Maturase Research Articles

CURRENT PERSPECTIVES OF DNA BARCODING IN BOSNIA AND HERZEGOVINA THROUGH BOLD DATABASE

UDK: 577.212:574]:007.5(497.6)
 DNA barcoding is a method designed to provide rapid and precise species identifications by using one or more of short gene sequences called barcodes. In most plant and fungi studies, the standard barcodes of choice are three plastid (rbcL, matK and trnH-psbA) and one nuclear (ITS) gene regions. The relatively high, but comparatively conserved rate of sequence evolution of mtDNA has made COI the marker of choice in animals. BOLD is a freely available cloud-based data storage and analysis platform developed with the aim to advance biodiversity science through DNA barcoding species identification. To date, over 6 million barcodes have been deposited in BOLD with 196,000 animal species, 68,000 plant species and 22,000 species of fungi and other organism entries. In this database, there are currently 447 entries for organisms from Bosnia and Herzegovina, which makes 0.0067% of the total number of BOLD entries. According to BOLD statistics, only 1.11% of all organism entries from B&H were submitted by B&H institutions.
 Despite the fact that Bosnia and Herzegovina has valuable natural resources with a high percentage of endemic and autochthonous species, BOLD statistics elucidated the lack of coordinated and systematic DNA barcoding research so far. It is necessary to establish continuous progress of molecular-genetic characterization of these resources in the future. It is up to B&H institutions to decide if they want to continue the practice of submitting the data sporadically or if they will animate the research community to actively participate in this global project.

Molecular and morphological evidence for a new species of Leptopus (Phyllanthaceae) from Southeast Yunnan, China.

Leptopus malipoensis, a new species of Phyllanthaceae from Southeast Yunnan Province, China, is described. The phylogenetic position of the new species within the genus Leptopus was analyzed based on nuclear ribosomal Internal Transcribed Spacer (nrITS) and plastid matK sequence data. The results show that L. malipoensis is highly supported to be the sister of L. fangdingianus (P. T. Li) Voronts. & Petra Hoff., a species endemic to western Guangxi Province, China. Morphologically, the new species can be distinguished from all known congeneric taxa by its long and slim branches usually pendulous or procumbent, some of its leaf laminas up to 15 cm long and 7 cm wide. It further differs from its sister species by its hirsute stems, leaves and pedicel of female flowers, longer pedicel of male flowers, 3-locular ovary and three styles. A key to all 10 accepted Leptopus species is provided.

Chichimecactus (Cactoideae, Cactaceae), a new genus based on molecular characterisation of highly endangered Strombocactus species

Molecular characterisation of the three taxa currently circumscribed under Strombocactus (Cactaceae, Cactoideae) based on the analysis of the plastid matK, psbA-trnH and atpB-rbcL datasets, provided unambiguous identification of the two endangered and highly wanted cacti species: S. corregidorae and S. disciformis (including subsp. disciformis and subsp. esperanzae). The combined autapomorphies in each of the three markers and even the autapomorphies in each of the single molecular datasets provide a positive and clear-cut identification for each of the taxa. The Bayesian, maximum likelihood and parsimony phylogenetic analyses of the three datasets including 46 terminals of cacti, recover a paraphyletic Strombocactus with S. corregidorae as sister to a clade containing Ariocarpus, Turbinicarpus, and Strombocactus disciformis subsp. disciformis + subsp. esperanzae. Autapomorphies for each of the three taxa for every dataset are identified, and as a consequence, the new genus Chichimecactus, based on S. corregidorae, is proposed.

Big fruits with tiny tepals: An unusual new species of Lauraceae from southwestern China.

We collected an unusual new plant of Phoebe (Lauraceae) from southeastern Yunnan, China, which possesses more or less oblong leaves, paniculate inflorescences with strictly opposite lateral cymes, trimerous flowers with 4-locular stamens, and large fruits with tiny, equal, persistent tepals. Our molecular phylogenetic study based on nrITS, LEAFY and plastid matK sequences suggests that this species belongs to a clade of Phoebe including P. puwenensis, P. megacalyx, and P. macrocarpa. However, this species differs from the latter three species by subglabrous twigs, leaves and inflorescences (vs. pubescent twigs, leaves and inflorescences in the latter three species), larger fruits (5–8 cm long vs. 1–4 cm long in the latter three species), and smaller tepals (1–2.5 mm long vs. 5–15 mm long in the latter two species). As a result, Phoebe jinpingensis sp. nov. is described and illustrated here as new to science.

<p><strong>An expanded concept of <em>Madisonia</em> including miscellaneous species of Pleurothallidinae (Orchidaceae): evidence from molecular analysis<br /></strong></p>

Prior taxonomic studies in subtribe Pleurothallidinae have suggested a close relationship between miscellaneous species featuring long-repent, segmented rhizomes, abbreviated ramicauls, few-flowered inflorescences, and flowers with partially connate sepals and trilobed lip. The lack of phylogenetic information for most species has prevented further conclusions or changes in their taxonomy; and as a result, they are currently assigned to several unrelated genera: Anathallis, Madisonia, Pabstiella, Pleurothallis, Sansonia and Specklinia. We performed phylogenetic analyses using nuclear (nrITS) and five plastid (matK, psbD-trnT, rps16-trnQ, trnH-psbA and trnS-trnG) markers and demonstrated that these species form an isolated clade which requires generic recognition. The name Madisonia, previously a monotypic genus endemic of the Amazon basin, is re-circumscribed and expanded to include nine species distributed in the Atlantic Rainforest and the Caribbean. Eight new nomenclatural combinations are proposed.

A LIKELY INTERSECTIONAL HYBRID IN VACCINIUM (ERICACEAE) ON SAN BRUNO MOUNTAIN, SAN MATEO COUNTY, CALIFORNIA

A population of Vaccinium from San Bruno Mountain in San Mateo County, California has been confused with V. cespitosum Michx. (V. sect. Myrtillus), a species documented from the mountain, since its initial collection in 1961. These plants resemble V. cespitosum and other species in V. sect. Myrtillus in several characters, but differ most notably in their evergreen habit and well developed calyx lobes. The latter characters are shared by V. ovatum Pursh (V. sect. Pyxothamnus), the only other species of Vaccinium known from San Bruno Mountain, suggesting that the population is a hybrid between V. cespitosum and V. ovatum. We used data from gross morphology, leaf anatomy, and DNA sequences from the nuclear ribosomal internal transcribed spacer (ITS) and plastid matK and ndhF regions to test the hybrid status of this population. Hybrid status is supported by: 1) a plastid sequence profile identical to that of V. cespitosum from San Bruno Mountain and different from the profiles of all other Vaccinium samples in the study, 2) an ITS profile that differs from V. cespitosum from the mountain by only two polymorphic sites, and 3) the possession of gross morphological and anatomical characters that are either shared with one putative parent or the other, or are intermediate between them. Although ITS variation was non-additive and closely matched one of the putative parents, uniparental inheritance has been observed in other hybrids. Two novel gross morphological characters were also observed in the hybrid. The study documents a case of likely intersectional hybridization within Vaccinium, only rarely observed under natural conditions. Vaccinium cespitosum may have been outcompeted by the hybrid to the point of its extirpation from San Bruno Mountain. The population is here newly described as the nothospecies Vaccinium ×brunoense P.W.Fritsch, occurring in an area of only ca. 200 m2 with the number of individuals remaining uncertain because of clonal growth.

An Indomalesian origin in the Miocene for the diphyletic New World jewel orchids (Goodyerinae, Orchidoideae): molecular dating and biogeographic analyses document non-monophyly of the Neotropical genera

AbstractThe jewel orchids (Goodyerinae), named after their often colourful leaves, have a pantropical distribution with a clear Asian centre of diversity. However, the Nearctic and Neotropical America together form a second centre of diversity, with one-third of known species of Goodyerinae. Previously, only a few American samples have been included in phylogenetic studies, and their putatively Asian origins and American divergence times were poorly known. To elucidate these topics, we inferred phylogenetic trees, performed molecular dating and reconstructed biogeographic history using nuclear ribosomal ITS and plastid matK sequences for 34 species of Goodyerinae from the New World and 76 previously published accessions of Cranichideae. Our well-supported phylogenetic topology suggests two independent dispersal events to the New World from the Indomalesian region during the Miocene. The first inferred dispersal of a Neotropical clade diverged c. 11 Mya from their most recent common ancestor (MRCA), comprising three highly supported subclades that do not match the limits of Aspidogyne, Kreodanthus and Microchilus as previously circumscribed. The second dispersal involved a largely Nearctic clade of Goodyera s.l. diverging c. 8.4 Mya from the MRCA and exhibiting a complex biogeographic history with subsequent dispersals between the Nearctic and Indomalesia. The occurrence of these species in gallery forests putatively prevented vicariance events imposed by the expansion of the Chacoan region as previously detected for epiphytic Orchidaceae. Eighty-nine nomenclatural combinations and three new names in Microchilus are proposed.

<strong>A new species of <em>Pabstiella</em> (Pleurothallidinae, Orchidaceae) from Ecuador</strong>

Pabstiella elegans is newly described based on cultivated material originally collected near Chaucha in Ecuador. It belongs to the group of small, creeping species of Pabstiella section Mentosae and differs from its closest relatives by the two-times larger flower and unusual colour of its sepals, which are creamy white with red dots. It also differs in the genome size (1C-value = 0.537 pg), which is 10.5% higher than its sister species, P. aryter. Phylogenetic placement is supported by an analysis based on nuclear ribosomal ITS and plastid matK regions.

Using the nuclear LEAFY gene to reconstruct phylogenetic relationships among invasive knotweed (Reynoutria, Polygonaceae) populations

AbstractKnotweed species in the genus Reynoutria are native to eastern Asia but have become noxious weeds in Europe and North America. In the United States, invasive populations of Japanese knotweed (Reynoutria japonica Houtt.), giant knotweed [Reynoutria sachalinensis (F. Schmidt) Nakai], and their interspecific hybrid known as Bohemian knotweed (R. × bohemica Chrtek & Chrtková) continue to expand their ranges. Although these plants are among the most invasive terrestrial species, there are relatively few molecular tools for identifying the parental species, the F1 hybrid, or subsequent hybrids or introgressed individuals. We studied Reynoutria populations in Wisconsin, a state where all three taxa grow, to determine whether molecular data would be useful for distinguishing species and identifying hybrids. We obtained DNA sequence data from the plastid matK gene and the nuclear LEAFY gene and compared these to previously published sequences. Data from the uniparentally inherited matK region included haplotypes attributable to R. japonica and R. sachalinensis. Nuclear data indicated that R. sachalinensis plants are most similar to native plants in Japan, with two Wisconsin accessions exhibiting a monomorphic genotype for the LEAFY gene. Three Wisconsin accessions of R. japonica were each characterized by having three distinct kinds of LEAFY sequence. Most plants in our study were found to possess two or three phylogenetically distinct copies of the LEAFY gene, with the copies being most closely related to R. japonica and R. sachalinensis, respectively, and these were inferred to be interspecific hybrids. Altogether, five kinds of interspecific hybrids were identified, reflecting various combinations of LEAFY sequence types from the parental species. The widespread existence of hybrid plants in Wisconsin, many of which are morphologically identifiable as R. japonica, indicates a cryptic genetic diversity that should be examined more broadly in North America using molecular tools.

Antimicrobial Activity of Necklace Orchids is Phylogenetically Clustered and can be Predicted With a Biological Response Method.

Necklace orchids (Coelogyninae, Epidendroideae) have been used in traditional medicine practices for centuries. Previous studies on a subset of unrelated orchid species utilized in these traditional practices revealed they possessed antimicrobial, anti-inflammatory, and anti-oxidant activity, providing experimental proof for their medicinal properties. To date however none of these species have been investigated ethno-botanically in a phylogenetic context. This study carried out comparative bioprospecting for a group of wild orchids using EBDCS (the Economic Botany Data Collection Standards) organ targeted and biological response methods. The traditional medicinal use of necklace orchids was recorded from books and journals published between 1984 and 2016. Two orchids, Coelogyne cristata and Coelogyne fimbriata, were selected, cultivated both indoors and outdoors, and the antimicrobial properties on extracts from their leaves and pseudobulbs tested against a selection of human pathogens. A molecular phylogeny of Coelogyninae based on nuclear ribosomal ITS and plastid matK DNA sequences obtained from 148 species was reconstructed with Maximum Likelihood (ML) using RAxML, Maximum Parsimony (MP) using PAUP and Bayesian Inference using MrBayes. Bioprospecting comparison of EBDCS and biological response was carried out using customized R scripts. Ethanolic extracts obtained from leaves of C. fimbriata inhibited growth of Bacillus cereus, Staphylococcus aureus, and Yersinia enterocolitica, confirming the antimicrobial properties of these extracts. Leaf extracts were found to have slightly stronger antimicrobial properties for plants cultivated outdoors than indoors. These differences were not found to be statistically significant though. Three hot nodes with high potency for antimicrobial activities were detected with the EBDCS organ targeted classification method, and eight hot nodes were detected with the biological response classification method. The biological response classification method is thus a more effective tool in finding hot nodes amongst clades of species with high medicinal potential.

Three new species of Liparis s.l. (Orchidaceae: Malaxideae) from Southwest China based on morphological characters and phylogenetic evidence

Liparis aureolabella and L. mengziensis, two new species from the karst region of southwestern China, and L. bingzhongluoensis, a new species from montane region in Yunnan, are described and illustrated. L. aureolabella is easily distinguished from its relatives by having abaxially purple leave with purple reticulate veins prominent adaxially, a lip auriculate at base, and falcate-lanceolate pollinia. Liparis mengziensis is closely related to L. petiolata and L. auriculata, but differs from them by having an ovate to broadly ovate leaf, purple lip and apex connate along the margins. Liparis bingzhongluoensis is similar to Liparis nanlingensis, but the new species is characterized by having a lip with two transparent ridges on its disc, longitudinally concave basal callus and triangular column wings. Phylogenetic analyses based on nuclear ribosomal ITS and plastid matK sequences showed that L. aureolabella and L. mengziensis are nested with L. petiolata or L. auriculata in a monophyletic clade. L. bingzhongluoensis is sister to a clade formed by L. nanlingensis, L. tsii, L. sasakii and L. krameri. Moreover, morphological comparisons strongly support that the three species as separated species newly to science.

Taxonomy notes on Vandeae (Orchidaceae) from China: Five new species and two new records

Five new species (Gastrochilus yei, Gastrochilus minimus, Luisia simaoensis, Taeniophyllum xizangense, Tuberolabium subulatum) and two newly recorded species (Cleisostoma tricornutum, Luisia inconspicua) of Vandeae (Orchidaceae) from China are described and illustrated. Gastrochilus yei is similar to G. affinis and G. nepalensis, but differs from them by having an epichile not lobed, the apex of the hypochile not bilobed, and a tine on the apex of the leaf. Gastrochilus minimus is similar to G. acinacifolius, but can be distinguished from the latter by having a flabellate epichile that is densely hirsute on the adaxial surface and an inconspicuous central cushion; in addition, the hypochile of G. minimus has a keel that extends to the apex of the epichile. Taeniophyllum xizangense is similar to T. stella and T. radiatum, but it is distinguished from them by having much bigger flowers, inflorescences densely covered with short-bristly hairs, papillae on the external surface of sepals, and bigger triangular-ovate viscidium. Luisia simaoensis is similar to L. magniflora and L. ramosii, but can be easily distinguished from them by having lateral sepals longer than dorsal sepals and petals, lip with irregular and waved margins, and lip with bilobed apex. Luisia inconspicua is moved from Gastrochilus to Luisia based on phylogenetic analyses of plastid matK sequence data. Tuberolabium subulatum is similar to T. carnosum, but it can be easily distinguished from the latter by having an inflorescence much shorter than the leaves, yellow sepals and petals, and many small papillae outside the lip lobes.

Maturase K (matK) as a Barcode in Bamboos

Maturase K (matK) as a Barcode in Bamboos

Evidence for two genetic groups within the arctoalpine sedges Carex bicolor All. and C. atrofusca Schkuhr (Cyperaceae)

C. bicolor and C. atrofusca are sedge species characteristic for arctoalpine habitats. They have almost circumpolar distributions; they are found in Europe, Northern Asia, and North America, as well as in Middle Asia (C. atrofusca). We hypothesized that certain genetic and morphological differences between populations may be expected across this large area. We tested a set of geographically remote populations of C. bicolor and C. atrofusca. We sequenced a fragment of the plastid matk gene for 15 specimens of C. bicolor and 10 specimens for C. atrofusca from the Asian Russia, and also extracted sequences of this species from GenBank. We found that for both C. bicolor and C. atrofusca, plants from the Arctic and boreal zones of North America and Eurasia had identical matk sequences, while there was certain nucleotide diversity in the mountain ranges of the southern Siberia. Therefore, based on the obtained data we may hypothesize that the mountains of the East Siberia are the center of diversity for some arctoalpine sedge species, and might have served as the ancestral area of the populations colonizing the Arctic.

Molecular phylogeny and chromosomal evolution of endemic species of Sri Lankan Anacardiaceae

Family Anacardiaceae comprises 70 genera and approximately 985 species distributed worldwide. Sri Lanka harbours 19 species in seven genera, among these 15 are endemics. This study focuses on regionally restricted endemics and native Anacardiaceae species, which have not been investigated before at molecular and cytological level. Nuclear rDNA ITS and plastid matK regions were sequenced for ten species, having nine endemics and one native, and incorporated into the existing sequence data for phylogenetic analyses. The topologies resulting from maximum parsimony, maximum likelihood and Bayesian inference are congruent. Family Anacardiaceae forms a monophyletic group having monophyletic subfamily Anacardioideae and paraphyletic subfamily Spondioideae. Tribes Anacardieae, Semecarpeae and Rhoeae form subclades within the major clade of Anacardioideae. All the endemic species occupy correct position in the molecular phylogeny as per the existing classification except for Campnosperma zeylanica, which shows a close relationship to members of the subfamily Spondioideae. The position of non-native species Trichoscypha acuminata also remains unclear. Chromosome counts and karyograms were constructed for five endemic species. The chromosome numbers incorporated in the tree range from 2n = 28–58. Species of tribe Rhoeae have the lowest chromosome number (2n = 24, 28, 30) while species of tribe Semecarpeae have the higher numbers (2n = 50, 52, 58). Chromosome numbers mapped on the phylogeny shows that dysploidy had played a role in the evolution of the species of the family Anacardiaceae in Sri Lanka.

DNA barcode of Metroxylon sagu and others palm species using matK gene

Abstract. Abbas B, Kabes RJ, Mawikere NL, Ruimassa RMR, Maturbong RA. 2020. DNA barcode of Metroxylon sagu and other palm species using matK gene. Biodiversitas 21: 4047-4057. Palm family encompasses numerous species, and they disperse broadly across tropical and subtropical countries. The palm family is generally used as an ornamental plant, food, oil, and industrial raw materials. Species of palm that accumulate large amount carbohydrate in the trunk is sago palm (Metroxylon sagu Rottb). The objectives of this study were to explore the plastid sequence associated with matK genes in the palm family and to reveal DNA barcode of 16 genera and 28 species of the palm. Plant materials used in the studies were derived from Sago Research Center (SRC), and other palm sequences were retrieved from the GenBank, NCBI accessions. The PCR product was sequenced by the 1st Base Asia, Singapore. Sequences of the matK gene that were observed in the plastid genome of M. sagu were registered into the NCBI GenBank as DNA barcode of M. sagu. Percent query cover of Blast analysis range from 98% to 100%, and identity range from 97.70% to 100%. Plastid nucleotides associated with matK genes in the chloroplast genome of palm family were shown substantial differences in inter-genera and small differences in inter-species. Genetic distance among palm family range from 0 to 0.026 with nucleotide variation observed was of 0.008822 value. The result of molecular phylogenetic analysis showed that the palm family separated into three clades and three sub-clades based on the plastid matK gene. Species of M. sagu and M. warburgii were considered closely related as compared to other palm species. The matK gene barcoding method is one powerful tool for identification inter-genera and inter-species of the palm.

<p><strong><em>Cymbidium</em></strong><strong> <em>codonanthum</em> (Orchidaceae; Epidendroideae; Cymbidiinae), a new species from China: evidence from morphological and molecular analyses</strong></p>

A new orchid species, Cymbidium codonanthum, from Yunnan Province, China, is described and illustrated based on morphological and molecular analyses. A detailed comparison between the newly discovered orchid and other members of Cymbidium was performed. The new plant what is similar to C. cochleare, but it is characterized by several morphological features that distinguish it from the latter as well as all other known species of Cymbidium. A molecular study based on nuclear ribosomal ITS and plastid matK and rbcL DNA sequence data indicates that C. codonanthum is genetically distinct from other species and a member of Cymbidium section Cyperochis.

New insight into the molecular phylogeny of the genus Liparis s.l. (Orchidaceae: Malaxideae) with a new generic segregate: Blepharoglossum

Molecular studies have shown that Liparis s.l. is polyphyletic, with the epiphytic Liparis alliance well separated from the clade representing Liparis in its restricted sense and further forming a phylogenetically heterogeneous assemblage. The generic status of Cestichis, as the key member of the epiphytic Liparis alliance, remains contentious, and the relationships between Cestichis, Stichorkis and Platystyliparis are still unclear and in need of further studies. We herein employ DNA sequence data from nuclear ITS and plastid matK regions to clarify the generic boundaries of Cestichis and its relationship to the allied genera. Results from both Bayesian inference and maximum likelihood analysis congruently indicate that Cestichis as currently circumscribed is not monophyletic. The Blepharoglossum clade, corresponding to commonly recognized sect. Blepharoglossum, forms a monophyletic lineage closely related to the genus Oberonia instead of the core Cestichis clade. A re-evaluation of the diagnostic morphological characters reveals that this lineage represents a morphologically distinct group. Based on these results, Blepharoglossum is removed from Cestichis and elevated to generic status. Our study also sheds light on the homoplastic nature of some diagnostic morphological characters used traditionally in the taxonomy of the Malaxidinae.

<p><strong>A new species of <em>Andinia</em> (Pleurothallidinae, Orchidaceae) with unusual bearded flowers from Ecuador</strong></p>

Andinia barbata is newly described based on cultivated material originally collected near Shaglli in Ecuador. It belongs to subgenus Aenigma and differs from all others in this group by the lanceolate lip, 2.5 times longer than wide, and unusually long and thick projections from the synsepal which gives a bearded appearance to the flowers. Phylogenetic placement under the genus is supported with reconstruction of a molecular phylogeny using nuclear ribosomal ITS and plastid matK regions and the genome size estimation (1C-value = 1.38 pg) is provided.

Radiation history of Asian Asarum (sect. Heterotropa, Aristolochiaceae) resolved using a phylogenomic approach based on double-digested RAD-seq data.

The genus Asarum sect. Heterotropa (Aristolochiaceae) probably experienced rapid diversification into 62 species centred on the Japanese Archipelago and Taiwan, providing an ideal model for studying island adaptive radiation. However, resolving the phylogeny of this plant group using Sanger sequencing-based approaches has been challenging. To uncover the radiation history of Heterotropa, we employed a phylogenomic approach using double-digested RAD-seq (ddRAD-seq) to yield a sufficient number of phylogenetic signals and compared its utility with that of the Sanger sequencing-based approach. We first compared the performance of phylogenetic analysis based on the plastid matK and trnL-F regions and nuclear ribosomal internal transcribed spacer (nrITS), and phylogenomic analysis based on ddRAD-seq using a reduced set of the plant materials (83 plant accessions consisting of 50 species, one subspecies and six varieties). We also conducted more thorough phylogenomic analyses including the reconstruction of biogeographic history using comprehensive samples of 135 plant accessions consisting of 54 species, one subspecies, nine varieties of Heterotropa and six outgroup species. Phylogenomic analyses of Heterotropa based on ddRAD-seq were superior to Sanger sequencing-based approaches and resulted in a fully resolved phylogenetic tree with strong support for 72.0-84.8 % (depending on the tree reconstruction methods) of the branches. We clarified the history of Heterotropa radiation and found that A. forbesii, the only deciduous Heterotropa species native to mainland China, is sister to the evergreen species (core Heterotropa) mostly distributed across the Japanese Archipelago and Taiwan. The core Heterotropa group was divided into nine subclades, each of which had a narrow geographic distribution. Moreover, most estimated dispersal events (22 out of 24) were between adjacent areas, indicating that the range expansion has been geographically restricted throughout the radiation history. The findings enhance our understanding of the remarkable diversification of plant lineages in the Japanese Archipelago and Taiwan.