scholarly journals Molecular Divergence and Species Delimitation of the Cultivated Oyster Mushrooms: Integration of IGS1 and ITS

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Farhat Ahmadi Avin ◽  
Subha Bhassu ◽  
Yee Shin Tan ◽  
Pedram Shahbazi ◽  
Sabaratnam Vikineswary
Keyword(s):  
Phylogenetic Tree ◽  
Dna Barcode ◽  
Evolutionary Process ◽  
Species Group ◽  
Its Sequences ◽  
Species Differentiation ◽  
Separate Species ◽  
Variable Regions ◽  
Sufficient Variation

Identification of edible mushrooms particularlyPleurotusgenus has been restricted due to various obstacles. The present study attempted to use the combination of two variable regions of IGS1 and ITS for classifying the economically cultivatedPleurotusspecies. Integration of the two regions proved a high ability that not only could clearly distinguish the species but also served sufficient intraspecies variation. Phylogenetic tree (IGS1 + ITS) showed seven distinct clades, each clade belonging to a separate species group. Moreover, the species differentiation was tested by AMOVA and the results were reconfirmed by presenting appropriate amounts of divergence (91.82% among and 8.18% within the species). In spite of achieving a proper classification of species by combination of IGS1 and ITS sequences, the phylogenetic tree showed the misclassification of the species ofP. nebrodensisandP. eryngiivar.ferulaewith other strains ofP. eryngii. However, the constructed median joining (MJ) network could not only differentiate between these species but also offer a profound perception of the species’ evolutionary process. Eventually, due to the sufficient variation among and within species, distinct sequences, simple amplification, and location between ideal conserved ribosomal genes, the integration of IGS1 and ITS sequences is recommended as a desirable DNA barcode.

Morphological and molecular delineation of a new species in the Ceratina dupla species-group (Hymenoptera: Apidae: Xylocopinae) of eastern North America

Zootaxa ◽  
2011 ◽  
Vol 2873 (1) ◽  
pp. 35 ◽  
Author(s):  
SANDRA M. REHAN ◽  
CORY S. SHEFFIELD
Keyword(s):  
New Species ◽  
North America ◽  
North American ◽  
Dna Barcode ◽  
Species Group ◽  
North American Species ◽  
Eastern North America ◽  
Separate Species ◽  
Carpenter Bees ◽  
A New Species

DNA barcoding is used to verify characters to morphologically differentiate genetically distinct species of eastern North American small carpenter bees, Ceratina. Here we reveal that the common eastern North American species, Ceratina dupla s. l., is actually three separate species based on fixed differences in DNA barcode sequences and morphological characters. This study adds a new species, C. mikmaqi Rehan & Sheffield, to the Ceratina dupla species-group of eastern North America, and raises another form, C. floridana formerly C. dupla floridana, to full species. Temporal niche partitioning between C. dupla and C. mikmaqi and geographic isolation of C. floridana further support the division of the C. dupla s. l. group into three species. A diagnosis and description of the new species are provided, as is a key for eastern North American species of Ceratina.

scholarly journals Discovery of Eubasilissa signata Wiggins, 1998 (Trichoptera, Phryganeidae) from Taiwan

Zoosymposia ◽  
2019 ◽  
Vol 14 (1) ◽  
pp. 103-107
Author(s):  
RYOICHI B. KURANISHI ◽  
LI-PENG HSU
Keyword(s):  
Dna Barcode ◽  
Species Group ◽  
Coi Gene ◽  
Single Female ◽  
Separate Species ◽  
Other Information ◽  
Group A ◽  
Morphological Differences ◽  
Male Morphology ◽  
First Time

The phryganeid caddisfly Eubasilissa signata Wiggins, 1998 was originally described based on a single female specimen from Korea, and no other information on the species was available. Here we record an additional five male and five female specimens of E. signata from Taiwan and describe the male morphology for the first time. Based on morphological differences with other Eubasilissa species, E. signata should be regarded as a separate species and also not a member of the “tibetana” species group. A 658-bp fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene of the new specimens of E. signata is provided as a DNA barcode.

scholarly journals DNA barcoding of different Triticum species

2019 ◽  
Vol 43 (1) ◽  
Author(s):  
Samira A. Osman ◽  
Walaa A. Ramadan
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequence ◽  
Phylogenetic Tree ◽  
Dna Barcoding ◽  
Critical Role ◽  
Dna Barcode ◽  
Species Group ◽  
Amino Acid Sequences ◽  
Pairwise Distance ◽  
Multiple Sequence

Abstract Background The genus Triticum L. includes diploid, tetraploid, and hexaploid species. DNA barcoding is a new method to identify plant taxa by using short sequences of DNA and within a short time. In this investigation, we determined a phylogenetic analysis of 20 different Triticum species by partial chloroplast Maturase encoding gene (matK). Materials and methods Twenty accessions of different Triticum species diploid, tetraploid, and hexaploid were obtained from different countries. Genomic DNA was isolated from young leaves of studied samples and then used as a template for PCR reaction. PCR products were checked by electrophoresis, purified, sequenced, and submitted in the GenBank nucleotide sequence database, the nucleotide sequence was translated into an amino acid sequence. The nucleotide and amino acid sequences were aligned with Clustal W multiple sequence alignment programs to obtain the phylogenetic tree depending on two statistical data analysis such as bootstrapping and pairwise distance from both nucleotide and amino acid sequences. Results The phylogenetic tree obtained from both nucleotide and amino acid sequences divided the 20 Triticum species into two groups, A and B. Group A represented the diploid Triticum species. Group B was divided into two subgroup, I and II. Subgroup I represented the hexaploid Triticum species and subgroup II represented the tetraploid species. Conclusion The matK gene sequence has a critical role in discriminating the closely related Triticum species. So these sequences could be used as a DNA barcode for detecting the evolutionary history of Triticum species.

TAXONOMY OF ENTEROCOCCI BY COMPUTER ANALYSIS

1966 ◽  
Vol 12 (2) ◽  
pp. 353-362 ◽  
Author(s):  
H. Raj ◽  
R. R. Colwell
Keyword(s):  
Computer Analysis ◽  
Numerical Taxonomy ◽  
Species Group ◽  
Separate Species ◽  
Homogeneous Cluster ◽  
Pure Cultures ◽  
Electronic Computers ◽  
Taxonomic Groups ◽  
Formal Recognition

A total of 48 pure cultures of Streptococcus (including 12 ATCC strains) belonging to the fecal, pyogenic, and viridans groups was studied in an effort to derive a numerical taxonomy of the enterococci based on Adansonian principles. Each of these cultures was subjected to a variety of tests. The data so obtained was encoded and analyzed by electronic computers, ft showed two major taxonomic groups: a large homogeneous cluster of all enterococcal strains tested and a discrete cluster of streptococci belonging to the pyogenic and viridans groups, showing the least cross relationships with all of the enterococcal strains including S. bovis. The large enterococcus group comprised S. faecalis, unclassified enterococci, S. bovis, S. durans, and S. faecium within the major group. The S. faecalis cluster of strains showed three discernible subgroupings of S. faecalis (typical), var. liquefaciens, and var. zymogenes. The "unclassified" types formed a rather homogeneous cluster which may warrant formal recognition as a separate species. S. bovis was most closely related to the unclassified species group. The results of analysis support the proposed determinative classification of enterococci (16).

scholarly journals Validation of Automated Chromosome Recovery in the Reconstruction of Ancestral Gene Order

Algorithms ◽  
2021 ◽  
Vol 14 (6) ◽  
pp. 160
Author(s):  
Qiaoji Xu ◽  
Lingling Jin ◽  
James H. Leebens-Mack ◽  
David Sankoff
Keyword(s):  
Phylogenetic Tree ◽  
Gene Order ◽  
Evolutionary Process ◽  
Gene Content ◽  
Ancestral Genome ◽  
Maximum Weight ◽  
Ancestral Gene ◽  
Maximum Weight Matching

The RACCROCHE pipeline reconstructs ancestral gene orders and chromosomal contents of the ancestral genomes at all internal vertices of a phylogenetic tree. The strategy is to accumulate a very large number of generalized adjacencies, phylogenetically justified for each ancestor, to produce long ancestral contigs through maximum weight matching. It constructs chromosomes by counting the frequencies of ancestral contig co-occurrences on the extant genomes, clustering these for each ancestor and ordering them. The main objective of this paper is to closely simulate the evolutionary process giving rise to the gene content and order of a set of extant genomes (six distantly related monocots), and to assess to what extent an updated version of RACCROCHE can recover the artificial ancestral genome at the root of the phylogenetic tree relating to the simulated genomes.

Discovery of New Genera Challenges the Subtribal Classification of Tok-Tok Beetles (Coleoptera: Tenebrionidae: Sepidiini)

2021 ◽  
Vol 5 (2) ◽  
Author(s):  
Olivia M Gearner ◽  
Marcin J Kamiński ◽  
Kojun Kanda ◽  
Kali Swichtenberg ◽  
Aaron D Smith
Keyword(s):  
Dna Sequences ◽  
Species Group ◽  
Phylogenetic Placement ◽  
Darkling Beetles ◽  
Species Groups ◽  
Taxonomic Groups ◽  
Inference Methods ◽  
A New Species ◽  
Coleoptera Tenebrionidae

Abstract Sepidiini is a speciose tribe of desert-inhabiting darkling beetles, which contains a number of poorly defined taxonomic groups and is in need of revision at all taxonomic levels. In this study, two previously unrecognized lineages were discovered, based on morphological traits, among the extremely speciose genera Psammodes Kirby, 1819 (164 species and subspecies) and Ocnodes Fåhraeus, 1870 (144 species and subspecies), namely the Psammodes spinosus species-group and Ocnodes humeralis species-group. In order to test their phylogenetic placement, a phylogeny of the tribe was reconstructed based on analyses of DNA sequences from six nonoverlapping genetic loci (CAD, wg, COI JP, COI BC, COII, and 28S) using Bayesian and maximum likelihood inference methods. The aforementioned, morphologically defined, species-groups were recovered as distinct and well-supported lineages within Molurina + Phanerotomeina and are interpreted as independent genera, respectively, Tibiocnodes Gearner & Kamiński gen. nov. and Tuberocnodes Gearner & Kamiński gen. nov. A new species, Tuberocnodes synhimboides Gearner & Kamiński sp. nov., is also described. Furthermore, as the recovered phylogenetic placement of Tibiocnodes and Tuberocnodes undermines the monophyly of Molurina and Phanerotomeina, an analysis of the available diagnostic characters for those subtribes is also performed. As a consequence, Phanerotomeina is considered as a synonym of the newly redefined Molurina sens. nov. Finally, spectrograms of vibrations produced by substrate tapping of two Molurina species, Toktokkus vialis (Burchell, 1822) and T. synhimboides, are presented.

scholarly journals Application of internal transcribed spacer (ITS) sequences for identifying Anoectochilus setaceus Blume in Thanh Hoa, Vietnam

2020 ◽  
Vol 181 (2) ◽  
pp. 108-116
Author(s):  
B. B. Thinh ◽  
L. D. Chac ◽  
L. T.M. Thu
Keyword(s):  
Internal Transcribed Spacer ◽  
Molecular Taxonomy ◽  
Gene Segment ◽  
Dna Barcode ◽  
Its Sequences ◽  
Gene Region ◽  
Its Gene ◽  
Ctab Method ◽  
Young Leaves ◽  
Total Dna

Background. The term “DNA barcode” is used extensively in molecular taxonomy. Basically, this technique is based on the use of a DNA sequence (about 400–800 bp) as a standard to identify and determine the species relation of organisms quickly and accurately. Therefore, DNA barcodes not only help taxonomists in classifying and identifying species, but also improve their ability to control, understand and utilize biodiversity. In this study, the authors conducted identification of samples of Anoectochilus setaceus Blume collected in Thanh Hoa through the isolated sequence of ITS gene regions.Materials and methods. Total DNA was extracted from young leaves of A. setaceus samples using CTAB method. The ITS gene segment was amplified by PCR and sequenced. This genetic sequence was analyzed, compared and used to establish a phylogenetic tree using BioEdit, BLAST and DNASTAR programs.Results and conclusion. We isolated 4 sequences of the ITS gene region in 4 A. setaceus samples collected at Xuan Lien and Pu Luong of Thanh Hoa province; the ITS gene region was 667 nucleotide long. The findings identified the samples as the same species and showed 99% similarity to the ITS gene sequence of A. roxburghii (Wall.) Lindl. published in GenBank, GQ328774. This study also demonstrates that the method employing internal transcribed spacer (ITS) sequences is an effective tool to identify A. setaceus taxa.

scholarly journals A Comparative Study of Plasma Proteins from Twenty-Nine Species of Albatrosses And Petrels (Order Procellariiformes)

2021 ◽  
Author(s):  
◽  
Peter C Harper
Keyword(s):  
Plasma Proteins ◽  
Species Group ◽  
Reference Points ◽  
Evolutionary Significance ◽  
Group Level ◽  
Family Level ◽  
Phylogenetic Conservatism ◽  
History Of ◽  
Biochemical Research

<p>The plasma proteins of 29 species of albatrosses and petrels were electrophoretically separated in acrylamide gels to clarify relationships at the species-group to family-group levels. Little in the resulting data from 472 birds seriously contests the present classification of the Procellariiformes; much of the biochemical evidence supports, confirms, and clarifies the proposals of conventional taxonomic methodology. The biochemical data give fresh insights into the interrelationships of procellariiform taxa, and highlight intriguing new problems. Sex, season, age, and other sources of non-genetic protein variation are insignificant for taxonomic purposes. Proteins of comparable value include the transferrins, some α and β globulins, albumins, prealbumins, and non-specific esterases. Genetic variations in the mobility of these proteins are useful at the genus-group level and below. Other proteins are monomorphic at genus and family level, and three are monomorphic in both number and mobility throughout the Procellariiformes; these are useful reference points for calibrating samples on different gels. One conspicuous α protein is absent in the Hydrobatidae but present in all other families; the implications of this are discussed. Polymorphic proteins at the population or species level were not detected; this conspicuous phylogenetic conservatism is discussed with regard to its possible evolutionary significance. Following a summary of the protein data; three categories of, defined probability statements, based on the biochemical and other evidence, allow speculative comment on the evolutionary relationships and history of the taxa within the Procellariiformes. The value of further biochemical research into the marine birds is emphasised.</p>

scholarly journals Berlian, SOJ A3 and Jawa Local Rice Varieties Phylogenetically Distinct From Oryza sativa Indica and Oryza sativa Japonica

el–Hayah ◽  
2019 ◽  
Vol 6 (4) ◽  
pp. 112-125
Author(s):  
Yudrik Lathif ◽  
Riri Wiyanti Retnaningtyas ◽  
Dwi Listyorini ◽  
Suharti Suharti
Keyword(s):  
Oryza Sativa ◽  
Phylogenetic Tree ◽  
Dna Barcode ◽  
Rbcl Gene ◽  
Tree Reconstruction ◽  
Rice Varieties ◽  
Local Varieties ◽  
Precise Position ◽  
Total Dna ◽  
Taxonomical Position

The genetic resources identification of Indonesian local rice varieties is a crucial work should be done to conserve our native germplasm. This research aimed to know the taxonomical position of East Java local rice varieties including Jawa (JW), Berlian (BR), and SOJ A3 (SJ) using DNA barcode based on rbcL gene. Total DNA of each sample was isolated from leaves. A pair of forward 5'-ATG TCA CCA CAA ACA SJA AC-3' and reverse 5'-TCG GTA CCT GCA GTA GC-3' primers were used to amplify fragments of rbcL gene resulting in 751bp, 755bp, and 754bp fragments from BR, SJ, and JW varieties, respectively. Phylogenetic tree reconstruction revealed that our three local varieties were forming a cluster separated from the widely cultivated subspecies Oryza sativa Indica and Oryza sativa Japonica. However, further studies are necessary to reveal a more precise position of the local varieties in a phylogenetic tree on the species level.

CONTRIBUTIONS TO THE KNOWLEDGE OF CAMBODIAN CYPERACEAE

2019 ◽  
Vol 76 (2) ◽  
pp. 197-220
Author(s):  
K. Tremetsberger ◽  
S. Hameister ◽  
D. A. Simpson ◽  
K.-G. Bernhardt
Keyword(s):  
Phylogenetic Analysis ◽  
Southeast Asia ◽  
Phylogenetic Tree ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Sequences ◽  
Cryptic Variation ◽  
The Family ◽  
History Of ◽  
Rapid Radiations

To date, there are very few sequence data for Cyperaceae from mainland Southeast Asia. The aim of the present study was to contribute nuclear ribosomal internal transcribed spacer (ITS) sequences of selected species of Cambodian Cyperaceae to the overall phylogeny of the family. We generated ITS sequences of 38 accessions representing 26 species from Cambodia and used these sequences for phylogenetic analysis together with similar sequences from the National Center for Biotechnology Information GenBank. Our results corroborate recent phylogenetic work in the family and largely confirm established tribal relationships. The backbone of the phylogenetic tree of species-rich genera that have undergone rapid radiations is often weakly resolved (e.g. in Fimbristylis and in the C4 clade of Cyperus). Cryptic variation was revealed in the taxonomically difficult group of Fimbristylis dichotoma, with samples of this taxon appearing in two distinct clades within Fimbristylis. Further addition of geographically spread accessions of taxa will improve our understanding of the complex biogeographical history of the genera in the family. Eleocharis koyamae Tremetsb. & D.A.Simpson is proposed as a new name for E. macrorrhiza T. Koyama.

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