Molecular identification and phylogenetics of local pearl millet cultivars using internal-transcribed spacers of nuclear ribosomal DNA

2021 ◽  
pp. 1-8
Author(s):  
Zainab M. Almutairi
Keyword(s):  
Pearl Millet ◽  
Phylogenetic Trees ◽  
Secondary Structures ◽  
Its2 Sequence ◽  
Internal Transcribed Spacers ◽  
The Other ◽  
Nuclear Ribosomal Dna ◽  
Its2 Region ◽  
Local Cultivars ◽  
Pearl Millet Cultivars

Abstract Local cultivars of pearl millet in Saudi Arabia are known to tolerate extreme heat and drought stress. In the current study, the sequences of internal-transcribed spacers (ITSs) of six pearl millet cultivars were sequenced and analysed to investigate the genetic diversity among the local cultivars. The nucleotide polymorphism, secondary structures and phylogenetics were analysed for ITS sequences of the six local cultivars. The obtained sequences were 772–774 base pairs (bp) in length, including complete sequences of the ITS1–5.8S–ITS2 region and partial sequences of 18S and 26S rRNA. The nucleotide diversity among cultivars was higher in ITS2 sequences than ITS1 sequences. The ITS2 had four variable nucleotide sites in three native cultivars, whereas the ITS1 contained one base insertion. The secondary structures of the ITS1 and 5.8S region were highly conserved among the six cultivars and contained some motifs that are conserved across Viridiplantae. However, the ITS2 secondary structure for the two native cultivars, Sayah and Jazan, was distinct from the other cultivars, which confirms the applicability of the ITS2 sequence in distinguishing between genetically close taxa. Additionally, the phylogenetic analysis of the six investigated cultivars and 31 pearl millet accessions from the NCBI database showed close relationships between the local accessions and NCBI accessions from India and France. However, the local cultivar Sayah appeared to be distinct from the other cultivars in the phylogenetic trees. This study provides insights into the polymorphism within local pearl millet cultivars which is important for the identification and conservation of these cultivars.

Parasite hybridization in African Macrogyrodactylus spp. (Monogenea, Platyhelminthes) signals historical host distribution

Parasitology ◽  
2010 ◽  
Vol 137 (10) ◽  
pp. 1585-1595 ◽  
Author(s):  
MAXWELL BARSON ◽  
IVA PŘIKRYLOVÁ ◽  
MAARTEN P. M. VANHOVE ◽  
TINE HUYSE
Keyword(s):  
Clarias Gariepinus ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Hybrid Origin ◽  
Its2 Region ◽  
Rrna Gene ◽  
Intermediate Form ◽  
Its1 Sequence ◽  
Haptoral Sclerite ◽  
Partial 18S

SUMMARYMacrogyrodactylus spp. from the gills of Clarias gariepinus in Zimbabwe and Kenya, and C. anguillaris in Senegal were identified using haptoral sclerite morphology and by sequencing the nuclear ribosomal DNA internal transcribed spacers (ITS) 1 and 2, partial 18S and the complete 5·8S rRNA gene. A molecular phylogeny was constructed using all sequenced Macrogyrodactylus species to date. Based on morphology, Macrogyrodactylus congolensis, M. heterobranchii, M. clarii, and M. karibae were identified, with one specimen from Zimbabwe displaying morphological features that were intermediate between M. heterobranchii and M. clarii. In the intermediate form, the partial 18S and ITS1 sequence was identical to that of M. clarii while the remaining ITS1 and complete ITS2 region was almost identical to M. heterobranchii as was the partial cox1 fragment, thus strongly suggesting a hybrid origin. At present, the catfish host of M. heterobranchii and M. clarii do not co-occur in southern Zimbabwe; this hybridization event is therefore proof of historical sympatry of both fish species.

scholarly journals Multigene-Based Analyses of the Phylogenetic Evolution of Oligotrich Ciliates, with Consideration of the Internal Transcribed Spacer 2 Secondary Structure of Three Systematically Ambiguous Genera

2013 ◽  
Vol 12 (3) ◽  
pp. 430-437 ◽  
Author(s):  
Jiamei Li ◽  
Weiwei Liu ◽  
Shan Gao ◽  
Alan Warren ◽  
Weibo Song
Keyword(s):  
Secondary Structure ◽  
Phylogenetic Trees ◽  
Internal Transcribed Spacers ◽  
Morphological Data ◽  
Its2 Region ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Content Type ◽  
Ssu Rrna Gene ◽  
The Family

ABSTRACT Oligotrichs are ciliates of great abundance, but their molecular systematics are rarely studied. In this study, nine species representing three genera ( Strombidium , Novistrombidium , and Omegastrombidium ) of marine oligotrich ciliates were collected from coastal waters of China. The small subunit (SSU) rRNA gene of two species and the internal transcribed spacers and 5.8S region (ITS1-5.8S-ITS2) for all nine species were sequenced for the first time. Phylogenetic trees using both the SSU rRNA gene and ITS1-5.8S-ITS2 region sequences were generated. In addition, the secondary structures of ITS2 RNA transcripts of 11 taxa representing four genera ( Novistrombidium , Strombidium , Omegastrombidium , and Laboea ) were investigated. The phylogenetic analyses show that (i) the family Strombidiidae is polyphyletic, (ii) the genus Novistrombidium is probably paraphyletic, containing at least two subclades, which is consistent with recent cladistic analyses based on morphological data, and (iii) the tail-less genus Laboea is separate from other genera of Strombidiidae, clustering instead with the tontoniids. Comparisons of the secondary structure of ITS2 regions also show that Laboea is clearly different from other strombidiids. These findings cast doubt on the monophyly of the family Strombidiidae.

MOLECULAR PHYLOGENY AND CHARACTER EVOLUTION OF DIDYMOCARPUS (GESNERIACEAE) IN THAILAND

2006 ◽  
Vol 63 (2-3) ◽  
pp. 231-251 ◽  
Author(s):  
P. PALEE ◽  
J. DENDUANGBORIPANT ◽  
V. ANUSARNSUNTHORN ◽  
M. MÖLLER
Keyword(s):  
Molecular Phylogeny ◽  
Geographical Origin ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Internal Transcribed Spacers ◽  
The Other ◽  
Nuclear Ribosomal Dna ◽  
Wide Sense ◽  
Corolla Colour ◽  
Pigment Glands

Until recently the genus Didymocarpus Wall. (Gesneriaceae) was used in an unwarrantably wide sense and included more than 180 species. It has now been remodelled and restricted to around 70 species. Of these, 18 species and one variety are known to occur in Thailand. To clarify the relationships among Thai species of Didymocarpus we sequenced the internal transcribed spacers (ITS) of nuclear ribosomal DNA (nrDNA) from a sample of 23 taxa, including 15 from Thailand, four from China, three from Malaysia and one from Bhutan. Seventeen morphological characters were coded for all 23 taxa and optimized onto a retention index (RI) reweighted maximum parsimony (MP) tree. The phylogenetic analyses suggested that Didymocarpus taxa formed a strongly supported monophyletic clade, with several supported subclades. The combination of molecular phylogeny and optimization of morphological characters suggests the presence of three distinct groups: the first, corresponding to Didymocarpus sect. Elati Ridl., includes plants with tall stems, yellow or white flowers and one-celled conoid or two-celled headed pigment glands; the other two groups, which represent Didymocarpus sect. Didymocarpus, both contain plants with dwarfed stems and violet or purple flowers, but are distinguished by the presence of both four-celled conoid or onecelled globose glands in one, and the absence in the other. Optimization of geographical locality onto the phylogeny led us to propose the hypothesis that, based on this sample, the geographical origin of Didymocarpus is the Malay Peninsula, and the ancestral corolla colour is white/yellow. Subsequent dispersal northward through southern and northern Thailand to China and Bhutan was accompanied by the evolution of a purple/violet corolla colour.

scholarly journals (269) Taxonomic Relationship of Korean Native Aster, Based on Internal Transcribed Spacer (ITS) Sequences of Nuclear Ribosomal DNA

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1017A-1017
Author(s):  
Su-Young Hong ◽  
Kwang-Soo Cho ◽  
Ki-Oug Yoo ◽  
Jong-Taek Suh ◽  
Dong-Lim Yoo
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Its Region ◽  
Sister Group ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Position ◽  
Its2 Region ◽  
Base Pairs ◽  
Total Length

There are 25 species of aster in Korea. There is a controversy about the taxonomical classification of Aster. The genus Aster was classified into four genera, Aster, Gymnaster, Kalimeris, and Heteropappus, by morphological characters. In order to clarify the phylogenetic position of aster, the nucleotide sequence of the nuclear ribosomal DNA internal transcribed spacer (ITS) region was compared among 11 taxa in Korean native aster. The size of ITS1 and ITS2 ranged from 283 to 286 bp and from 251 to 257 bp, respectively. The size of 5.8S region was 164 bp in 11 taxa. The total length of ITS1, 5.8S and ITS2, A. tripolium was shown to be the shortest length, 701 bp; and A. scaber was shown to be the longest length, 706 bp. The G+C content of ITS1 ranged from 47.9% to 51.2% and ITS2 ranged from 52.2% to 55.1%. The range of each taxon was narrow. The total length of the character matrix was 708 characters. Among them, total indel showed 9; in the ITS1 region indel showed 6 it was 67%; and in the ITS2 region, indel showed 3. Most of the indels showed deletion or insertion of only one base pair, but in A. spathulifolius deleted two base pairs and in A. tripolium deleted five base pairs. But in A. yomena, A. hayatae, A. koraiensis, and A. hispidus, the indel was not detected. Phylogenetic trees did not even make a difference inter-genus, but A. yomena and A. koraiensis called genus Kalimeris and genus Gymnaster, respectively; these constituted a clade. A. hispidus called genus Heteropappus was placed as a sister group to the clade of A. ageratoides and A. glehni.

scholarly journals Assessing the Genetic Diversity of Alternaria Bataticola in South Africa using Molecular Markers

2017 ◽  
Vol 5 (2) ◽  
Author(s):  
J. Chalwe ◽  
P. Adebola ◽  
M. Pillay
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Ipomoea Batatas ◽  
Cultural Practices ◽  
Sequence Data ◽  
Control Measure ◽  
Secondary Structures ◽  
Its2 Sequence ◽  
Its2 Region ◽  
Alternaria Blight

Sweetpotato (Ipomoea batatas) an economically important food crop is affected by viral and fungal diseases. The most important fungal disease is Alternaria blight caused by Alternaria bataticola. Alternaria blight can be controlled using fungicides and cultural practices in the short-term. A sustainable control measure is the development of resistant sweetpotato cultivars. A prerequisite to this approach is the knowledge of the genetic diversity of this fungal pathogen. This study assessed the genetic diversity of A. bataticola in South Africa using RAPD analysis, DNA sequencing and secondary structures of the ITS2 region. Samples were collected from 25 different localities and the pathogen was identified in the laboratory. Both RAPD and ITS2 sequence data showed that there is high levels of genetic diversity among the isolates of A. bataticola. Although the dendrograms generated from the RAPD and ITS2 sequences clustered some isolates according to their place of origin, the majority of isolates did not group according to their geographic origins. The predicted ITS2 secondary structure models were variable ranging from simple to complex. The unique secondary structures of each isolate can be used to identify and distinguish each of the isolates used in this study.  

Reviewing lymnaeid vectors of fascioliasis by ribosomal DNA sequence analyses

2005 ◽  
Vol 79 (3) ◽  
pp. 257-267 ◽  
Author(s):  
M.D. Bargues ◽  
S. Mas-Coma
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Fasciola Hepatica ◽  
Rdna Sequence ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Nuclear Rdna ◽  
Natural Classification ◽  
The Family

AbstractSnails of the family Lymnaeidae are of great parasitological importance due to the numerous helminth species they transmit, mainly trematodiases (such as fascioliasis) of considerable medical and veterinary impact. The present knowledge of the genetics and host–parasite relationships of this gastropod group is far from adequate. Fascioliasis is caused by two species, Fasciola hepatica and F. gigantica, which, as in the case of other trematodes, show a marked snail host specificity. Many lymnaeid species involved in fascioliasis transmission still show a confused systematic-taxonomic status. The need for tools to distinguish and characterize species and populations of lymnaeids is evident and the present review concerns new molecular tools developed in recent years using nuclear ribosomal DNA sequences. The small subunit or 18S gene and the internal transcribed spacers ITS-2 and ITS-1 are analysed and evaluated as markers for taxon differentiation and relationships within the Lymnaeidae from genus and species levels to subspecies and population levels. rDNA sequence differences and genetic distances, and their value for reconstructing phylogenetic trees using different methods are considered. Nuclear rDNA sequences are appropriate tools on which to base a review of the systematics and taxonomy of the family Lymnaeidae, without excluding other valuable snail characteristics already available. A reconstruction of the lymnaeid system towards a more natural classification will undoubtedly be helpful in understanding parasite transmission and epidemiological features as well the dispersion of an emerging-reemerging disease such as fascioliasis. Nomenclature for nuclear rDNA genotyping in lymnaeids includes the main rDNA sequence regions able to furnish important information on interspecific differentiation and grouping as well as intraspecific variability of lymnaeid species. The composite haplotype code includes the rDNA markers arranged in order according to their well-known usefulness, in its turn related to their respective, more or less rapid evolutionary ratios, to distinguish between different taxonomic levels, from supraspecific taxa to the species level and up to the population level.

scholarly journals rDNA ITS sequences of Uncinaria spp. from Tsushima leopard cat (Prionailurus bengalensis euptilura)

2012 ◽  
Vol 49 (3) ◽  
pp. 123-127 ◽  
Author(s):  
Y. Shimono ◽  
S. Taharaguchi ◽  
K. Taira ◽  
N. Miyoshi ◽  
N. Yasuda
Keyword(s):  
Its2 Sequence ◽  
The Other ◽  
Its2 Region ◽  
Morphological Identification ◽  
Rdna Its ◽  
Rdna Its Sequences ◽  
Small Intestines ◽  
Prionailurus Bengalensis ◽  
Second Internal Transcribed Spacer ◽  
Pcr Techniques

AbstractUncinaria spp. parasites were collected from two Tsushima leopard cats found on Tsushima Island, Nagasaki prefecture, Japan. One Uncinaria sp. was observed in the large intestines, and the other was observed in the small intestines. The nematode found in the large intestines was determined to be Uncinaria felidis by morphological identification. The other Uncinaria sp. found in the small intestines was morphologically different from U. felidis in the short-length of prevulvar flap. After isolation of genomic DNA of these worms, a second internal transcribed spacer (ITS2) of ribosomal DNA was amplified and sequenced using PCR techniques. The ITS2 region of U. felidis had 222 nucleotide sequences in length. The alignments of ITS2 sequence for Uncinaria felidis and Uncinaria sp. showed one nucleotide (0.45 %) replacement. These differrences may be regarded as intraspecific variation.

scholarly journals Two species of Leymus (Poaceae) are artificial as inferred from the molecular-genetic data

2021 ◽  
Vol 908 (1) ◽  
pp. 012024
Author(s):  
N K Badmaeva
Keyword(s):  
Ribosomal Dna ◽  
Genetic Study ◽  
Molecular Genetic ◽  
Genetic Data ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Morphological Data ◽  
Its2 Region ◽  
Molecular Genetic Study ◽  
Molecular Genetic Data

Abstract The results of studying taxonomic relationships between five species of the aggregate Leymus secalinus (Georgi) Tzvel. of the genus Leymus Hochst. are presented. The research is based on the study of the ITS1-5.8S-ITS2 region obtained by sequencing the nuclear ribosomal DNA internal transcribed spacers, and on the anatomical and morphological data. A molecular-genetic study of the L. secalinus aggregate has revealed that the two species L. ovatus and L. jenisseiensis are artificial.

Phylogenetic relationships in Dermocybe and related Cortinarius taxa based on nuclear ribosomal DNA internal transcribed spacers

1997 ◽  
Vol 75 (4) ◽  
pp. 519-532 ◽  
Author(s):  
Y. J. Liu ◽  
S. O. Rogers ◽  
Y. J. Liu ◽  
J. F. Ammirati
Keyword(s):  
Ribosomal Dna ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Molecular Data ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Herbarium Specimens ◽  
Data Reorganization ◽  
Taxonomic Groups

The genus Cortinarius Fr. (Cortinariaceae, Agaricales) is divided into four or more subgenera. Dermocybe (Fr.) Sacc. has been recognized as either a subgenus of Cortinarius or a separate genus, distinguished in part by the presence of various anthraquinonic pigments. Nucleotide sequences of ribosomal DNA 5.8S and internal transcribed spacers were used to investigate the phylogenetic relationships among species of Dermocybe and selected taxa from subgenera of Cortinarius. Sequence data from 47 herbarium specimens representing 31 taxa (28 species plus 3 varieties) of Dermocybe and Cortinarius were analyzed using parsimony, maximum likelihood, and neighbor joining. In general, molecular data support the morphological groupings of the taxa, although they more closely correspond to biochemical (anthraquinone and other) analyses. Phylogenetic trees showed that, while the sections Dermocybe and Malicoriae are monophyletic, and the concolorous or almost concolorous red species (section Sanguineae, such as D. sanguinea and relatives) together formed a coherent clade, the subgenus Dermocybe sensu lato itself is polyphyletic. Cortinarius californicus clusters with taxa in Cortinarius, subgenus Telamonia, section Armillati. Dermocybe olivaceopicta is more closely related to other subgenera of Cortinarius than to Dermocybe. Within the genus Cortinarius, certain of the subgenera may actually represent coherent genera. Of the subgenera examined, Telamonia, Phlegmacium, and possibly Sericeocybe appear to represent well defined taxonomic groupings. However, current assignments of taxa within Leprocybe and Myxacium were inconsistent with the molecular data. Reorganization of some taxa and taxonomic groups is suggested. Key words: Dermocybe, Cortinarius, molecular phylogeny, rDNA, ITS1, ITS2.

scholarly journals Multigene Phylogeny and Morphology Reveal Three Novel Species and a Novel Record of Agaricus From Northern Thailand

2021 ◽  
Vol 12 ◽  
Author(s):  
Chanyawat Jaichaliaw ◽  
Jaturong Kumla ◽  
Santhiti Vadthanarat ◽  
Nakarin Suwannarach ◽  
Saisamorn Lumyong
Keyword(s):  
Phylogenetic Trees ◽  
Large Subunit ◽  
Elongation Factor ◽  
Morphological Characteristics ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Translation Elongation ◽  
Northern Thailand ◽  
Three New Species ◽  
First Time

Agaricus is a saprophytic mushroom genus widely distributed throughout the world. In this study, a survey of the Agaricus species carried out around Chiang Mai University in northern Thailand from 2018 to 2019 yielded 12 collections. Morphological characteristics and phylogenic analyses based on the internal transcribed spacers (ITS) and a fragment of the large subunit (LSU) of the nuclear ribosomal DNA (rDNA), and a fragment of the translation elongation factor 1-alpha (tef1) genes were investigated. The results revealed that these collections belong to six species including Agaricus erectosquamosus, Agaricus pallidobrunneus, Agaricus subrufescens, and three new species. Agaricus thailandensis sp. nov. was found to belong to Agaricus sect. Minores, which is placed in Agaricus subg. Minores. Aagricus pseudoerectosquamosus sp. nov. was placed in Agaricus sect. Brunneopicti within Agaricus subg. Pseudochitonia. Furthermore, Agaricus lannaensis remains an incertae sedis in Agaricus subg. Pseudochitonia. Additionally, this study was proposed that A. pallidobrunneus was discovered in Thailand for the first time. Full descriptions, color photographs, illustrations, and phylogenetic trees are provided.

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