DNA Barcoding Reveals Intra-Species Genetic Diversity of Amphiesma stolatum

2021 ◽  
Vol 9 (2) ◽  
pp. 139-145
Author(s):  
Lalbiak zuala ◽  
◽  
H.T. Lalremsanga ◽  
Lalrin sanga ◽  
Lalmuan sanga ◽  
...  
Keyword(s):  
16S Rrna ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Northeast India ◽  
Morphological Data ◽  
Cox1 Gene ◽  
History Museum ◽  
The Mean ◽  
Elevational Range ◽  
First Time

Amphiesma stolatum is a widely distributed snake species. But the intra-species genetic information is still limited from India. This paper provides the first-time barcode data of A. stolatum (cox1 and 16s rRNA) sampled from Mizoram State, India. We compare the newly generated sequences with the conspecies sequences from the Indo-Malayan region, and establishes its phylogenetic relationship with its sister genera. We diagnosed a total of five haplotypes from the cox1 gene fragment with 0.844 and 0.004 as the haplotype diversity (hd) and nucleotide diversity (Pi), respectively. The specimens from Mizoram showed a Kimura 2 parameter genetic distance of 0.21% (16s rRNA) and 1.05–1.22% (cox1) with the sequences from Guangdong Province, China; 1.22% (cox1) with the sequences from Hubei Province, China; 0.87–1.05% (cox1) with that from Taiwan; 8.05% with the specimen vouchered in the Natural History Museum, London. The mean intra-specific K2P distances are 4% and 0.36% in 16s rRNA and cox1, respectively. We also contribute new distributional records and elevational range, with notes on additional morphological data and occurrence of the two distinct morphs in Mizoram, Northeast India.

scholarly journals New insights into the prevalence and phylogenetic diversity of Cysticercus ovis isolates in sheep from Sulaymaniyah, Iraq

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Aram Ahmad Mohammed
Keyword(s):  
Sequence Analysis ◽  
Phylogenetic Diversity ◽  
Nucleotide Diversity ◽  
Control Strategies ◽  
Economic Losses ◽  
Cox1 Gene ◽  
Conventional Pcr ◽  
Single Clade ◽  
First Time ◽  
Cysticercus Ovis

Abstract Introduction Although ovine cysticercosis is not a zoonotic problem, it results in substantial economic losses due to the condemnation of infected tissues or entire carcasses. This study aimed to record preliminary data on the prevalence, and phylogenetic diversity of Cysticercus ovis isolates from slaughtered sheep in the province of Sulaymaniyah, Iraq. Material and Methods From January to September 2020, 6, 411 slaughtered sheep were examined for C. ovis by routine meat inspection. The amplification and sequence analysis of the COX1 gene for up to 35 specimens of C. ovis was performed using conventional PCR. Results The overall prevalence rate was 1.3%, and the prevalence was significantly higher in older sheep (>1 year) than younger ones (<1 year) (P< 0.05). The cardiac muscle showed a higher tendency to carry C. ovis infection compared to other examined muscles. Sequence analysis of the COX1 gene revealed six haplotypes, and the level of pairwise nucleotide diversity between individual haplotypes was 1–2%. Five out of six of the Taenia ovis haplotypes recovered could have been recorded for the first time globally. Phylogenetic interpretation indicated that all the T. ovis haplotypes clustered in a single clade, and it also indicated an extremely close similarity to Iranian and New Zealand isolates. Conclusions Globally, this report adds new data on C. ovis genetic diversity, which provide an extremely useful molecular background with regard to future preventive as well as control strategies.

scholarly journals GENETIC CHARACTERIZATION OF KISSING GOURAMI (Helostoma temminckii Cuvier, 1829) IN OGAN RIVER, SOUTH SUMATRA INFERRED FROM 16S rRNA AND COI MITOCHONDRIAL GENES

2019 ◽  
Vol 25 (1) ◽  
pp. 37
Author(s):  
Tuty Arisuryanti ◽  
Gregorius Altius Pratama ◽  
Lukman Hakim ◽  
Johan Putra Koentjana ◽  
Fitria Kurnia Nazira
Keyword(s):  
16S Rrna ◽  
Genetic Divergence ◽  
Nucleotide Diversity ◽  
Genetic Characterization ◽  
Haplotype Diversity ◽  
Mitochondrial Genes ◽  
Coi Gene ◽  
Fish Stock ◽  
Fish Samples

Genetic characterization data of kissing gourami are important to understand historical lineage thus enhancing sustainability of the species and to establish regulation for sustainable management of the fish stock in their habitat. However, investigation of genetic characterization of kissing gourami, one of native Indonesian freshwater fishes has poorly understood. Therefore, the aim of this study was to examine genetic characterization of the fish species collected from Ogan River, South Sumatra using partial sequences of two mitochondrial genes, 16S rRNA and COI. The results revealed that for the 621 bp determined in 16S rRNA gene of the samples, five sites were variable, of which one was parsimony informative. Concatenate data revealed three haplotypes with an overall haplotype diversity of 0.833±0.222 and nucleotide diversity of 0.003±0.001. The genetic divergence varied from 0-0.49%. Next, sequence analysis of COI gene exhibited 609 bp which can be translated into 203 amino acids. For the 609 bp sequence determined in the fish samples, three haplotypes were revealed with nine variable sites and two parsimony informatives. Haplotype diversity and nucleotide diversity of the fish samples were 0.833±0.22 and 0.00794±0.0025, respectively. The haplotype divergence between the fish samples was also supported by three nonsynonymous codons. In addition, the genetic divergence varied from 0 % to 1.16 %. The results suggest that genetic variation of the kissing gourami has to be monitored and further studies are needed to compare the same species from different location to know the historical lineage and demography.

scholarly journals Occurrence of Tamdil Leaf-litter Frog Leptobrachella tamdil (Sengupta et al., 2010) (Amphibia: Megophryidae) from Manipur, India and its phylogenetic position

2021 ◽  
Vol 13 (6) ◽  
pp. 18624-18630
Author(s):  
Ht Decemson ◽  
Vanlalsiammawii ◽  
Lal Biakzuala ◽  
Mathipi Vabeiryureilai ◽  
Fanai Malsawmdawngliana ◽  
...  
Keyword(s):  
16S Rrna ◽  
Leaf Litter ◽  
Gene Sequence ◽  
Marker Gene ◽  
Genetic Data ◽  
Range Extension ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
First Time ◽  
Distribution Record

We present a new state record of Leptobrachella tamdil from Manipur State, northeastern India based on three individuals collected from Chakpi stream, Chandel District.  This record represents the range extension of the species as well as the easternmost distribution record.  We also provide additional morphological data as well as the first time genetic data for the species and inferred its phylogenetic position using mitochondrial 16S rRNA marker gene sequence.

scholarly journals Is the Goat a New Host for the G3 Indian Buffalo Strain ofEchinococcus granulosus?

2012 ◽  
Vol 2012 ◽  
pp. 1-5 ◽  
Author(s):  
Pietro Calderini ◽  
Simona Gabrielli ◽  
Gabriella Cancrini
Keyword(s):  
Genetic Markers ◽  
Reference Strain ◽  
Central Italy ◽  
Original Description ◽  
Morphological Data ◽  
12S Rrna ◽  
Cox1 Gene ◽  
New Host ◽  
Specific Pcr ◽  
First Time

Four goats bred in Central Italy (province of Rieti) revealed, in the liver, metacestodes ofEchinococcus granulosus. The cysts, unilocular and fertile, were examined by microscopy and molecular diagnostics. Morphological data on the rostellar hooks are in agreement with the original description of the strain found in buffaloes and are largely compatible with those reported in Europe for cattle and humans. Specific PCR followed by DNA sequencing of the mitochondrial cox1 gene revealed for all the isolates 99.5% identity to the reference strain G3 genotype and 99.3% and 99.1% to G2 and G1, respectively. Further genetic markers (nad1 and 12S rRNA) confirmed the identity of the goat isolates to the G3 strain. This genotype, here reported for the first time in goats, proved to have a wider than previously supposed host range, therefore its relevance in human hydatidosis is expected to be more often evidenced.

A new country record of Raorchestes cangyuanensis Wu, Suwannapoom, Xu, Murphy & Che 2019 and additional record of Kurixalus yangi Yu, Hui, Rao & Yang 2018 (Anura: Rhacophoridae: Rhacophorinae) from India

Zootaxa ◽  
2021 ◽  
Vol 4974 (2) ◽  
pp. 383-390
Author(s):  
SAMUEL LALRONUNGA ◽  
VANRAMLIANA VANRAMLIANA ◽  
LALRAMLIANA LALRAMLIANA ◽  
ESTHER LALHMINGLIANI
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Barcoding ◽  
Northeast India ◽  
Rrna Gene ◽  
Identification Of Species ◽  
Mitochondrial 16S Rrna Gene ◽  
Faunal List ◽  
First Time ◽  
The 16S Rrna Gene

Most studies on the diversity of amphibians in northeast India were based on classical morpho-taxonomy, which have a high probability of errors in species identification. DNA barcoding of amphibians using the mitochondrial 16S rRNA gene has been used successfully for the identification of species and detection of cryptic species. In the present study, we carry out DNA barcoding of two rhacophorid species of the genus Raorchestes and Kurixalus that are not readily identifiable to the species level based on their morphology. Our analysis on the 16S rRNA gene revealed that these species were Raorchestes cangyuanensis and Kurixalus yangi, species which were recorded for the first time and second time from India respectively. We discuss on the records of R. longchuanensis from Bangladesh and India, which were based on the misidentification of R. cangyuanensis. We therefore propose to delist this species from the faunal list of Bangladesh and India. We further raise a question as to why the population of Kurixalus from Motuo, Xizang province of China was assigned as K. naso and not the population described as K. yangi, which is morphologically similar to K. naso and is also recorded from a locality close to the type locality of K. naso. 

scholarly journals Patterns of nucleotide diversity for different domains of centromeric histone H3 (CENH3) gene in Secale L.

2019 ◽  
Vol 23 (2) ◽  
pp. 135-139
Author(s):  
S. S. Gatzkaya ◽  
E. V. Evtushenko
Keyword(s):  
Nucleotide Diversity ◽  
Histone H3 ◽  
Haplotype Diversity ◽  
Nucleotide Polymorphisms ◽  
Mean Values ◽  
Geographic Ranges ◽  
Histone Fold ◽  
Histone Fold Domain ◽  
Commercial Breeding ◽  
The Mean

Rye (Secale) is among staple cereals along with other members of the Triticeae tribe: wheat and barley. The genus Secale includes perennial and annual, cross-pollinating and self-pollinating species, and they can be donors of valuable genes in wheat and rye breeding programs. Studies of the structure of the gene for centromeric histone H3 (CENH3), essential for centromere functions, are relevant to the breeding of agronomically important crops. We have investigated the nucleotide diversity of sequences of two variants of the rye CENH3 gene inside the N-terminal tail (NTT) and the conservative HFD (histone fold domain) domain in the genus Secale. The mean values of nucleotide diversity in the NTT and HFD of wild cross- and self-pollinating taxa are close in αCENH3: πtot = 0.0176–0.0090 and 0.0136–0. 0052, respectively. In the case of βCENH3, the mean values for NTT (πtot = 0.0168–0.0062) are lower than for HFD (πtot = 0.0259–0.084). The estimates of nucleotide and haplotype diversity per site for the CENH3 domains are considerably lower in taxa with narrow geographic ranges: S. cereale subsp. dighoricum and S. strictum subsp. kuprijanovii. Commercial breeding reduces the nucleotide sequence variability in αCENH3 and βCENH3. Cultivated rye varieties have π values within 0.0122–0.0014. The nucleotide and haplotype diversity values in αCENH3 and βCENH3 are close in S. sylvestre, which is believed to be the oldest rye species. The results of this study prove that the frequency of single nucleotide polymorphisms and nucleotide diversity of sequences in genes for CENH3 in Secale species are influenced by numerous factors, including reproduction habits, the geographic isolation of taxa, breeding, and the evolutionary age of species.

Phylogenetic position of Tropidophorus assamensis Annandale, 1912 with updated morphological data and distributional records

2022 ◽  
pp. 1-4
Author(s):  
Hmar T. Lalremsanga
Keyword(s):  
16S Rrna ◽  
Genetic Data ◽  
Type Locality ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Eastern India ◽  
North East India ◽  
North East ◽  
North Eastern ◽  
First Time

The poorly known northeastern water skink Tropidophorus assamensis is only known from the type locality (Harigaj Range, Sylhet District) in Bangladesh, and few localities in Assam and Mizoram States, north-eastern India. Little is known about the biology including the systematics of the species. In this study, we present for the first time, genetic data (16s rRNA) and inferred its phylogenetic position. In addition to this, we provide updated morphological data along with new distributional records of the species from Mizoram State of north-east India.

The identity of Indosylvirana nicobariensis (Stoliczka 1870) (Amphibia, Ranidae) from northeast India

Zootaxa ◽  
2021 ◽  
Vol 4952 (3) ◽  
pp. 596-600
Author(s):  
SAMUEL LALRONUNGA ◽  
VANRAMLIANA VANRAMLIANA ◽  
LALKHAWNGAIHA SAILO ◽  
ISAAC ZOSANGLIANA ◽  
LALMUANPUIA LALMUANPUIA ◽  
...  
Keyword(s):  
16S Rrna ◽  
Southeast Asia ◽  
West Bengal ◽  
Mitochondrial Gene ◽  
Northeast India ◽  
Morphological Data ◽  
Molecular Evidence ◽  
Arunachal Pradesh ◽  
Nicobar Islands

Stoliczka (1870) described Hylorana nicobariensis from the Nicobar Islands of India. The generic allocation of this enigmatic species is yet to be fully resolved (Chan et al. 2020b) and it has been placed in different genera (Boulenger 1885; Frost et al. 2006; Che et al. 2007; Oliver et al. 2015; Chan et al. 2020a; Chandramouli et al. 2020). As of now, the species is assigned to the genus Indosylvirana (Oliver et al. 2015; Chan et al. 2020b; Frost 2020). Apart from Nicobar archipelago, this species is distributed in the insular regions of southeast Asia (Oliver et al. 2015; Chandramouli et al. 2020; Frost 2020) and the states of Arunachal Pradesh, Assam, Mizoram, Tripura and West Bengal in northeast India (Sarkar et al. 1992, 2002; Sarkar & Ray 2006; Ahmed et al. 2009; Mathew & Sen 2010; Lalremsanga 2011; Lalremsanga et al. 2015, 2016). However, Frost (2020) doubted the records of this species in northeast India. Systematic studies on the herpetofauna of northeast India based on molecular evidence are scanty (Lalronunga et al. 2020a), and species recorded from the area need confirmation (Frost 2020). Recent studies revealed that many species previously recorded from northeast India were based on misidentifications (Das et al. 2019; Giri et al. 2019; Lalronunga et al. 2020b), therefore, a review and revalidation on the herpetofaunal list of the area is warranted. Herein, we examined the identity of the species recorded as I. nicobariensis from northeast India using morphological data and a fragment of 16S rRNA mitochondrial gene. 

Edward Heron-Allen FRS (1861–1943): a review of his scientific career, with an annotated bibliography of his foraminiferal publications

2004 ◽  
Vol 31 (1) ◽  
pp. 6-29 ◽  
Author(s):  
Richard L. Hodgkinson ◽  
John E. Whittaker
Keyword(s):  
Natural History ◽  
Royal Society ◽  
Annotated Bibliography ◽  
Natural History Museum ◽  
Scientific Career ◽  
History Museum ◽  
First Time

ABSTRACT: In spite of his many other interests, Edward Heron-Allen also worked for nearly 50 years as a scientist on minute shelled protists, called foraminifera, much of it in an unpaid, unofficial capacity at The Natural History Museum, London, and notably in collaboration with Arthur Earland. During this career he published more than 70 papers and obtained several fellowships, culminating in 1919 in his election to the Royal Society. Subsequently, he bequeathed his foraminiferal collections and fine library to the Museum, and both are housed today in a room named in his honour. In this paper, for the first time, an assessment of his scientific accomplishments is given, together with a full annotated bibliography of his publications held in the Heron-Allen Library. This is part of a project to produce a bibliography of his complete publications, recently initiated by the Heron-Allen Society.

First Records of Bufo luchunnicus (Yang et Rao, 2008) and Amolops wenshanensis Yuan, Jin, Li, Stuart et Wu, 2018 (Anura: Bufonidae, Ranidae) from Vietnam

2020 ◽  
Vol 27 (2) ◽  
pp. 81-86
Author(s):  
Cuong The Pham ◽  
Minh Duc Le ◽  
Chung Van Hoang ◽  
Anh Van Pham ◽  
Thomas Ziegler ◽  
...  
Keyword(s):  
Natural History ◽  
Genetic Divergence ◽  
Morphological Data ◽  
Type Series ◽  
Lao Cai ◽  
First Time ◽  
Nd2 Gene ◽  
Quang Ninh

We record two species of amphibians for the first time from Vietnam: Bufo luchunnicus from Lao Cai and Son La provinces and Amolops wenshanensis from Quang Ninh Province. Morphologically, the Vietnamese representatives of B. luchunnicus resemble the type series from China. The specimen of A. wenshanensis from Vietnam slightly differs from the type series from China by having a smaller size (SVL 33.2 mm vs. 35.7 – 39.9 mm in males) and the presence of distinct transverse bands on the dorsal surfaces of limbs. Genetic divergence between the sequence of the Vietnamese specimen and those of A. wenshanensis from China available from GenBank is 1.2 – 1.6% (ND2 gene). In addition, morphological data and natural history notes of aforementioned species are provided from Vietnam.

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