matK Gene Research Articles

The complete chloroplast genome of critically endangered Chimonobambusa hirtinoda (Poaceae: Chimonobambusa) and phylogenetic analysis

Chimonobambusa hirtinoda, a threatened species, is only naturally distributed in Doupeng Mountain, Duyun, Guizhou, China. Next-generation sequencing (NGS) is used to obtain the complete chloroplast (cp) genome sequence of C. hirtinoda. The sequence was assembled and analyzed for phylogenetic and evolutionary studies. Additionally, we compared the cp genome of C. hirtinoda with previously published Chimonobambusa species. The cp genome of C. hirtinoda has a total length of 139, 561 bp and 38.90% GC content. This genome included a large single -copy (LSC) region of 83, 166 bp, a small single-copy (SSC) region of 20, 811 bp and a pair of inverted repeats of 21,792 bp each. We discovered 130 genes in the cp genome, including 85 protein-coding genes, 37 tRNA, and 8 rRNA genes. A total of 48 simple sequence repeats (SSRs) were detected. The A/U preference of the third nucleotide in the cp genome of C. hirtinoda was obtained by measuring the codon usage frequency of amino acids. Furthermore, phylogenetic analysis using complete cp sequences and matK gene revealed a genetic relationship within the Chimonobambusa genus. This study reported the chloroplast genome of the C. hirtinoda.

Endorsement and phylogenetic analysis of some Fabaceae plants based on DNA barcoding

BackgroundDNA barcoding have been considered as a tool to facilitate species identification based on its simplicity and high-level accuracy in compression to the complexity and subjective biases linked to morphological identification of taxa. MaturaseK gene (MatK gene) of the chloroplast is very vital in the plant system which is involved in the group II intron splicing. The main objective of this study is to determine the relative utility of the “MatK” chloroplast gene for barcoding in 15 legume as a tool to facilitate species identification based on their simplicity and high-level accuracy linked to morphological identification of taxa.Methods and ResultsMatK gene sequences were submitted to GenBank and the accession numbers were obtained with sequence length ranging from 730 to 1545 nucleotides. These DNA sequences were aligned with database sequence using PROMALS server, Clustal Omega server and Bioedit program. Maximum likelihood and neighbor-joining algorithms were employed for constructing phylogeny. Overall, these results indicated that the phylogenetic tree analysis and the evolutionary distances of an individual dataset of each species were agreed with a phylogenetic tree of all each other consisting of two clades, the first clade comprising (Enterolobium contortisiliquum, Albizia lebbek), Acacia saligna, Leucaena leucocephala, Dichrostachys Cinerea, (Delonix regia, Parkinsonia aculeata), (Senna surattensis, Cassia fistula, Cassia javanica) and Schotia brachypetala were more closely to each other, respectively. The remaining four species of Erythrina humeana, (Sophora secundiflora, Dalbergia Sissoo, Tipuana Tipu) constituted the second clade.ConclusionMoreover, their sequences could be successfully utilized in single nucleotide polymorphism or as part of the sequence as DNA fragment analysis utilizing polymerase chain reaction in plant systematic. Therefore, MatK gene is considered promising a candidate for DNA barcoding in the plant family Fabaceae and provides a clear relationship between the families.

Identification and Molecular Phylogeny of Morphologically of the Medicinal Plant Calligonum L’Herit

Aim: The rare gem species of Calligonum comosum contains highly therapeutic compounds collected from Al-Qassim region, Saudi Arabia. It has various biological properties that used for antimicrobial, antioxidant, anti-inflammatory, anti-gastric ulcer, anti-hyperglycemic, abdominal ailments as well as against toothache. Methods: Calligonum L. (Polygonaceae) genus consists of 158 species dispersed in Asia, Africa and Middle East. Remarkably a very few researches found molecular phylogeny of Calligonum comosum, it is one of the significant medicinal plants used in various herbal preparations and most commonly adulterated by the morphologically similar species, viz C. ebinuricum. The species C. junceum, C. Colubrinum and C. arborescens is often misidentified as Calligonum comosum hence, thereby accurate identification of this medicinal herb are very crucial which ensures the drug effectively as well as biosafety. Thus, in this study, DNA barcoding tool was used for precise identification, its conservation development and differentiating from analogous species of C. comosum. Results: The barcode genes like nuclear internal transcribed spacer region ITS2, the chloroplast plastid gene matK and rbcL were used for phylogenetic analysis of Calligonum species. From the sequence alignment the nuclear internal transcribed spacer ITS2 regions shows 9.5% of polymorphic sites, indicates higher range of transition/transversion (ts/tv) ratio and percentage of variation which aids to discriminate Calligonum comosum from its closely related species. Conclusion: The present phylogeny proves that the nuclear internal transcribed spacer ITS2 region distinguishes the closely related species of Calligonum comosum from its morphologically similar species. Keywords: Calligonum, Phylogeny, ITS2, matK, rbcL.

Morphological description and DNA barcoding study of Paramignya trimera collected in Khanh Hoa, Vietnam

Paramignya trimera is a valuable traditional medicinal plant, typically distributing in Khanh Hoa, Vietnam. In recent years, P. trimera has been exploited to treat liver diseases such as hepatitis, cirrhosis and liver cancers. The recorded during the investigation, in Khanh Hoa currently appears a number of species with similar phenotypes known collectively as P. trimera and appeared some morphology with differences in leaf morphology and thorns. Therefore, this study was carried out for identification, breeding and propagation conservation.This study has been described, characterized morphological characteristics and analyzed DNA barcodes based on ITS, matK and rbcL gene markers. About the morphology, P. trimera is distinguished from other species of the genus Paramignya with the following characteristics: elongated, single leaf, leaf-shaped lobe end, leaf veins shaped like a feather. Petiole with big, pointed and straight spines. Corolla 3, 6 stamens, upper election, with three sepals and two ovule leaves, the seed has a seed coat. The analysis of DNA barcodes shows that the results combination of the analysis of the three regions of ITS, matK and rbcL can be used to determine the genetic relationship between five samples of P. trimera. The nucleotide sequence lengths of the samples for the three regions of the ITS, matK and rbcL genes are 850 bp, 850 bp and 500 bp, respectively. On the basis of phenotypic tree analysis, the samples (X1, X2, X3, X4, X5) have the same evolutionary origin in ITS, matK and rbcL. Base on to identified the five morphological forms of P. trimera distributed in Khanh Hoa as the same species and expanded the distribution area as well as in-depth research on P. trimera morphologies in Khanh Hoa, Vietnam.

Molecular phylogeny of Ruppia maritima L. from Chilika Lake, Odhisa using nuclear and plastid genes

Aim: The present study aims to confirm the molecular identification of Ruppia maritima L. from Chilika Lake, Odhisa using different molecular markers and find out the evolutionary lineage of Ruppia species. Methodology: For molecular identification, R. maritima was collected from Chilika Lake and the rbcL, matK, and ITS gene sequences were investigated and analyzed using BLAST to verify the gene fragment. Phylogenetic tree was constructed using MEGA X software following Neighbor joining (NJ) and Maximum parsimony (MP) methods. Results: The nucleotide (ITS) and plastid gene (rbcL and matK) sequences of Ruppia maritima were examined. The tree topology of R. maritima rbcL and matK gene sequences revealed a paraphyletic cluster at 99 and 100% bootstrap. The conserved region was high in matK (74.8%), followed by rbcL (45.2%) and ITS (19.1%) with seagrass and freshwater species. ITS had the most significant proportion of variable sites (79.7%), followed by rbcL (52.4%) and matK (25.2%). The ITS region showed less parsimonious-informative character (66.1) than rbcL and matK region. Interpretation: The study concludes that the R. maritima was identified through molecular markers, which was a closed lineage with seagrasses than freshwater species.

DNA BARCODING OF THE EGYPTIAN MEDICINAL PLANT Astragalus spinosus

Medicinal plants have served as the basis of alternative medicine and have become the primary source for developing new medications. Astragalus spinosus (Forssk.) Muschl. belongs to family Fabaceae and due to its active constituent’s composition, it is used traditionally to treat various ailments. Additionally, various Astragalus-based dietary supplements were sold for supporting immunity and cardiovascular system. Therefore, authentication of the medicinal plant material is important and vital to provide an extensive database with DNA data for easy identification, adulteration detection and conservation of genetic resources. In the current study, three partial chloroplast coding genes were examined in A.spinosus; ribulose 1,5biphosphate carboxylase large subunit (rbcL), RNA polymerase (rpoC1) and maturase K (matK). When compared to the National Center for Biotechnology Information (NCBI) database, the results showed that rbcL was successful in identifying and discriminating A.spinosus at the genus and species levels. The, rpoC1 and matK genes revealed a high level of identity with Astragalus species, indicating that they are capable of identifying A.spinosus at the genus level. Phylogenetic trees were established based on the expected amino acids sequence of each coding gene, demonstrating the extent of relatedness with recorded plant species in the NCBI database.

Paracladopuschiangmaiensis (Podostemaceae), a new generic record for China and its complete plastid genome.

The genus Paracladopus was established based on the type species P.chiangmaiensis in 2006. The two Paracladopus species are distributed in Thailand and Laos; however, neither of them has been documented in China to date. During our field work in 2020, we collected a river-weed in Wuzhi Mountain, Hainan Province of China. After checking the morphological characters, it was identified as P.chiangmaiensis. Then, we assembled and annotated its chloroplast genome based on the genome skimming data. The results showed that the complete chloroplast genome was 133,748 bp with 35% GC content, consisting of 76 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. A maximum-likelihood tree constructed based on the matk genes showed that WuMS109 was clustered with P.chiangmaiensis (AB537420, AB698348) without base difference and together with the remains of Paracladopus formed a sister clade to Cladopus. This is the first report of P.chiangmaiensis that represents a new generic record for China. The discovery of this river-weed could lay the foundation for investigating their biogeographical patterns and species evolution in further studies.

Reconstructing an historical pollination syndrome: keel flowers

BackgroundKeel flowers are bilaterally symmetrical, pentamerous flowers with three different petal types and reproductive organs enclosed by keel petals; generally there is also connation of floral parts such as stamens and keel petals. In this study, the evolution of keel flowers within the order Fabales is explored to investigate whether the establishment of this flower type within one of the species-rich families, the Fabaceae (Leguminosae), preceded and could have influenced the evolution of keel flowers in the Polygalaceae. We conducted molecular dating, and ancestral area and ancestral state analyses for a phylogeny constructed for 678 taxa using published matK, rbcL and trnL plastid gene regions.ResultsWe reveal the temporal and spatial origins of keel flowers and traits associated with pollinators, specifically floral symmetry, the presence or absence of a pentamerous corolla and three distinct petal types, the presence or absence of enclosed reproductive organs, androecium types, inflorescence types, inflorescence size, flower size, plant height and habit. Ancestral area reconstructions show that at the time keel flowers appeared in the Polygaleae, subfamily Papilionoideae of the Fabaceae was already distributed almost globally; at least eight clades of the Papilionoideae had keel flowers with a functional morphology broadly similar to the morphology of the first evolving Polygaleae flowers.ConclusionsThe multiple origins of keel flowers within angiosperms likely represent convergence due to bee specialization, and therefore pollinator pressure. In the case of the Fabales, the first evolving keel flowers of Polygaleae have a functional morphology that corresponds with keel flowers of species of the Papilionoideae already present in the environment. These findings are consistent with the keel-flowered Polygaleae exploiting pollinators of keel-flowered Papilionoideae. The current study is the first to use ancestral reconstructions of traits associated with pollination to demonstrate that the multiple evolutionary origins of the keel flower pollinator syndrome in Fabales are consistent with, though do not prove, mimicry.

Morpho-anatomical characterization and DNA barcoding of Achillea millefolium L.

Abstract. Ilham M,Mukarromah SR, Rakashiwi GA, Indriati DT, Yoku BF, Purnama PR, Junairiah, Prasongsuk S,Purnobasuki H, Wahyuni DK. 2022. Morpho-anatomical characterizationand DNA barcoding of Achillea millefolium L. Biodiversitas 23: 1958-1969. One of the important things to study the distribution of secondary metabolites in the plant body is to carry out the identification process. Morphological markers have several limitations to recognize plants, therefore supporting data is needed so that the information becomes more comprehensive. This study aims to identify Achillea millefolium L. based on morphological, anatomical, and DNA barcoding markers to obtain specific data and avoid confusion. Morphological studies were carried out descriptively using vegetative organs, while anatomical studies of rhizomes, stems, and leaves used the paraffin method. The DNA barcoding was performed by analyzinggenes from 3 different individuals. The research was carried out by amplifying and sequencing the partial gene in the ribulose-bisphosphate carboxylaselarge subunit (rbcL) regions and maturase-K (matK). The results showed that the plant had taproots, short stems due to root rosette and the leaves were double compound. The rhizome and stem tissues had almost the same structure, while the leaves had a tissue arrangement that was similar to other plants in general, except that the mesophyll tissue was undifferentiated. The results of DNA barcoding showed a percentage of identity above 98% for both the rbcLand matK genes.

The evolution of the Aristolochia pallida complex (Aristolochiaceae) challenges traditional taxonomy and reflects large-scale glacial refugia in the Mediterranean.

The taxonomy of the Mediterranean Aristolochia pallida complex has been under debate since several decades with the following species currently recognized: A. pallida, A. lutea, A. nardiana, A. microstoma, A. merxmuelleri, A. croatica, and A. castellana. These taxa are distributed from Iberia to Turkey. To reconstruct phylogenetic and biogeographic patterns, we employed cpDNA sequence variation using both noncoding (intron and spacer) and protein‐coding regions (i.e., trnK intron, matK gene, and trnK‐psbA spacer). Our results show that the morphology‐based traditional taxonomy was not corroborated by our phylogenetic analyses. Aristolochia pallida, A. lutea, A. nardiana, and A. microstoma were not monophyletic. Instead, strong geographic signals were detected. Two major clades, one exclusively occurring in Greece and a second one of pan‐Mediterranean distribution, were found. Several subclades distributed in Greece, NW Turkey, Italy, as well as amphi‐Adriatic subclades, and a subgroup of southern France and Spain, were revealed. The distribution areas of these groups are in close vicinity to hypothesized glacial refugia areas in the Mediterranean. According to molecular clock analyses the diversification of this complex started around 3–3.3 my, before the onset of glaciation cycles, and the further evolution of and within major lineages falls into the Pleistocene. Based on these data, we conclude that the Aristolochia pallida alliance survived in different Mediterranean refugia rarely with low, but often with a high potential for range extension, and a high degree of morphological diversity.

Gene loss, genome rearrangement, and accelerated substitution rates in plastid genome of Hypericum ascyron (Hypericaceae)

BackgroundComparative genomic analysis exhibits dynamic evolution of plastid genome (plastome) in the clusioid clade of Malpighiales, which comprise five families, including multiple inversions and gene losses. Little is known about the plastome evolution in Hypericaceae, a large family in the clade. Only the plastome of one species, Cratoxylum cochinchinense, has been published.ResultsWe generated a complete plastome sequence for Hypericum ascyron, providing the first complete plastome from the tribe Hypericeae (Hypericaceae). The H. ascyron plastome exhibits dynamic changes in gene and intron content, structure, and sequence divergence compared to the C. cochinchinense plastome from the tribe Cratoxyleae (Hypericaceae). Transcriptome data determined the evolutionary fate of the missing plastid genes infA, rps7, rps16, rpl23, and rpl32 in H. ascyron. Putative functional transfers of infA, rps7, and rpl32 were detected to the nucleus, whereas rps16 and rpl23 were substituted by nuclear-encoded homologs. The plastid rpl32 was integrated into the nuclear-encoded SODcp gene. Our findings suggested that the transferred rpl32 had undergone subfunctionalization by duplication rather than alternative splicing. The H. ascyron plastome rearrangements involved seven inversions, at least three inverted repeat (IR) boundary shifts, which generated gene relocations and duplications. Accelerated substitution rates of plastid genes were observed in the H. ascyron plastome compared with that of C. cochinchinense plastid genes. The higher substitution rates in the accD and clpP were correlated with structural change, including a large insertion of amino acids and losses of two introns, respectively. In addition, we found evidence of positive selection of the clpP, matK, and rps3 genes in the three branches related to H. ascyron. In particular, the matK gene was repeatedly under selection within the family Hypericaceae. Selective pressure in the H. ascyron matK gene was associated with the loss of trnK-UUU and relocation into the IR region.ConclusionsThe Hypericum ascyron plastome sequence provides valuable information for improving the understanding of plastome evolution among the clusioid of the Malpighiales. Evidence for intracellular gene transfer from the plastid to the nucleus was detected in the nuclear transcriptome, providing insight into the evolutionary fate of plastid genes in Hypericaceae.

Complete chloroplast genome sequences of three aroideae species (Araceae): lights into selective pressure, marker development and phylogenetic relationships

BackgroundColocasia gigantea, Caladium bicolor and Xanthosoma sagittifolium are three worldwide famous ornamental and/or vegetable plants in the Araceae family, these species in the subfamily Aroideae are phylogenetically perplexing due to shared interspecific morphological traits and variation.ResultThis study, for the first time ever, assembled and analyzed complete chloroplast genomes of C. gigantea, C. bicolor and X. sagittifolium with genome sizes of 165,906 bp, 153,149 bp and 165,169 bp in length, respectively. The genomes were composed of conserved quadripartite circular structures with a total of 131 annotated genes, including 8 rRNA, 37 tRNA and 86 protein-coding genes. A comparison within Aroideae showed seven protein-coding genes (accD, ndhF, ndhK, rbcL, rpoC1, rpoC2 and matK) linked to environmental adaptation. Phylogenetic analysis confirmed a close relationship of C. gigantea with C. esculenta and S. colocasiifolia, and the C. bicolor with X. sagittifolium. Furthermore, three DNA barcodes (atpH-atpI + psaC-ndhE, atpH-atpI + trnS-trnG, atpH-atpI + psaC-ndhE + trnS-trnG) harbored highly variable regions to distinguish species in Aroideae subfamily.ConclusionThese results would be beneficial for species identification, phylogenetic relationship, genetic diversity, and potential of germplasm resources in Aroideae.

Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics.

Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one of the most extraordinarily diverse clades among angiosperms. Papilionoids are a major source of food and forage, are ecologically successful in all major biomes, and display dramatic variation in both floral architecture and plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding of relationships among the major groups of Papilionoideae, yet the backbone of the subfamily phylogeny remains unresolved. In this study, we sequenced and assembled 39 new plastomes that are covering key genera representing the morphological diversity in the subfamily. From 244 total taxa, we produced eight datasets for maximum likelihood (ML) analyses based on entire plastomes and/or concatenated sequences of 77 protein-coding sequences (CDS) and two datasets for multispecies coalescent (MSC) analyses based on individual gene trees. We additionally produced a combined nucleotide dataset comprising CDS plus matK gene sequences only, in which most papilionoid genera were sampled. A ML tree based on the entire plastome maximally supported all of the deep and most recent divergences of papilionoids (223 out of 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, and Amburaneae), Cladrastis, Andira, and Exostyleae clades formed a grade to the remainder of the Papilionoideae, concordant with nine ML and two MSC trees. Phylogenetic relationships among the remaining five papilionoid lineages (Vataireoid, Dermatophyllum, Genistoid s.l., Dalbergioid s.l., and Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because of insufficient support and/or conflicting relationships among trees. Our study fully resolved most of the deep nodes of Papilionoideae, however, some relationships require further exploration. More genome-scale data and rigorous analyses are needed to disentangle phylogenetic relationships among the five remaining lineages.

Analysis of the Complete Plastomes of 31 Species of Hoya Group: Insights Into Their Comparative Genomics and Phylogenetic Relationships.

Hoya is a genus in Apocynaceae-Asclepiadoideae, known for its showy wax flowers, making it a popular ornamental plant. However, phylogenetic relationships among most Hoya species are not yet fully resolved. In this study, we sequenced 31 plastomes of Hoya group species using genome skimming data and carried out multiple analyses to understand genome variation to resolve the phylogenetic positions of some newly sequenced Chinese endemic species. We also screened possible hotspots, trnT-trnL-trnF, psba-trnH, and trnG-UCC, ndhF, ycf1, matK, rps16, and accD genes that could be used as molecular markers for DNA barcoding and species identification. Using maximum likelihood (ML) and Bayesian Inference (BI), a species phylogeny was constructed. The newly assembled plastomes genomes showed the quasi-tripartite structure characteristic for Hoya and Dischidia with a reduced small single copy (SSC) and extremely enlarged inverted repeats (IR). The lengths ranged from 175,404 bp in Hoya lacunosa to 179,069 bp in H. ariadna. The large single copy (LSC) regions ranged from 80,795 bp (Hoya liangii) to 92,072 bp (Hoya_sp2_ZCF6006). The massively expanded IR regions were relatively conserved in length, with the small single-copy region reduced to a single gene, ndhF. We identified 235 long dispersed repeats (LDRs) and ten highly divergent hotspots in the 31 Hoya plastomes, which can be used as DNA barcodes for species identification. The phylogeny supports Clemensiella as a distinct genus. Hoya ignorata is resolved as a relative to Clade VI species. This study discloses the advantages of using Plastome genome data to study phylogenetic relationships.

Astragalus sect. Elvendia (Fabaceae), a new tragacanthic section recorded from Mt. Alvand, a center of endemism in W Iran

A new section of Astragalus from Mt. Alvand, W Iran, was recognized namely Astragalus sect. Elvendia Bagheri & Maassoumi, sect. nov., which is described here based on A. leucargyreus Bornm. A full description and diagnosis of the new section are given and taxonomic relationships of the section and its allied taxa are discussed. Molecular phylogenetic data obtained from the nuclear ribosomal DNA internal transcribed spacer (ITS) region as well as plastid ycf1 and matK genes strongly support that the species of the new section is separated from sections Hymenostegis and Adiaspastus, where A. leucargyreus was placed before, and forms a distinct clade. In addition, we discuss the floristic, endemism, and conservation status of the Mt. Alvand region (type locality of the new section). Supplemental data for this article is available online at https://doi.org/10.1080/11263504.2022.2036846 .

Uncovering the first complete plastome genomics, comparative analyses, and phylogenetic dispositions of endemic medicinal plant Ziziphus hajarensis (Rhamnaceae)

BackgroundZiziphus hajarensis is an endemic plant species well-distributed in the Western Hajar mountains of Oman. Despite its potential medicinal uses, little is known regarding its genomic architecture, phylogenetic position, or evolution. Here we sequenced and analyzed the entire chloroplast (cp) genome of Z. hajarensis to understand its genetic organization, structure, and phylogenomic disposition among Rhamnaceae species.ResultsThe results revealed the genome of Z. hajarensis cp comprised 162,162 bp and exhibited a typical quadripartite structure, with a large single copy (LSC) region of 895,67 bp, a small single copy (SSC) region of 19,597 bp and an inverted repeat (IR) regions of 26,499 bp. In addition, the cp genome of Z. hajarensis comprises 126 genes, including 82 protein-coding genes, eight rRNA genes, and 36 tRNA genes. Furthermore, the analysis revealed 208 microsatellites, 96.6% of which were mononucleotides. Similarly, a total of 140 repeats were identified, including 11 palindromic, 24 forward, 14 reverse, and 104 tandem repeats. The whole cp genome comparison of Z. hajarensis and nine other species from family Rhamnaceae showed an overall high degree of sequence similarity, with divergence among some intergenic spacers. Comparative phylogenetic analysis based on the complete cp genome, 66 shared genes and matK gene revealed that Z. hajarensis shares a clade with Z. jujuba and that the family Rhamnaceae is the closest family to Barbeyaceae and Elaeagnaceae.ConclusionAll the genome features such as genome size, GC content, genome organization and gene order were highly conserved compared to the other related genomes. The whole cp genome of Z. hajarensis gives fascinating insights and valuable data that may be used to identify related species and reconstruct the phylogeny of the species.

DNA barcoding analysis and phylogenetic relationships of Indian wild coffee species

Wild coffee species are the reservoirs of genetic diversity and could play a critical role in the genetic improvement of coffee. However, the conservation and genetic assessment of wild coffee species has been largely neglected. In the present study, DNA barcoding approaches were employed to assess the phylogenetic relationships between five indigenous wild coffee species from India and compared with two cultivated, and four wild coffee species of African origin. The efficacy of three barcoding loci namely matK,rbcL, and trnL-trnF was investigated using PCR amplification and sequence characterization. The intergenic spacer trnL-trnF is the highly polymorphic loci followed by matK and rbcL chloroplast gene. Among the three barcoding loci, the matK locus has the maximum number of parsimony informative sites, whereas the trnL-trnF locus contains maximum singleton variable sites. Although all the three loci contain a few unique fixed nucleotides (UFNs), no individual barcode locus has the critical nucleotide sequence tags for all the five Indian wild coffee species that help in species discrimination. However, the multilocus combinations are efficient in discriminating the species due to the presence of SNPs and specific sequence tags. The phylogenetic tree constructed using the maximum likelihood analysis of the combined barcoding loci separated all the Indian wild coffee species from African wild coffee species compared to phylogeny inferred using individual barcoding loci. Our study supports the utility of DNA barcoding as a useful tool for coffee species identification, which can be used for conservation purposes.

Lamium cappadocicum, a new species from Central Anatolia, Turkey: evidence from molecular and morphological studies

Lamium is a taxonomically convoluted genus of about 34 species. Within Lamium, the L. garganicum species complex is particularly challenging. Here, based on morphological and molecular studies, Lamium cappadocicum Celep & Karaer sp. nova (Lamiaceae) is separated from L. garganicum and L. bilgilii and described as a new species, and L. garganicum subsp. rectum (= L. garganicum subsp. pulchrum) is resurrected. The new species is only known from the Hasan Mountain (Aksaray) in Central Anatolia, Turkey. Lamium cappadocicum is closely related to L. garganicum subsp. rectum but differs from it by its mat-forming caespitose habit, reniform (rarely ovate in upper part) and deeply cordate leaves with dense white villous hairs, deeply crenate and undulate leaf margins, subglabrous to sparsely pilose stems, and densely white villous calyces. Lamium cappadocicum also differs from L. bilgilii by its matforming caespitose habit, smaller corollas (25-33 mm versus 40-52 mm in L. bilgilii), subglabrous to sparsely pilose stems and smaller leaves (3-20 (-30) mm long × 3-20 (-30) mm wide, versus 5-45 mm long × 5-45 mm wide in L. bilgilii). Molecular phylogenetic analyses from nuclear ribosomal (nrITS) and chloroplast (matK, rpoA and psbA-trnH) gene regions support the morphological results. The IUCN conservation status, ecology, phenology, etymology, and notes on biogeography of the new species are also given and diagnostic features are discussed.

Phylogenetic Relationship Between the Bamboo Species of Tribe Bambuseae and Arundinarieae Based on matK Gene Sequences

Phylogenetic Relationship Between the Bamboo Species of Tribe Bambuseae and Arundinarieae Based on matK Gene Sequences

Morphological and Molecular Characterization of Some Egyptian Six-Rowed Barley (Hordeum vulgare L.).

Barley production is essential in Egypt. In the present study, 15 different six-rowed Egyptian barley cultivars were studied. To differentiate between the different cultivars under study in terms of morphological characteristics and ISSR, molecular characterization reactions were carried out. Moreover, four cultivars (Giza 123, Giza 126, Giza 136, and Giza 138) were selected for further studies using scanning electron microscopy (SEM). Computational analysis of the DNA barcoding sequences of the two plastid markers rbcL and matK was executed, and the results were deposited in the NCBI database. The morphological traits showed low statistical significance among the different cultivars under study via the data collected from two seasons, suggesting that the mean field performance of these Egyptian cultivars may be equal under these conditions. The results showed that the phylogenetic tree was divided into four groups, one of which contained the most closely related genotypes in the genetic distance, including Giza 124, Giza 130, Giza 138, Giza 136, and Giza 137, which converge in the indicative uses of farmers. The seed coat of the studied cultivars was “rugose”. The elevation folding of the rugose pattern ranged from 11 ± 1.73 µm (Giza 126) to 14.67 ± 2.43 µm (Giza 123), suggesting variation in seed quality and its uses in feed and the food industry. According to the similarity matrix of ISSR analysis, the highest similarity value (93%) was recorded between Giza 133 and Giza 132, as well as between Giza 2000 and Giza 126. On the other hand, the lowest similarity value (80%) was recorded between Giza 130 and (Giza 133 and Giza 132), indicating that these cultivars were distantly related. Polymorphism information content (PIC) ranged from 0.26 for the primer ISSR UBC 835 to 0.37 for the primers ISSR UBC 814 and ISSR UBC 840. The current study showed that the matK gene is more mutable than the rbcL gene among the tested cultivars.