rbcL Sequences Research Articles

Taxonomic contributions to Hapalidiales (Corallinophycidae, Rhodophyta): Boreolithothamnion gen. nov., Lithothamnion redefined and with three new species and Roseolithon with new combinations.

Phylogenetic analyses of rbcL gene sequences and of concatenated rbcL, psbA, and nuclear SSU rRNA gene sequences resolved the generitype of Lithothamnion, L. muelleri, in a clade with three other southern Australian species, L. kraftii sp. nov., L. saundersii sp. nov., and L. woelkerlingii sp. nov. Cold water boreal species currently classified in Lithothamnion and whose type specimens have been sequenced are transferred to Boreolithothamnion gen. nov., with B. glaciale comb. nov. as the generitype. The other species are B. giganteum comb. nov., B. phymatodeum comb. nov., and B. sonderi comb. nov., whose type specimens are newly sequenced, and B. lemoineae comb. nov., B. soriferum comb. nov., and B. tophiforme comb. nov., whose type specimens were already sequenced. Based on rbcL sequences from the type specimens of Lithothamnion crispatum, L. indicum, and L. superpositum, each is recognized as a distinct species and transferred to the recently described Roseolithon as R. crispatum comb. nov., R. indicum comb. nov., and R. superpositum com. nov., respectively. To correctly assign species to these three genera based only on morpho-anatomy, specimens must have multiporate conceptacles and some epithallial cells with flared walls. The discussion provides examples demonstrating that only with phylogenetic analyses of DNA sequences can the evolution of morpho-anatomical characters of non-geniculate corallines be understood and applied at the correct taxonomic rank. Finally, phylogenetic analyses of DNA sequences support recognition of the Hapalidiales as a distinct order characterized by having multiporate tetra/bisporangial conceptacles, and not as a suborder of Corallinales whose tetra/bisporangial conceptacles are uniporate.

Morphology and molecular phylogeny of Pleurosigmapacificum sp. nov. (Pleurosigmataceae), a new tropical pelagic species from the Western Pacific Ocean.

A new species of pelagic diatom, Pleurosigmapacificumsp. nov., is described from the tropical Western Pacific Ocean. It has the typical features of Pleurosigma, including a slightly sigmoid raphe, intersected transverse and oblique striae, and loculate areolae with external opening slits and internal poroids. Morphologically, P.pacificum belongs to a species group of Pleurosigma with lanceolate valves, including P.atlanticum Heiden & Kolbe, P.nubecula W. Smith, P.indicum Simonsen, and P.simonsenii Hasle. However, P.pacificum differs by its smaller lanceolate valve and smaller intersection angle as well as elliptical areolae without a silica bar. The SSU rDNA and rbcL sequence data place P.pacificum in a basal position relative to other species of Pleurosigma. Our molecular phylogenetic analyses did not support the monophyly of lanceolate and slightly sigmoid species. Thus, the sigmoidality of valve outline cannot be considered as a criterion to define the species group.

Molecular analyses of turf algae reveal a new species and an undetected introduction in the Pterosiphonieae (Rhodomelaceae, Rhodophyta).

Introduced seaweeds and undescribed species often remain undetected because marine regional floras are as yet poorly understood. DNA sequencing facilitates their detection, but databases are incomplete, so their improvement will continue to lead the discovery of these species. Here we aim to clarify the taxonomy of two turf-forming red algal Australian species that morphologically resemble the European Aphanocladia stichidiosa. We also aim to elucidate whether either of these species could have been introduced in Europe or Australia. We studied their morphology, analyzed 17 rbcL sequences of European and Australian specimens, examined their generic assignment using a phylogeny based on 24 plastid genomes, and investigated their biogeography using a taxon-rich phylogeny including 52 rbcL sequences of species in the Pterosiphonieae. The rbcL sequences of one of the Australian species were identical to A. stichidiosa from Europe, considerably expanding its known distribution. Unexpectedly, our phylogenetic analyses resolved this species in the Lophurella clade rather than in Aphanocladia and the new combination L. stichidiosa is proposed. The other Australian species is described as L. pseudocorticata sp. nov. Although L. stichidiosa was originally described in the Mediterranean ca. 70 years ago, our phylogenetic analyses placed it in a lineage restricted to the southern hemisphere, showing that it is native to Australia and introduced to Europe. This study confirms that further work using molecular tools is needed to characterize seaweed diversity, especially among the poorly explored algal turfs, and showcases the usefulness of phylogenetic approaches to uncover introduced species and to determine their native ranges.

Taxonomic Confirmation of Rare Fruits in West Kalimantan Using rbcL and matK Sequences

Phylogenetic analysis for plants can be very helpful in determining species identification or taxonomic status morphologically. rbcL and matK are widely used as genetic markers in constructing seed plant phylogenies. Different identification and new collection during the re-inventory from the previous study were found in two and four types of rare fruits in Sibohe Forest, West Kalimantan. The six types include pisang karok (Musa sp.) and Kandis (Garcinia sp.), as well as nubik (Artocarpus sp.), tehengan (Artocarpus sp.), smallest arok (Ficus sp.), and amok (Alpinia sp.). This study aimed to analyze the phenetic relationship of six rare fruits from Kalimantan based on rbcL and matK genes. DNA samples were obtained from dried body parts of the previous study and amplified by PCR using both forward and reverse primers for rbcL and matK genes. Amplification was observed on electrophoresis gel for rbcL gene of nubik, tehengan, smallest arok, amok, and pisang karok, while only pisang karok in matK gene. However, matK gene sequence was also obtained for amok even though the band was not seen on the gel. Phylogenetic analysis using the two genes confirmed the morphological identification reported in the previous study; however, using matK as a single gene for taxonomic confirmation must be reconsidered. The information of rbcL and matK sequences of six rare fruits from West Kalimantan could be the first information for building the DNA barcodes of the rare fruits in West Kalimantan.

Phylogenetic analysis based on the ITS, matK and rbcL DNA barcodes and comparison of chemical contents of twelve Paeonia taxa in Türkiye

Twelve taxa of herbaceous Paeonia species were recorded in Türkiye. All definitions were performed morphologically and/or anatomically and there is no study based on DNA barcode sequences. Three barcode regions were sequenced to determine the phylogenetic relationships of Turkish Paeonia taxa. The chemical comparison of roots was also investigated. The taxons were collected between May and June 2021 from nine cities. Leaf materials were used for DNA isolation and ITS, matK and rbcL regions were amplified and sequenced. There was no difference among taxa in terms of rbcL sequences. But the ITS and matK regions distinguished 12 taxa and structured them in two groups. ITS region distinguished P. peregrina, P. arietina, and P. tenuifolia from other taxa, while matK region distinguished P. arietina and P. witmanniana from other taxa. Both barcode sequences actually showed that the registration of P. mascula subsp. arasicola was actually 100% similar to P. arietina. ITS was the most polymorphic region (n = 54) followed by matK (n = 9). These sequences could successfully discriminate Paoenia species from each other and diploid P. tenuifolia. The methanolic root (100 gr) extracts were examined for total phenolic and flavonoid content, and antioxidant activities. Significant variation was found for polyphenolic content, and antioxidant properties (TPC from 204.23 to 2343.89mg, TFC from 7.73 to 66.16mg, and FRAP from 523.81 to 4338.62mg). SC50 values of ABTS and DPPH were ranged from 115.08 to 1115.52μg/ml and 73.83 to 963.59μg/ml, respectively. It was concluded that 11 of 12 taxa had differences in terms of ITS and matK sequences and these region must be used for the correct identification of Turkish Paeonia.

Morphology and molecular phylogeny of the marine diatom genus Nagumoea (Bacillariophyceae) from Japan

SUMMARYThe canal‐bearing diatom genus Nagumoea, described based on only morphological evidence, was tentatively assigned to the order Bacillariales, although its phylogenetic position remained unclear. Because three isolates of Nagumoea (SK002, SK024 and SK053) were successfully established from Japanese coasts, we performed their morphological observations and molecular phylogenetic analyses to discuss the phylogeny and taxonomic position of this genus. Strains SK002 and SK024 were identified as Nagumoea africana, whereas SK053 conformed with Nagumoea serrata. There was high interspecific divergence between N. africana and N. serrata in the rbcL sequences (8.03–8.17%), indicating their distinctness. Furthermore, intraspecific variations were detected within N. africana (2.35%) in the rbcL, implying its cryptic diversity. The maximum likelihood and Bayesian phylogenetic trees inferred from the plastid rbcL, psbC and nuclear 18S rDNA genes recovered Nagumoea as monophyletic with strong statistical support and embedded within an unresolved, poorly supported lineage containing Achnanthes, Craspedostauros, Staurotropis and Undatella in the canal‐bearing order Bacillariales (= the family Bacillariaceae). Although the constrained tree based on the monophyly of Nagumoea and the other canal‐bearing clade (Surirellales and Rhopalodiales) was statistically rejected by the topology tests, the phylogenetic position of Nagumoea with other Bacillarialean members remains equivocal. The possession of two plastids positioned fore and aft, observed in the present study, and lack of keel, typical of the Bacillariales, indicate the possibility of Nagumoea being part of the ingroup of the Bacillariales or its closely related outgroup.

Barking up the wrong tree: the dangers of taxonomic misidentification in molecular phylogenetic studies

Background and aims – Keraunea is a Brazilian endemic genus that has sat uncomfortably in Convolvulaceae where it was placed due to an enlarged and adnate fruit bract typical of Neuropeltis. A recent molecular phylogeny suggested that two of its five morphologically almost identical species actually belong to two different families, Malpighiaceae (superrosids) and Ehretiaceae (superasterids). Later studies have demonstrated that Keraunea effectively belongs to Ehretiaceae, but the proposal of one species belonging to Malpighiaceae has remained problematic. In this study, we re-assess this hypothesis, discuss the issues that have led to this assumption, and offer insights on the importance of carefully using herbarium collections and incorporating morphological evidence in systematic studies. Material and methods – Sequences of matK, rbcL, and ITS for all 77 currently accepted genera of Malpighiaceae, K. brasiliensis and Elatinaceae (outgroup) were compiled from GenBank and analysed with Maximum Likelihood and Bayesian Inference criteria for nuclear, plastid and combined datasets. Additional database and herbarium studies were performed to locate and analyse all duplicates of the holotype of K. brasiliensis to check for misidentified or contaminated material. Key results – Our examination of expanded DNA datasets and herbarium sheets of all K. brasiliensis isotypes revealed that a mistake in tissue sampling was, in fact, what led to this species being proposed to belong in Malpighiaceae. Kew’s isotype had a leaf of Malpighiaceae (likely Mascagnia cordifolia) stored in the fragment capsule, which was sampled and sequenced instead of the actual leaves of K. brasiliensis. Recently published studies have settled the placement of Keraunea in Ehretiaceae (Boraginales) and proposed three additional species. Conclusions – DNA sequences can be helpful in classifying taxa when morphology is conflicting or of a doubtful interpretation, with molecular phylogenetic placement being established as a popular tool accelerating the discovery of systematic relationships. Nonetheless, molecular techniques are also susceptible to methodological mistakes, which necessitates building a solid foundation of plant morphology and taxonomy to avoid artefacts in phylogenetic studies.

Genetic diversity analysis in wheat cultivars using SCoT and ISSR markers, chloroplast DNA barcoding and grain SEM

BackgroundWheat is a major cereal that can narrow the gap between the increasing human population and food production. In this connection, assessing genetic diversity and conserving wheat genetic resources for future exploitation is very important for breeding new cultivars that may withstand the expected climate change. The current study evaluates the genetic diversity in selected wheat cultivars using ISSR and SCoT markers, the rbcL and matK chloroplast DNA barcoding, and grain surface sculpture characteristics. We anticipate that these objectives may prioritize using the selected cultivars to improve wheat production. The selected collection of cultivars may lead to the identification of cultivars adapted to a broad spectrum of climatic environments.ResultsMultivariate clustering analyses of the ISSR and SCoT DNA fingerprinting polymorphism grouped three Egyptian cultivars with cultivar El-Nielain from Sudan, cultivar Aguilal from Morocco, and cultivar Attila from Mexico. In the other group, cultivar Cook from Australia and cultivar Chinese-166 were differentiated from four other cultivars: cultivar Cham-10 from Syria, cultivar Seri-82 from Mexico, cultivar Inqalab-91 from Pakistan, and cultivar Sonalika from India. In the PCA analysis, the Egyptian cultivars were distinct from the other studied cultivars. The rbcL and matK sequence variation analysis indicated similarities between Egyptian cultivars and cultivar Cham-10 from Syria and cultivar Inqalab-91 from Pakistan, whereas cultivar Attila from Mexico was distinguished from all other cultivars. Combining the data of ISSR and SCoT with the rbcL and matK results retained the close resemblance among the two Egyptian cultivars EGY1: Gemmeiza-9 and EGY3: Sakha-93, and the Moroccan cultivar Aguilal, and the Sudanese cultivar El-Nielain and between Seri-82, Inqalab-91, and Sonalika cultivars. The analysis of all data distinguished cultivar Cham-10 from Syria from all other cultivars, and the analysis of grain traits indicated a close resemblance between cv. Cham-10 from and the two Egyptian cultivars Gemmeiza-9 and Sakha-93.ConclusionsThe analysis of rbcL and matK chloroplast DNA barcoding agrees with the ISSR and the SCoT markers in supporting the close resemblance between the Egyptian cultivars, particularly Gemmeiza-9 and Sakha-93. The ISSR and SCoT data analyses significantly expressed high differentiation levels among the examined cultivars. Cultivars with closer resemblance may be recommended for breeding new wheat cultivars adapted to various climatic environments.

Potential distribution of two economic laver species-Neoporphyra haitanensis and Neopyropia yezoensis under climate change based on MaxEnt prediction and phylogeographic profiling

Climate change is altering geographic and phylogeographic distribution of macroalgae, laying great impacts on their conservation and sustainable utilization. The potential distribution of two dominant cultured seaweeds-Neoporphyra haitanensis and Neopyropia yezoensis was predicted under present and three representative concentration pathways (RCP 2.6, 4.5, 8.5) for 2050 s using the maximum entropy model (MaxEnt). The area under the receiver operating characteristic curve (AUC) was 0.998 forN. haitanensis and 0.992 for N. yezoensis, indicating high modelling accuracy. Sea surface temperature contributed mainly to the models. In addition to the predominant distribution in their native habitats in Northwest Pacific, high suitability along the east coast of North America and trans-hemispheric distribution was predicted for both species. In 2050 s, high-latitudinal and offshore expansion was observed, increasing over the present distribution area by 10.75%∼26.13% for N. haitanensis and 18.97%∼26.48% for N. yezoensis. Current geographic distribution centroid of N. yezoensis was located in Seocheon and the centroid shifted northeastward to the Sea of Japan in 2050 s. The most specific haplotypes or high genetic variations (based on chloroplast rbcL sequences) were identified in both regions. Current and future centroids of N. haitanensis were located in East China Sea, where the highest genetic diversity was identified. The overall haplotype and nucleotide diversity of both species was at low levels while the haplotype distribution showed spacial heterogeneity, more diversified at the convergence zones of warm and cold ocean currents. The overlapping between N. yezoensis and N. haitanensis geographic distribution centers and species’ genetic diversity hotspots implied their ability to adapt to future climate change. These findings provided vital information for conservation and sustainable utilization of these important intertidal seaweeds to address the global climate challenges.

Potential application of a newly isolated microalga Desmodesmus sp. GXU-A4 for recycling Molasses vinasse

The development of cost-effective and energy-efficient technologies for the stabilization of organic wastewater by microalgae has been essential and sought after. In the current study, GXU-A4 was isolated from an aerobic tank treating molasses vinasse (MV) and identified as Desmodesmus sp. based on its morphology, rbcL, and ITS sequences. It exhibited good growth with a high lipid content and chemical oxygen demand (COD) when grown using MV and the anaerobic digestate of MV (ADMV) as the growth medium. Three distinct COD concentrations for wastewater were established. Accordingly, GXU-A4 removed more than 90% of the COD from molasses vinasse (MV1, MV2, and MV3) with initial COD concentrations of 1193 mgL−1, 2100 mgL−1, and 3180 mgL−1, respectively. MV1 attained the highest COD and color removal rates of 92.48% and 64.63%, respectively, and accumulated 47.32% DW (dry weight) of lipids and 32.62% DW of carbohydrates, respectively. Moreover, GXU-A4 grew rapidly in anaerobic digestate of MV (ADMV1, ADMV2, and ADMV3) with initial COD concentrations of 1433 mgL−1, 2567 mgL−1, and 3293 mgL−1, respectively. Under ADMV3 conditions, the highest biomass reached 13.81 g L-1 and accumulated 27.43% DW of lipids and 38.70% DW of carbohydrates, respectively. Meanwhile, the removal rates of NH4–N and chroma in ADMV3 reached 91.10% and 47.89%, respectively, significantly reducing the concentration of ammonia nitrogen and color in ADMV. Thus, the results demonstrate that GXU-A4 has a high fouling tolerance, a rapid growth rate in MV and ADMV, the ability to achieve biomass accumulation and nutrient removal from wastewater, and a high potential for MV recycling.

Reinstatement of Corallina chilensis (Corallinaceae, Rhodophyta) based on DNA sequencing of the type material collected by Darwin

ABSTRACT To determine whether Corallina chilensis is a distinct species or a variety (i.e. C. officinalis var. chilensis) of the generitype of Corallina, molecular phylogenetic analyses were performed using psbA, COI-5P, rbcL, or some combination of these gene regions from 75 voucher specimens representing Corallina collections from around the world. Names were applied by comparing these DNA sequences with sequences obtained from type specimens, including a 263 bp rbcL sequence from an isotype of C. chilensis collected by Darwin (C. Darwin 2151) from Valparaiso, Chile. DNA sequences from the C. chilensis isotype matched unnamed coralline DNA sequences from British Columbia, Canada, and previously published DNA sequences from the northeast and southeast Pacific. The clade containing the isotype of C. chilensis was distinct from C. officinalis specimens in phylogenetic analyses. Although morphologically variable, fronds of C. chilensis from British Columbia populations matched Kützing’s original description of C. officinalis var. chilensis. These data support the conclusion that C. chilensis is a distinct species, not a variety of C. officinalis, and is distributed in both hemispheres. While this study strongly supported C. chilensis as a distinct species, phylogenetic relationships among Corallina species remain elusive because individual gene trees are not congruent.

Insight into the species identification and distribution of Grateloupiaceae (Halymeniales, Rhodophyta) having Grateloupia filicina-like morphology in the Northwest Pacific

Accurately identifying species is the basis of all biological studies. There has been much confusion in the identification of Grateloupiacean species, which have finely pinnate gross morphology similar to Grateloupia filicina (the type species of the family). The objective of this study was to comprehensively investigate species identification and distribution of G. filicina-like species in the Northwest Pacific, based on the rbcL sequences. A total of 118 specimens from 78 sites in Korea and Japan were collected from 2001 to 2021 and analyzed for their rbcL sequences. Additional 341 sequences downloaded from the GenBank were included in our comprehensive dataset. Based on these sequences, we documented the nomenclatural history and geographical distribution of the species, and commented on the application of species name. G. asiatica was the most abundant G. filicina-like species in the Northwest Pacific, and its high degree of morphological variation caused many misidentifications. In particular, G. dalianensis, G. serra and G. variata require reconsideration of their conspecificity with G. asiatica using more specimens from China. By contrast, G. oligoclora was presumed to be a heterotypic synonym of G. subpectinata. The occurrence of G. acuminata, G. ramosissima, and G. livida in Korea resulted from misidentifications with other species.

Insight into the species identification and distribution of Grateloupiaceae (Halymeniales, Rhodophyta) having Grateloupia filicina-like morphology in the Northwest Pacific

Accurately identifying species is the basis of all biological studies. There has been much confusion in the identification of Grateloupiacean species, which have finely pinnate gross morphology similar to Grateloupia filicina (the type species of the family). The objective of this study was to comprehensively investigate species identification and distribution of G. filicina-like species in the Northwest Pacific, based on the rbcL sequences. A total of 118 specimens from 78 sites in Korea and Japan were collected from 2001 to 2021 and analyzed for their rbcL sequences. Additional 341 sequences downloaded from the GenBank were included in our comprehensive dataset. Based on these sequences, we documented the nomenclatural history and geographical distribution of the species, and commented on the application of species name. G. asiatica was the most abundant G. filicina-like species in the Northwest Pacific, and its high degree of morphological variation caused many misidentifications. In particular, G. dalianensis, G. serra and G. variata require reconsideration of their conspecificity with G. asiatica using more specimens from China. By contrast, G. oligoclora was presumed to be a heterotypic synonym of G. subpectinata. The occurrence of G. acuminata, G. ramosissima, and G. livida in Korea resulted from misidentifications with other species.

Genetic Diversity and Phylogeography of a Turf-Forming Cosmopolitan Marine Alga, Gelidium crinale (Gelidiales, Rhodo-Phyta).

Cosmopolitan species are rare in red algae, which have a low-dispersal capacity unless they are dispersed by human-mediated introductions. Gelidium crinale, a turf-forming red alga, has a widespread distribution in tropical and temperate waters. To decipher the genetic diversity and phylogeography of G. crinale, we analyzed mitochondrial COI-5P and plastid rbcL sequences from collections in the Atlantic, Indian, and Pacific Oceans. Phylogenies of both markers statistically supported the monophyly of G. crinale, with a close relationship to G. americanum and G. calidum from the Western Atlantic. Based on the molecular analysis from these materials, Pterocladia heteroplatos from India is here merged with G. crinale. Phylogeny and TCS networks of COI-5P haplotypes revealed a geographic structure of five groups: (i) Atlantic-Mediterranean, (ii) Ionian, (iii) Asian, (iv) Adriatic-Ionian, and (v) Australasia-India-Tanzania-Easter Island. The most common ancestor of G. crinale likely diverged during the Pleistocene. The Bayesian Skyline Plots suggested the pre-LGM population expansion. Based on geographical structure, lineage-specific private haplotypes, the absence of shared haplotypes between lineages, and AMOVA, we propose that the cosmopolitan distribution of G. crinale has been shaped by Pleistocene relicts. The survival of the turf species under environmental stresses is briefly discussed.

Nitzschia captiva sp. nov. (Bacillariophyta), the essential prey diatom of the kleptoplastic dinoflagellate Durinskia capensis, compared with N. agnita, N. kuetzingioides and other species

ABSTRACT Durinskia capensis is a kleptoplastic dinoflagellate species from high intertidal marine rock pools, which can use a variety of diatoms for photosynthesis. However, very few of the diatoms permit indefinite survival of the dinoflagellate and rbcL sequences show that D. capensis isolated from nature contains one of two closely related Nitzschia species as its kleptoplastids. In culture, without a supply of these ‘essential’ Nitzschia cells to replenish the intracellular store of diatom plastids and other organelles, D. capensis eventually loses all its kleptoplastids and dies. Inside Durinskia, diatoms do not possess frustules and so cannot be compared morphologically with free-living forms. Recently, one of the essential Nitzschia species was isolated from the type locality of D. capensis and grown in culture, allowing comparison with similar Nitzschia species, particularly N. agnita and N. kuetzingioides, examined from type material. We conclude that the ‘essential diatom’ of D. capensis differs morphologically from these and other Nitzschia species and it is therefore described as N. captiva sp. nov. Nitzschia agnita and N. kuetzingioides, on the other hand, are conspecific and N. agnita has priority. Nitzschia captiva and N. agnita are extremely similar in valve shape, dimensions, pattern and ultrastructure, but can be separated by their girdle structure. Nitzschia agnita appears to be a freshwater species, though somewhat salt-tolerant. In contrast, N. captiva, which is known principally from records of the kleptoplastids of D. capensis rather than from frustules, is so far marine.

Diversity of aquatic plants in the Rote Dead Sea area, East Nusa Tenggara, Indonesia, based on rbcL marker

Abstract. Lonthor DW, Miftahudin, Kayat, Julzarika A, Subehi L, Iswandono E, Dima AOM, Dianto A, Setiawan F, Nugraha MFI. 2023. Diversity of aquatic plants in the Rote Dead Sea area, East Nusa Tenggara, Indonesia, based on rbcL marker. Biodiversitas 24: 810-818. The Rote Dead Sea area in Rote Islands has two freshwater and 24 saltwater lakes. The saltwater lakes have salinity levels varied between 0-100 ppt. Every lake has specific aquatic plant species. Species identification through morphological analysis only has its limitations; therefore, DNA barcoding is a preference due to an effective, accurate, and faster method for species identification. In this study, we used the rbcL marker to identify and analyze the diversity of the aquatic plant species in lakes Ledulu, Oenduy, Oemasapoka, Oesotimori, and Landu Leko. Plants samples' DNA was amplified using rbcL primers, and the amplicons were sequenced. Species identification was based on morphological study and the rbcL sequence database. Diversity analyses were performed based on pairwise genetic distances, analysis of molecular variance, and genetic relationships based on the Kimura 2 parameter. The results showed that all 20 aquatic plants were correctly identified, and high genetic diversity was discovered. AMOVA analysis showed that genetic variations within the population were higher than among the population. All plant species were grouped into four groups based on the phylogenetic tree and fractional component analyses. The species belonging to the certain family were grouped in the same clade and the closely related plant families. The rbcL marker can be used to discriminate aquatic plant species and analyze their genetic diversity and relationships.

Evolutionary Trend in Passiflora Species Revealed by RAPD-PCR, Gene Specific ITS and rbcl Markers

Background: The present study represents a preliminary analysis of genetic diversity among Passiflora species using amplified genotypic data of specific ITS and rbcL sequences and non-specific RAPD-PCR markers for investigation of the molecular phylogeny.
 Methods: The PCR-RAPD uses ten primers for polymorphic DNA, which are compiled on NTSYS software to construct dendrogram. The gene specific ITS and rbcL primers are used for specific amplification from genomic. The amplified ITS and rbcL markers assembled using Maximum Parsimony (MP) and Maximum likelihood (ML) methods. The BLAST, CLUSTAL W, and MEGA 6.0 have been used to conclude final genetic relation tree.
 Results: The PCR-RAPD primers translate 133 random amplified polymorphic DNA. NTSYS dendrogram placed P. vitifolia from Ramdaspeth and Shankar Nagar Nagpur, India in same clade (similarity coefficient 0.609) confirming same origin Nagpur India. Moreover, P. foetida from England is not coming in same clade with Indian P. foetida showing geographically intra-specific variation. In addition, the change in a constructed tree was observed with respect to change in phylogeny methods MS/ML. The ITS MP consensus tree is supported by strong 100 bootstrap value, clusters P. vitifolia (HNI and RNI) and P. foetida (UAI and UGI) in equivalent clade. However, no single species have been recovered using rbcL in MP and ML method. Thus, it is inference that rbcL have tendency to differentiate Passiflora species not allowing clustering around same species in same clade and the ITS region having parsimony informative sites that provide valid resolution and identification at inter-intra species level.
 Conclusions: The evaluation of properties of RAPD indicates 100% PCR success, sometimes with low rate of amplification. The ITS region found to be best for identification at inter-intra species, On the contrary, rbcL region is good to distinguished inter species, making it best as local DNA barcode for marking a Passiflora species in phylogenetic community.

New record of Sporochnus dotyi (Sporochnales, Phaeophyceae) from Kii Peninsula, Japan

SUMMARYThe subtidal brown algal species Sporochnus dotyi Brostoff (Sporochnales, Phaeophyceae), which has been regarded as a Hawaiian endemic, is reported from Kushimoto, Kii Peninsula, Pacific coast of central Honshu, Japan, for the first time outside Hawai'i. The species grew on subtidal rocks ca. 5–20 m deep attached by a small conical holdfast. The erect thalli were 5–30 cm high, terete, robust and alternately branched in 1–2 orders. When mature, pedicellate receptacles developed on the branches, and formed elliptical sori 1 mm long with a pedicel 3–5 mm long. The apical parts of the thalli and the receptacles were terminated with a tuft of simple assimilatory filaments of up to 4 mm long and showed prominent green to yellow underwater iridescence. Reproductive filaments (paraphyses) were densely packed, simple, up to 200 μm long and bore 4–6 mostly unilateral unilocular zoidangia 20–22 μm long and 5–6 m in diameter. In the genetic analyses, the Sporochnus alga from Kushimoto had partial rbcL sequence identical to S. dotyi from Hawai'i. The cox3 phylogeny revealed that this alga formed a fully supported clade with S. dotyi. Therefore, we identified the alga from Kushimoto as S. dotyi. This finding of S. dotyi from Japan, together with the recent reports of the mesophotic macroalgae Ryuguphycus kuaweuweu (=Umbraulva kuaweuweu), Ulva iliohaha and Newhousia imbricata from various localities in the Pacific Ocean including Japan, suggest closer biogeographical connections of subtidal/mesophotic macroalgae in the Pacific than previously recognized.

‘Unfinished’ Morphogenesis Hides Different Speciation Pathways in Charophytes: Evidence from the 190-Year-Old Original Material of Chara denudata (Charales, Charophyceae)

Several Chara L. species have ‘unfinished’ morphogenesis that is recognizable because of their imperfect stem and branchlet cortication compared to the perfectly corticated species. Chara denudata A. Braun, described from South Africa, is one of these species, assumed for a long time to be conspecific with C. dissoluta A. Braun ex Leonhardi, as described from Central Europe. An attempt to resolve this long-lasting uncertainty in the framework of integrative taxonomy is implemented here. The restudy of the original material of both species showed similarities but did not identify a hiatus in their morphological traits, which represents evidence for their placement in the subsection Chara R.D. Wood according to morphology. Bifid adaxial bract cells, a trait rarely encountered among charophytes, were found for the first time in C. dissoluta. According to the rbcL and matK sequences, C. denudata was unexpectedly placed within the section Grovesia R.D. Wood, far from the clusters of the section Chara with C. dissoluta. This is in obvious disagreement with the position of C. denudata according to morphology. Both species were distinct according to their biology, habitat preference, and distribution and were accepted as distinct species. Therefore, the ‘unfinished’ morphogenesis resulting in morphological similarity hides different speciation pathways in charophytes.

The geography of genetic data: Current status and future perspectives

The biogeography field benefits more and more from the growth and application of genetic data such as nucleotide sequences and whole genomes. It has been perceived by scientists that genetic data may be imbalanced among different geographical regions and taxonomic groups. However, the lack of empirical evidence prevents the understanding of current data volume and distribution of genetic data. Based on the construction of a dataset including records for 365 millions of nucleotide sequences of Animalia, Plantae, and Fungi kingdoms, 6 millions of COI sequences of insects, 77 thousands of COI sequences of mammals, 220 thousands of rbcl sequences of Magnoliopsida, and 44 thousands of ITS sequences of Dothideomycetes, here we present evidence on geographical and taxonomical imbalance of the genetic data, identify major gaps and inappropriate practices in the production, application and sharing of genetic data. We then discuss our perspectives on how to fill up gaps and improve the quantity and quality of genetic data.