Nuclear ITS Research Articles

A new, disjunct species of Bahiana (Euphorbiaceae, Acalyphoideae): Phytogeographic connections between the seasonally dry tropical forests of Peru and Brazil, and a review of spinescence in the family.

Bahiana is expanded from 1 to 2 species with the description of B.occidentalis K. Wurdack, sp. nov. as a new endemic of the seasonally dry tropical forests (SDTFs) of Peru. The disjunct distribution of Bahiana with populations of B.occidentalis on opposite sides of the Andes in northwestern Peru (Tumbes, San Martín) and B.pyriformis in eastern Brazil (Bahia) adds to the phytogeographic links among the widely scattered New World SDTFs. Although B.occidentalis remains imperfectly known due to the lack of flowering collections, molecular phylogenetic results from four loci (plastid matK, rbcL, and trnL-F; and nuclear ITS) unite the two species as does gross vegetative morphology, notably their spinose stipules, and androecial structure. Spinescence in Euphorbiaceae was surveyed and found on vegetative organs in 25 genera, which mostly have modified sharp branch tips. Among New World taxa, spines that originate from stipule modifications only occur in Bahiana and Acidocroton, while the intrastipular spines of Philyra are of uncertain homologies.

DNA Barcoding of Wild Plants with Potential Medicinal Properties from Faifa Mountains in Saudi Arabia.

Wild medicinal plants are the main source of active ingredients and provide a continuous natural source for many folk medicinal products, a role that is important for society's health with an impressive record of utilization. Thus, surveying, conserving, and precisely identifying wild medicinal plants is required. The current study aimed to precisely identify fourteen wild-sourced medicinal plants from southwest Saudi Arabia, within the Fifa mountains area located in Jazan province, using the DNA barcoding technique. Two DNA regions (nuclear ITS and chloroplast rbcL) were sequenced and analyzed for the collected species using BLAST-based and phylogeny-based identification methods. Based on our analysis, ten of the fourteen species were successfully identified by DNA barcoding, five were identified as morphologically inspected, and three were morphologically indifferent. The study was able to distinguish some key medicinal species and highlight the importance of combining morphological observation with DNA barcoding to ensure the precise identification of wild plants, especially if they are medicinally relevant and associated with public health and safety usage.

An integrative approach to explore species limits in Laelaps mazzai Fonseca, 1939 (Mesostigmata, Laelapidae), a South American widespread mite parasitizing the cricetid Calomys Waterhouse, 1837

Laelaps mazzai Fonseca, 1939 (Mesostigmata, Laelapidae) parasitizes several species of the widespread South American rodent genus Calomys Waterhouse, 1837. Morphological variation has been noticed within this laelapid but has yet to be analyzed. Since several other species of laelapids that initially were considered generalists have resulted in host-specific species, after further analyses, herein we explored, through morphology and genetics, the variation of this parasite across six species of Calomys, trying to establish if it constitutes a polymorphic species or a complex of cryptic host specific-species. An integrative approach was applied, including principal component and discriminant analyses of females and males and DNA sequences (nuclear region ITS and the COI gene). The obtained results indicate that female mites tend to differentiate only the sizes of their dorsal shield among host species but with extensive overlapping. At the same time the males lack metrical differentiation, and the genetic evidence failed to resolve specific-species clades. We conclude that L. mazzai is a single widespread mite with little genetic and phenotypic differentiation.

A new species of Habenaria (Orchidaceae, Orchideae) from Qinghai Province, China

Habenaria qinghaiensis, a new species of Orchidaceae from Qinghai Province, is described and illustrated. Molecular phylogenetic analysis based on nuclear ITS (nrITS) and two plastid (matK and rbcL) DNA markers indicates that H. qinghaiensis belongs to H. josephi group (sect. Diphyllae s.l.). It is morphologically similar to H. josephi and H. tibetica, but differs from the former by having petals shallowly 2-lobed at base, lateral lobes of lip 1.8–2.2 cm long, lip with cushion-like appendage at entrance of spur, and from the latter by having almost glabrous bracts, petals and ovary, lip with cushion-like appendage at entrance of spur, and three stigmas.

Plastome evolution and phylogeny of the tribe Ruteae (Rutaceae).

Rutaceae is a large family, and the genus-level classification in the subfamilies or tribes of this family is not unified based on different taxonomic treatments. Until now, phylogenetic relationships of some genera in traditional tribe Ruteae have not been clearly resolved. In this study, seven new complete plastomes of this tribe were sequenced, and a comparative analysis was performed to investigate their plastome characteristics and evolution. In addition, we inferred the phylogenetic relationships of Ruteae based on complete plastome and nuclear ITS data. All plastomes exhibited a typical quadripartite structure and were relatively conserved in their structure and gene arrangement. Their genome sizes ranged from 154,656 bp to 160,677 bp, and the size variation was found to be associated with differences in IR expansion and gene loss. A total of 112 to 114 genes were identified in the genomes, including 78 to 79 protein-coding genes, 30 tRNA genes, 4 rRNA genes, and 2 pseudogenes. Sequence divergence analysis indicated that non-coding regions exhibited a higher percentage of variable characters, and nine non-coding and six coding regions were identified as divergent hotspots. Phylogenetic results based on different datasets showed that this tribe was divided into three reciprocally exclusive groups. The phylogenetic analyses between plastome and nuclear ITS data were partly incongruent with each other. This study provides new insights into plastome evolution of Ruteae as well as Rutaceae. The availability of these plastomes provides useful genomic resources for molecular DNA barcodes and phylogenetically informative markers and deepens our understanding of the phylogeny in Ruteae.

Isolation, molecular characterization and first report of Dothiorella gregaria associated with fruit rot of walnuts of Jammu and Kashmir, India.

Walnuts are known for their high levels of antioxidants, which are linked to various health benefits. However, challenges related to distribution and storage, as well as the risk of fungal infections, can affect the quality of walnut kernels. Fungal pathogens from the Botryosphaeriaceae family, including Dothiorella species and Diplodia species, can damage fruit and reduce its antioxidant content. To comprehend the cause of fruit rot in walnuts, Dothiorella gregaria isolates were studied using polyphasic methods, including multiple gene sequences and morphological identification, as well as analysis of polyphenol content and pathogenicity. The walnuts kernels purchased from market places of Jammu and Kashmir (J&K), India were observed to be affected by Dothiorella gregaria species causing the quality detoriation and decrease in polyphenol content thus undeniably with decreased antioxidant properties. D. gregaria Infected walnut kernels were having some brown and black spots and some were having white mycelial growth and however, most samples were asymptomatic. Pathogenicity testing revealed that the pathogen was able to develop all the symptoms under experimental conditions and the reisolated pathogen was morphologically similar to D. gregaria. The samples infected with this pathogen showed considerable decrease in polyphenol content, 10.9±2.66 mgGAE/g (mean±standard deviation) thus decreased antioxidant quality as compared to the samples which showed zero incidence of this pathogen, 52.50±4.27 mgGAE/g (mean±standard deviation). Furthermore, the pathogen was studied using polyphasic approach involving morphological, molecular and phylogenetic analysis. Combined nucleotide dataset of nuclear ribosomal ITS and tef1-α revealed that Dothiorella gregaria (NY6) formed a clade with Dothiorlla iberica (MAEC33), Dothiorella sarmentorium (MAEC28) and Dothiorella iberica (CAA905) strains with 83% bootstrap support. Besides, we observed six nucleotide changes, four were insertions or deletions and two were substitutions in the 502-bp region of the ITS rRNA gene when we compared our isolate to the most equivalent sequences submitted to NCBI GenBank. This is the first report of Dothiorella gregaria affecting walnuts purchased from various markets in J&K, India, causing fruit rot in walnuts after harvest. Given that local farmers store and export walnuts, it could pose an emerging threat to their livelihood. Thus, creating post-harvesting interventions for D. gregaria and knowing more about the fruit rot in walnuts can be benefited from morphological and molecular identification using several gene loci, genetic variability in the ITS rRNA gene, and total phenol analysis.

Widespread, but less than assumed: Populations of Euphorbia amygdaloides (Euphorbiaceae) from western Asia represent two new cryptic species

The Hyrcanian forests positioned along the southern and south-western shores of the Caspian Sea and the Euxine-Colchic forests along the southern and eastern shores of the Black Sea (western Asia) are renowned as hotspots of biodiversity and represent major refugia of Eurasian Tertiary relict forest species. One of them was considered to be Euphorbia amygdaloides (Euphorbia sect. Patellares), a forest species with wide distribution from northern Africa across Europe to western Asia. Using nuclear ribosomal ITS and plastid ndhF–trnL sequences we here show that the western Asian populations previously treated as E. amygdaloides are clearly divergent from European E. amygdaloides and actually pertain to two new species, which are also morphologically different. The newly described E. sylvicola is widespread in the Hyrcanian and Euxine-Colchic forests and is morphologically most similar to E. amygdaloides, with which it also shares its genome size. On the other hand, E. caspica is endemic to the Hyrcanian forests in Iran and is most closely related to another western Asian species, E. macroceras, with which it partly overlaps in distribution. Both species have also similar genome size, slightly lower from that of E. amygdaloides and E. sylvicola, but morphologically E. caspica resembles more E. amygdaloides than E. macroceras. Our study uncovered cryptic diversity in the forests of western Asia that had remained hidden due to slow rates of morphological evolution, i.e. morphological stasis, commonly observed in other Tertiary forest relict species, and highlights the Euxine-Colchic and especially the Hyrcanian forests as important centres of biodiversity and endemism.

Genetic analysis reveals conspecificity of two nominal species of Anaphes fairyflies (Hymenoptera: Mymaridae), egg parasitoids of Oulema leaf beetle (Coleoptera: Chrysomelidae) pests of cereal crops in Europe and of rice in East Asia.

Anaphes (Anaphes) flavipes (Foerster), a fairyfly (Hymenoptera: Mymaridae) native of Europe, is an economically important egg parasitoid for the natural control of Oulema spp. leaf beetle (Coleoptera: Chrysomelidae) pests of cereal crops such as barley, oats, rye, and wheat in Europe, and for the classical biological control of the invasive Oulema melanopus (L.) in North America. A morphologically very similar Anaphes (Anaphes) nipponicus Kuwayama, known from mainland China, Japan, Republic of Korea, Far East of Russia and Taiwan, is an egg parasitoid of Oulema oryzae (Kuwayama), a pest of rice mainly in temperate parts of East Asia. The nuclear 28S-D2 and ITS2 and the mitochondrial COI genes were used as markers to compare specimens of A. (Anaphes) flavipes reared from eggs of an Oulema sp. on barley in Germany with those of A. (Anaphes) nipponicus reared from eggs of O. oryzae on rice in Honshu Island, Japan. Because the resulting sequences are practically identical, within an expected intraspecific genetic variability, conspecificity of these two nominal species has been confirmed, and consequently A. (Anaphes) nipponicus Kuwayama, 1932, syn. n. is synonymized with A. (Anaphes) flavipes (Foerster, 1841). Taxonomic notes and illustrations are provided for the specimens of both sexes of A. (Anaphes) flavipes from Japan to facilitate their recognition.

DNA barcoding and nutritional profiling of underutilized native indigenous plant species of Karnataka, India.

Locally adapted native indigenous plant species (NIPS) could restore the crop diversity in sustainable agriculture. Here, we report the molecular identification and nutritional profiling of some five NIPS of Karnataka; Musa paradisiaca cv. Nanjangud rasabale, Piper betle L. cv. Mysore betel leaf, Jasminum grandiflorum cv Mysore mallige, Solanum melongena L. cv. Udupi Mattu Gulla and S. melongena L. cv. Erangere badane of which the first four are Geographical Indication (GI) tagged. The samples were procured, authenticated and sequenced using two standard DNA barcodes: nuclear ITS2 and plastid rbcl. The phylogenetic analysis using Neighborhood joining method revealed all the ITS2 tree topologies with higher genetic divergence than rbcl. All the rbcl tree topologies were monophyletic indicating sequence conservation. Though the concatenated ITS2 + rbcl trees had higher bootstrap support (> 98% except Solanum sp.) differences were observed because of the lack of available sequence deposition at species level. The proximate and nutritional profiling of the NIPS displayed superiority in terms of their nutritional profile and their potential application in phytopharmaceutical sector as nutritional supplements. To our best knowledge this is the first study reporting the screening of five NIPS plant species of Karnataka for phylogeny and nutritional analysis. We also anticipate that if research towards the identification of NIPS species is accelerated, these nutritionally enhanced crops could be used as a safe and sustainable food in changing global climatic conditions.

Spatial and phylogenetic structure of Alpine stonefly assemblages across seven habitats using DNA-species.

Stream ecosystems are spatially heterogeneous, with many different habitat patches distributed within a small area. The influence of this heterogeneity on the biodiversity of benthic insect communities is well documented; however, studies of the role of habitat heterogeneity in species coexistence and assembly remain limited. Here, we investigated how habitat heterogeneity influences spatial structure (beta biodiversity) and phylogenetic structure (evolutionary processes) of benthic stonefly (Plecoptera, Insecta) communities. We sampled 20 sites along two Alpine rivers, including seven habitats in four different reaches (headwaters, meandering, bar-braided floodplain, and lowland spring-fed). We identified 21 morphological species and delineated 52 DNA-species based on sequences from mitochondrial cox1 and nuclear ITS markers. Using DNA-species, we first analysed the patterns of variation in richness, diversity, and assemblage composition by quantifing the contribution of each reach and habitat to the overall DNA-species diversity using an additive partition analysis and distance-based redundancy analysis. Using gene-tree phylogenies, we assessed whether environmental filtering could lead to the co-occurrence of DNA-species using a two-step analysis to detect a phylogenetic signal. All four reaches significantly contributed to DNA-species richness, with the meandering reach having the highest contribution. Habitats had an effect on DNA-species diversity, where glide, riffle and, pool influenced the spatial structure of stonefly assemblage possibly due to the high habitat heterogeneity. Among the habitats, the pool showed significant phylogenetic clustering, suggesting high levels of evolutionary adaptation and strong habitat filtering. This assemblage structure may be caused by long-term stability of the habitat and the similar requirements for co-occurring species. Our study shows the importance of different habitats for the spatial and phylogenetic structure of stonefly assemblage and sheds light on the habitat-specific diversity that may help improve conservation practices.

Molecular phylogeny of the spiny-surfaced species of the dinoflagellate Prorocentrum with the description of P. thermophilum sp. nov. and P.criophilum sp. nov. (Prorocentrales, Dinophyceae).

Spiny-surfaced species of Prorocentrum form harmful algal blooms, and its taxonomic identity is obscure due to the size and shape variability. Molecular phylogenies reveal two major clades: one for P. cordatum with sequences mainly retrieved as P. minimum, and the other for P. shikokuense with sequences also retrieved as P. dentatum and P. donghaiense. Several closely related clades still need to be characterized. Here, we provide nuclear SSU and LSU rRNA genes, and nuclear ITS region (ITS1-5.8S gene-ITS2) sequences of the strain CCMP3122 isolated from Florida (initially named P. donghaiense) and strains Prorocentrum sp. RCC6871-2 from the Ross Sea, Antarctica. We describe Prorocentrum thermophilum sp. nov. based on the strain CCMP3122, a species also distributed in the open waters of the Gulf of Mexico, New Zealand, and the Arabian Gulf; and Prorocentrum criophilum sp. nov. based on the strain RCC6872, which is distributed in the Antarctic Ocean and Arctic Sea. Prorocentrum thermophilum is roundish (~14 μm long, ~12 μm wide), with an inconspicuous anterior spine-like prolongation under light microscopy, valves with tiny, short knobs (5-7 per μm2 ), and several (<7) large trichocyst pores (~0.3 μm) in the right valve, as well as smaller pores (~0.15 μm). Prorocentrum criophilum is round in valve view (~11 μm long, 10 μm wide) and asymmetrically roundish in lateral view, the periflagellar area was not discernible under light microscopy, valves with very tiny, short knobs (6-10 per μm2 ), and at least 12 large pores in the right valve. Other potentially undescribed species of spiny-surfaced Prorocentrum are discussed.

Unraveling Polyphyly in Flourensia (Asteraceae, Heliantheae, Enceliinae) and the Establishment of a New Genus Austroflourensia

The monophyly of Flourensia was examined for the first time by sequencing the nuclear ITS and plastid psbA- trnH regions in 18 species of the genus, analyzing them along with representatives of the remaining genera of subtribe Enceliinae. Results showed strong evidence for the polyphyly of Flourensia identifying two well-supported groups: Flourensia, a clade from North America including the type F. laurifolia, and another clade, here designed as the new genus Austroflourensia, containing the South American species. Austroflourensia is related to the other four genera composing the subtribe Enceliinae, whereas Flourensia s.s. is sister to all of them. Austroflourensia can be mainly distinguished by having a shrubby or subshrubby habit, capitula always radiate usually arranged in weakly cymose-corymbose capitulescences, phyllaries 2-3-seriate, and disc corollas shortly dentate. This paper proposes twelve new combinations to accommodate species previously described in the genus Flourensia and provides emended descriptions of Flourensia and the new genus Austroflourensia. The illustration of the type of the new genus, a distribution map, and a key to the genera of Enceliinae are also provided.

Molecular characterization of schistosome cercariae and their Bulinus snail hosts from Niakhar, a seasonal transmission focus in central Senegal

Bulinus senegalensis and Bulinus umbilicatus, two sympatric freshwater snails found in temporal ponds in Senegal, were thought to be involved in the transmission of Schistosoma haematobium and/or Schistosoma curassoni. To better understand the role of these Bulinus species in the transmission of human and animal Schistosoma species, B. senegalensis and B. umbilicatus were collected in 2015, during a malacological survey, from a temporal pond in Niakhar, central Senegal. Snails were induced to shed cercariae on two consecutive days. Individual cercariae from each snail were collected and preserved for molecular identification. Infected snails were identified by analysis of a partial region of the cytochrome c oxidase subunit 1 (cox1) gene. Six individual cercariae shed from each infected snail were identified by analyses of the cox1, nuclear ITS and partial 18S rDNA regions. Of the 98 snails collected, one B. senegalensis had a mixed infection shedding S. haematobium, S. bovis and S. haematobium-S. bovis hybrid cercariae and one B. umbilicatus was found to be shedding only S. haematobium. These data provide molecular confirmation for B. senegalensis transmitting S. bovis and S. haematobium-S. bovis hybrids in Senegal. The multiple Bulinus species involved in the human urogenital schistosomiasis in Senegal provides a high force of transmission warranting detailed mapping, surveillance and regular treatment of at-risk populations.

Alleniella aegaea Blockeel &amp; Hugonnot (Neckeraceae), a new moss species from the Aegean islands of Greece

A new moss species, Alleniella aegaea (Neckeraceae) is described and illustrated from the Greek islands of Crete, Samos and Evvia based on morphological and molecular evidence. According to phylogenetic analysis of nuclear ITS and plastid trnS-F sequences it is sister to A. com planata, which it also morphologically resembles, but it differs from that species e.g. in its distinctly flattened habit, lack of caducous branchlets, more rounded leaf apices, and shorter median laminal cells. Alleniella aegaea is dioicous and the sporophytes remain unknown

Evolutionary history of Nasutitermes kemneri (Termitidae, Nasutitermitinae), a termite from the South American diagonal of open formations

Little is known about the phylogeography of termites in the Neotropical region. Here, we explored the genetic patterns and phylogeographical processes in the evolutionary history of Nasutitermes kemneri, an endemic termite of the South American diagonal of open formations (DOF) formed by the Chaco, Cerrado, and Caatinga phytogeographic domains. We sampled 60 individuals across the three domains of the DOF, and using the mitochondrial genes 16S, COI, and COII, as well as the nuclear gene ITS, evaluated the genetic diversity and divergence time of the populations, along with their genetic structure. The results show a strong genetic and spatial structure within the samples, evidencing the existence of two well-differentiated genetic groups: the Northeastern and the Southwestern populations, which diverged about 2.5 Mya, during the Pliocene-Pleistocene boundary. The Northeastern population, which encompasses Caatinga and northern portions of Cerrado, has an intricate structure and seems to have suffered repetitive retraction-expansion events due to climactic fluctuations during the Quaternary. The Southwestern population, which ranges from central-south Cerrado to the northeast peripherical portions of the Chaco, displays a star-shaped haplotype structure, indicating that this region may have acted as a refugia during interglacial periods.

Allium sulaimanicum: A new Allium species and section from Pakistan.

A new species, Allium sulaimanicum, is described from northern Balochistan and southern Khyber Pakhtunkhwa in Pakistan based on morphological, molecular, and cytological studies. The new species is characterised by long runner-like cylindrical rhizomes of adult plants, cylindrical bulbs, linear leaves with minute soft hairs along veins, campanulate perigonium, and white to creamy white, ovate to elliptical, 4.5-5-mm-long acute tepals, with brownish to purplish nerves, stamens as long as to slightly longer than tepals, yellow to brick red anthers, hexagonal ovary, and white and papillate/warty along angles. The presence of long herbaceous rhizomes indicated serious isolation of the new species; hence, a new section Sulaimanicum is proposed to accommodate the new species. The new species is diploid with a chromosome number of 2n = 16. Detailed morphological description, illustrations, phylogenetic analyses based on sequences of plastid spacers (rpl32-trnL (UAG) and trnQ-rps16) and nuclear ITS, karyotype features, and a distribution map of the new species are provided.

Phylogenetic Placement and Taxonomic Revision of the Genus Monochilus (Lamiaceae), a Rare Brazilian Endemic

Abstract— Monochilus (Lamiaceae) is an enigmatic genus endemic to Brazil with two rarely collected species currently recognized. Based on morphological features Monochilus is hypothesized to be closely related to Amasonia within subfamily Ajugoideae. However, Monochilus is one of the few genera within Lamiaceae never to be represented in a published molecular phylogenetic study, and thus has an uncertain placement with the subfamily. During recent herbarium exploration in association with the Flora of Brasil 2020 project, new specimens of Monochilus gloxinifolius and M. obovatus were uncovered. Based on this material, a new phylogeny of Ajugoideae was constructed based on nuclear ribosomal ITS and chloroplast matK and trnL-trnF markers. Monochilus, as previously hypothesized, is closely related to Amasonia and placed within Ajugoideae. We discuss the phylogenetic placement of the genus and provide a taxonomic revision with description, distribution maps, an identification key, preliminary conservation assessments, photographic plates, and comments on both the taxonomy and ecology of these two species. Additionally, we provide a lectotypification for M. gloxinifolius.

The enchytraeid fauna (Enchytraeidae: Clitellata) of the Fanjing Mountain National Nature Reserve (China) with description of two new species

ABSTRACT The first ever survey of the enchytraeid fauna in the Fanjing Mountain National Nature Reserve (Guizhou, China) yielded a total of eight species, two of them new to science: Xetadrilus prolixglandus sp. nov. and Hemienchytraeus tenuiculus sp. nov. One unidentified and possibly new species of Fridericia and five additional species, Achaeta brevivasa, Enchytraeus buchholzi, Fridericia loretensis, Henlea perpusilla and Hemienchytraeus stephensoni, are recorded and described, based on the collected material. The species records include morphological descriptions and molecular data (the mitochondrial cytochrome c oxidase subunit 1 (COI) gene, the nuclear ribosomal ITS region and the nuclear histone 3 (H3) gene). http://www.zoobank.org/urn:lsid:zoobank.org:pub:40F089F9-F332-438F-9A3F-4E25A877BDFE

Revisit Study of Freshwater Sponges Eunapius carteri (Bowerbank, 1863) and a New Record of Oncosclera asiatica Manconi and Ruengsawang, 2012 (Porifera: Spongillida) in Porong River, East Java, Indonesia

Distribution of freshwater sponges (Porifera: Spongillida) in Indonesia is currently insufficiently reported and underestimated compared to marine sponges. An inventory study on freshwater sponges in East Java after Indonesian independence in 1945 is yet to be carried out. For this reason, we reported new records of two freshwater species, Eunapius carteri (Bowerbank, 1863) and Oncosclera asiatica (Manconi and Ruengsawang, 2012) in Porong river, East Java, Indonesia. E. carteri species was originally described in Mumbai, India and its presence in Java was reported in 1927, 1928, and 1930. DNA barcoding and molecular phylogenetic analysis using mitochondrial COI was able to successfully identify our specimens as E. carteri, while analysis using the nuclear ITS markers placed our samples with other Eunapius species. Furthermore, in this study we report for the first time in East Java, Indonesia, the presence of O. asiatica. The O. asiatica species was originally described from Pong River located in Lower Mekong, Thailand. We concluded our specimens to be O. asiatica based on the morphology, skeleton, and spicule composition of the specimens that were similar to the samples recorded in Thailand. We were only successful in obtaining the COI sequence of O. asiatica. Furthermore, our samples did not group to the publicly available sequence of its congener, namely Oncosclera sp. Therefore, further molecular taxonomy and morphological analysis is needed to explore the diversity of freshwater sponges in general and to conduct species delimitation of E. carteri and O. asiatica in Java, Indonesia, and Asia

DNA Barcoding and ITS2 Secondary Structure Predictions in Taro (Colocasia esculenta L. Schott) from the North Eastern Hill Region of India.

Taro (Colocasia esculenta L. Schott, Araceae), an ancient root and tuber crop, is highly polygenic, polyphyletic, and polygeographic in nature, which leads to its rapid genetic erosion. To prevent the perceived loss of taro diversity, species discrimination and genetic conservation of promising taro genotypes need special attention. Reports on genetic discrimination of taro at its center of origin are still untapped. We performed DNA barcoding of twenty promising genotypes of taro indigenous to the northeastern hill region of India, deploying two chloroplast-plastid genes, matK and rbcL, and the ribosomal nuclear gene ITS2. The secondary structure of ITS2 was determined and molecular phylogeny was performed to assess genetic discrimination among the taro genotypes. The matK and rbcL genes were highly efficient (&gt;90%) in amplification and sequencing. However, the ITS2 barcode region achieved significant discrimination among the tested taro genotypes. All the taro genotypes displayed most similar sequences at the conserved matK and rbcL loci. However, distinct sequence lengths were observed in the ITS2 barcode region, revealing accurate discriminations among the genotypes. Multiple barcode markers are unrelated to one another and change independently, providing different estimations of heritable traits and genetic lineages; thus, they are advantageous over a single locus in genetic discrimination studies. A dynamic programming algorithm that used base-pairing interactions within a single nucleic acid polymer or between two polymers transformed the secondary structures into the symbol code data to predict seven different minimum free energy secondary structures. Our analysis strengthens the potential of the ITS2 gene as a potent DNA barcode candidate in the prediction of a valuable secondary structure that would help in genetic discrimination between the genotypes while augmenting future breeding strategies in taro.