL gene sequences were analyzed using neigbor joining method and minimum spanning tree. Molecular analyses of RAPD-PCR analysis revealed high genetic diversity of O. cumana populations which indicated high adaptive potential of this parasitic weed in Serbia. Further analyses of rbcL gene using minimum spanning tree revealed clear differences among diverse sections of Orobanche genus. Although this molecular marker lacked the resolution to display intrapopulation diversity it could be a useful tool for understanding the evolution of this parasitic plant. Our results suggested that O. cumana has great genetic potential which can lead to differentiation of more virulent races which is important for determining crop breeding strategies for their control.

First Molecular Record and Distribution of Padina pavonica (Linnaeus) Thivy from the Southern Black Sea

Padina is a brown algal genus widely distributed in warm-temperate and tropical regions. Species-level identification of specimens is often difficult due to intraspecific and interspecific morphological plasticity. This study reveals the results of the phylogenetic relationships of specimens, by analyzing the cytochrome oxidase subunit 3 (Cox3) and RuBisCO large subunit (rbcL) gene sequences. A total of 144 new sequences were analyzed together with other Padina sequences obtained from GenBank. Phylogenetic inference identified one well-resolved clade. All of these analyses showed that this genus has only one species in the Black Sea. This is the first study on the molecular diagnosis of macroalgae in the Black Sea, and it contains the first molecular records of Padina in the Black Sea Region.

Two New Benthic Diatoms of the Genus Achnanthidium (Bacillariophyceae) from the Hangang River, Korea

Two new benthic freshwater species belonging to the genus Achnanthidium were found in Korea. Achnanthidium ovale sp. nov. and A. cavitatum sp. nov. are described as new species based on light and scanning electron microscopy observations and molecular analyses. Both species are compared with the type material of morphologically similar taxa. Achnanthidium ovale differs from other species belonging to the A. pyrenaicum complex in outline, striation pattern, raphe central endings, and freestanding areolae at the apices. Achnanthidium cavitatum differs from other species in the A. minutissimum complex in outline, broad axial central area in the raphel ess valve, and slit-like areolae near the axial central area. We assessed their molecular characteristics by analyzing nuclear small subunit (SSU) rRNA and chloroplast-encoded rbcL gene sequences. Both the morphological comparison and the SSU and rbcL sequence analyses provide strong evidence to support the recognition of A. ovale and A. cavitatum as new species.

Molecular taxonomy of Indopiptadenia oudhensis (Brandis) Brenan (Leguminosae - Mimosoideae) - A threatened endemic monotypic genus

Indopiptadenia oudhensis (Brandis) Brenan is a threatened and an endemic legume forest tree genus of tropical moist deciduous forest of lower foothills of Himalaya. As population status of the species is declining at alarming rate, molecular characterization and germplasm conservation is urgently needed. This is the first attempt to draw its phylogeny based on molecular level and evolutionary closeness with other legumes. Among three barcode genes i.e rbcL, matK and ITS, only rbcLaF-rbcLaR gave satisfactory amplification and proved that rbcL is still working well than other barcode genes and justifies the evolutionary affinities with other legume species. Based on nucleotide homeology, the species is closely related to Prosopis cineraria and demonstrated nucleotide variation at only one site (552; A>G). Based on rbcL gene sequences and phylogeny, its evolutionary linkages found similar to the species placed in subfamilies Mimosaoideae and Caesalpiniodeae. However, researchers working on legume phylogeny clearly mentioned that Indopiptadenia is a part of clade mimosoid of Caesalpinioideae based on morphology. Hence, Indopiptadenia oudhensis may be the connecting species between subfamilies Mimosaoideae and Caesalpiniodeae.

VARIASI INFRASPESIES MACANG (Mangifera foetida) BERDASARKAN SEKUEN GEN rbcL

AbstrakMacang (Mangifera foetida) adalah jenis mangga kosmopolit dengan vigoritas yang kuat. Macang banyak ditemukan di perkarangan dan kebun dan bersifat semi liar. Penurunan luas lahan seperti deforestasi dapat mengakibatkan keanekaragaman kultivar macang juga mengalami penurunan secara cepat. Penelitian ini bertujuan untuk menganalisis dan merekonstruksi hubungan kekerabatan antar kultivar macang menggunakan sekuen gen rbcL. Sampel berasal dari koleksi hasil eksplorasi mangga Sumatera bagian Selatan, yaitu Provinsi Bengkulu, Lampung dan Sumatera Selatan. Ekstraksi DNA dilakukan dengan menggunakan metode CTAB yang dimodifikasi, kemudian DNA diamplifikasi dengan menggunakan primer spesifik rbcL forward dan reverse, dan dilakukan sekuensing serta analisis filogenetik. Rekontruksi pohon filogenetik menggunakan program PAUP* versi 4.0b10 dengan metode Maximum Parsimony (MP) dan Neighbor Joining (NJ). Kladogram dengan MP diperoleh dua klad, yaitu pada klad I terdiri dari kultivar Macang lonjong dan Macang lado, sedangkan klad II terdiri dari kultivar Macang bulat. Berdasarkan metode NJ, diperoleh Macang bulat memiliki jarak genetik lebih panjang sehingga dianggap sebagai individu yang lebih primitif daripada kultivar yang lain. Dengan demikian, dari penelitian ini diperoleh informasi dan bukti dari status taksonomi kultivar macang.Abstract Mangifera foetida is a species of cosmopolitan mango with strong vigor. Some M. foetida are found in some front houses and gardens and has a character of semi-wild in its cultivation. Decreases in land area, such as deforestation, can lead to a rapid decline in their diversity of cultivars. This study aimed to analyze and reconstructs the phylogenetic relationship among M. foetida cultivars using the rbcL gene sequences. Samples were collected from the exploration within the area of South Sumatra, such as Provinces of Bengkulu, Lampung and South Sumatra. The DNA extraction was carried out using the modified CTAB method, followed by DNA amplification using rbcL-specific primers, sequencing, and phylogenetic analysis. The phylogenetic trees were reconstructed using the PAUP* version 4.0b10 by using the method of Maximum Parsimony (MP) and Neighbor Joining (NJ). Cladogram of the MP tree showed two clades that the clad I consisted of M. foetida (Macang lonjong) and M. foetida (Macang lado) cultivars, whereas clad II consisted of M. foetida (Macang bulat) cultivar. The NJ tree showed that M. foetida (Macang bulat) has a longer genetic distance so it is considered as a more primitive cultivar than others. Therefore, information and evidences from the taxonomic status of the M. foetida cultivars were obtained from this study.

Species diversity and phylogenetic analysis of Heliconia spp. collections of Purwodadi Botanic Garden (East Java, Indonesia) inferred by rbcL gene sequences

Hapsari L, Trimanto, Wahyudi D. 2019. Species diversity and phylogenetic analysis of Heliconia spp. collections of Purwodadi Botanic Garden (East Java, Indonesia) inferred by rbcL gene sequences. Biodiversitas 20: 1266-1283. Heliconia L. is a single genus in the family Heliconiaceae, with approximate consists of 200 species. It has wide morphological variations among and within species which led to problems in species identification. Species diversity and phylogenetic analysis using morphology and rbcL marker subjected to 17 Heliconia spp. living collections of Purwodadi Botanic Garden (PBG) have been conducted. The rbcL gene located in chloroplast genome is one of appropriate proposed marker for plant barcoding assessment. This study aimed to study morphology and genetic variability of the PBG Heliconiaceae collections, to confirms the species name for a more accurate identity record and to reveal the diversity and phylogenetics of the species. Morphological characterization showed high variability among Heliconia species, which included 3 subgenera (Heliconia, Stenochlamys, and Griggsia) and 1 hybrid. Each species possessed unique morphological characteristics. The common morphological characters which distinguished among and within Heliconia species includes leaf form, inflorescence type, and bract characteristics. Key to the Heliconia species examined is presented in this paper. However, molecular confirmation using rbcL sequences showed high conservation level (0.932) and low genetic variability. About 656 nucleotides were monomorphic and 33 positions were polymorphic which comprised 18 singleton variable sites and 15 parsimony informative sites. Twelve haplotypes were produced with haplotype diversity value 0.8952. Pairwise distance analysis shows that they were shared high similarity of rbcL sequences with very low genetic distance (0.022 to 0.000). The topology of phylogenetic tree resulted by Neighbour-Joining algorithm has the best grouping and be able to explain the relationship among species of Heliconia, although supported by low bootstrap (65). It was separated into two clades following its subgen. classification. Clade 1 consists of subgen. Heliconia and Griggsia; while clade 2 consists of subgen. Heliconia and Stenochlamys; also hybrid species. Further, separation of deeper branchings (section) was inconsistent and unclear. Upon this study, rbcL marker was considered too conserved thus less valuable for phylogenetic analysis at lower taxa among and within Heliconia spp. However, rbcL was suggested to distinguish at higher level taxa between closely related genus and above.

Phylogenetic and phylogeographic patterns of Didymosphenia geminata on invaded sites in Chile

Understanding the population dynamics of invasive processes has become a pressing concern in a highly connected world faced with ongoing climate change and increased exotic species introduction. In Chile, the invasive freshwater benthic diatom Didymosphenia geminata (Lyngbye) Schmidt has become widespread, expanding across multiple river basins spanning over 3000 km in three years. Here we evaluate the phylogenetic and phylogeographic relationships of D. geminata samples collected throughout the invaded range in Chile, using specific rbcL gene sequence previously published. Genetic sequences for this marker were generated for 19 sample sites, and were compared with available freshwater diatom sequences, as well as with previously published rbcL gene sequences for D. geminata. We find that all genetic sequences collected within Chile present phylogenetic divergences from D. geminata samples collected in Siberia, as well as from samples of the genera Gomphonema, Cymbella and Encyonema. Thus, we validate the invasion by D. geminata, in agreement with existing morphological taxonomic criteria. In addition, a haplotype analysis showed a total of 13 haplotypes, two of which (halpotypes I and IX) found in 12 and 3 populations respectively, while each of the remaining haplotypes presents a single population. Thus, these results are consistent either with the introduction of multiple lineages, or with a rapid genetic differentiation in this invading freshwater diatom. Further genetic sampling, both within Chile and in countries that may have been potential sources of the invasion are needed to test these alternative hypotheses.

Phylogenetic and phylogeographic patterns of Didymosphenia geminata on invaded sites in Chile

Understanding the population dynamics of invasive processes has become a pressing concern in a highly connected world faced with ongoing climate change and increased exotic species introduction. In Chile, the invasive freshwater benthic diatom Didymosphenia geminata (Lyngbye) Schmidt has become widespread, expanding across multiple river basins spanning over 3000 km in three years. Here we evaluate the phylogenetic and phylogeographic relationships of D. geminata samples collected throughout the invaded range in Chile, using specific rbcL gene sequence previously published. Genetic sequences for this marker were generated for 19 sample sites, and were compared with available freshwater diatom sequences, as well as with previously published rbcL gene sequences for D. geminata. We find that all genetic sequences collected within Chile present phylogenetic divergences from D. geminata samples collected in Siberia, as well as from samples of the genera Gomphonema, Cymbella and Encyonema. Thus, we validate the invasion by D. geminata, in agreement with existing morphological taxonomic criteria. In addition, a haplotype analysis showed a total of 13 haplotypes, two of which (halpotypes I and IX) found in 12 and 3 populations respectively, while each of the remaining haplotypes presents a single population. Thus, these results are consistent either with the introduction of multiple lineages, or with a rapid genetic differentiation in this invading freshwater diatom. Further genetic sampling, both within Chile and in countries that may have been potential sources of the invasion are needed to test these alternative hypotheses.

Streblocladia (Rhodomelaceae) in New Zealand: recognition of a new species

The genus Streblocladia was described by early European collectors based on S. neglecta, a marine red alga from southern New Zealand currently treated as a taxonomic synonym of Streblocladia glomerulata. In New Zealand, Streblocladia includes two species and has always been considered distinct. To analyse the phylogenetic relationships of this genus with other Polysiphonia sensu lato, we conducted a molecular-assisted investigation using plastid rbcL gene sequences of recent collections of Streblocladia from New Zealand, as well as morphological observations. The molecular analyses indicated that Streblocladia species form a monophyletic clade sister to P. rhododactyla with strong support. The Streblocladia clade is clearly separated from other species of Polysiphonia sensu lato. Species of Streblocladia are characterized by sympodially branched, corticated main axes, the absence of vegetative trichoblasts, and spermatangial branches that are unilaterally arranged and replace the whole trichoblast. As a result, the New Zealand endemic Polysiphonia rhododactyla is transferred to the genus Streblocladia on the basis of genetic and morphological evidence and compared with the two other species from New Zealand, S. glomerulata and S. muelleriana.

DNA profiles to identify Dillenia species (Dilleniaceae) in Thailand

Surveying of the species throughout Thailand revealed 13 identified and one unidentified species including D. aurea, D. excelsa, D. grandifolia, D. hookeri, D. indica, D. obovata, D. ovata, D. parviflora, D. pentagyna, D. philippinensis, D. pulchella, D. reticulata, D. suffruticosa and Dillenia sp. They were phylogenetically examined based on RAPD profiles of 2,290 discrete characters including a monomorphic and 226 polymorphic characteristics. The phylogenetic relationships calculated from theses banding data show that the intraspecific genetic similarity (S) values ranged from 0.990 to 1.000, and the interspecific S values ranged from 0.520 to 0.790. The RAPD method can be effectively used in Dillenia study. However, its quality of unreproducible method, it cannot be reasonable used in any study on specific genes or areas. In additions, sequences from two molecular regions, rbcL gene and psbA-trnH spacer, were analyzed and determined for genetic distances. The rbcL gene sequences were rather ineffective, as all of the paired species displayed no or low genetic distance values. The psbA-trnH spacer sequences were rather effective, with only one pair (D. reticulata and D. parviflora) showing low genetic distance values. The other species pairs indicated rather far genetic distances, ranging from 0.006 (D. parviflora and D. grandifolia) to 0.376 (Dillenia specie and D. indica). Intraspecific genetic distance values ranged from 0–0.003 and 0–0.013 for rbcL and psbA-trnH spacer regions, respectively. Based on the results from both nucleotide variations and DNA fingerprinting, D. grandifolia and D. ovata were distinct Dillenia species.