Genetic characteristic of giant featherback, Chitala lopis (Bleeker, 1851) from Lampung and Kalimantan using COI Gene

DNA barcoding based on partial Cytochrome Oxidase subunit I (COI) gene in the mitochondrial has widely used in species identification and biodiversity studies. COI gene application is expected to obtain genetic characteristic, genetic variations and phylogeny of giant featherback. The aim of this research was to analyze genetic diversity of giant featherback Chitala lopis in Lampung and Kalimantan. To analyse genetic distance, Kimura two parameter (K2P) model was performed where to determine nucleotide variation & polymorphism and also reconstructed of phylogenetic tree was used MEGA 7.0 software. Total nine individuals were obtained from three populations, i.e. Lampung, West Kalimantan and South Kalimantan. The results showed that giant featherback has 689 bp conserve, 18 bp variation, 13 bp parsimony-informative, and 2 bp singleton sites from 707 bp COI partial gene. The average within-species, in-group, and out-group based on K2P distances were 1.24%, 1.43% & 1.58% (AP008922.1; KM213054.1), and 13.00% respectively. The Single Nucleotide Polymorphism (SNP) was obtaining from 13 SNP sites. West Kalimantan samples have two SNP (471 and 528 site). The South Kalimantan samples showed more specific nucleotides with nine SNP (120, 129, 144, 201, 306, 324, 474, 615 and 644). Based on genetic distance, the biggest difference was in the South Kalimantan sample (1.58%) compared with Lampung and West Kalimantan. The results of the K2P neighbour-joining phylogenetic tree reconstruction show that the South Kalimantan samples are in a different group. The West Kalimantan sample shows that it is closely related to the Lampung.

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Genetic structure and phylogenetic relationships of Phyllidiellapustulosa species from Seribu Islands, North Sulawesi, Halmahera, and West Papua

IOP Conference Series Earth and Environmental Science ◽

10.1088/1755-1315/944/1/012028 ◽

2021 ◽

Vol 944 (1) ◽

pp. 012028

Author(s):

N O Yonatika ◽

N Widiasih ◽

M Hamidah ◽

M D Nurhakim ◽

H Budiarto ◽

...

Keyword(s):

Phylogenetic Tree ◽

Genetic Distance ◽

Dna Sequence ◽

Maximum Likelihood Method ◽

Likelihood Method ◽

Neighbor Joining ◽

Tree Reconstruction ◽

Genetic Characteristics ◽

North Sulawesi ◽

West Papua

Abstract Phyllidiella pustulosa are brightly coloured gastropod molluscs frequently found in coral reefs of the tropical Indo-Pacific. Phyllidiella pustulosa is widely distributed in Indonesia, such as Seribu Island, North Sulawesi, West Papua, and Halmahera. Based on the genetic characteristics of an individual’s DNA sequence, differences between species can be identified. In this paper, we would like to provide the molecular analysis and phylogenetic relationship among nudibranchs from Indonesian waters. Identification was made by measuring the genetic distance between species. The phylogenetic tree reconstruction was made using the Kimura 2-parameter model with 1000 times bootstrap with neighbor-joining and maximum likelihood method. There is 46 DNA Sequence obtained from 4 different regions (Seribu Island, Halmahera, North Sulawesi, and West Papua). The genetic distance of West Papua and Halmahera has the smallest value among other populations, which is between 0.0051-1.4629, compared to the population in Halmahera. The phylogenetic tree also shows populations from West Papua and Halmahera are on the same lineage, indicating that the population in West Papua and Halmahera had the closest relation. The study suggested that North Sulawesi, Halmahera and West Papua have genetic mixing of the same region, which is distinctive from Seribu Island.

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Karyotype and COI sequences of Chironomus sokolovae Istomina, Kiknadze et Siirin, 1999 (Diptera,Chironomidae) from the bay of Orkhon River, Mongolia

Comparative Cytogenetics ◽

10.3897/compcytogen.v15.i2.66549 ◽

2021 ◽

Vol 15 (2) ◽

pp. 149-157

Author(s):

Viktor V. Bolshakov ◽

Alexander A. Prokin

Keyword(s):

Bayesian Inference ◽

Phylogenetic Tree ◽

Genetic Distance ◽

Dna Barcoding ◽

Molecular Genetic ◽

Species Level ◽

Coi Gene ◽

High Similarity ◽

Coi Sequences ◽

First Time

Chironomus sokolovae Istomina, Kiknadze et Siirin, 1999 (Diptera, Chironomidae) is recorded from Mongolia for the first time. Eleven banding sequences determined in the Mongolian population were previously known from Altai and Yenisei populations: sokA1, sokB1, sokB2, sokC1, sokC2, sokD1, sokD2, sokE1, sokF1, sokF2 and sokG1. The additional B-chromosomes are absent. DNA-barcoding of COI gene was carried out for this species for the first time. The phylogenetic tree estimated by Bayesian inference showed a high similarity of the studied species with Ch. acutiventris Wülker, Ryser et Scholl, 1983 from the Chironomus obtusidens-group. The estimated genetic distance K2P between Ch. sokolovae and Ch. acutiventris is much lower (0.38%) than the commonly accepted threshold of 3% for species of genus Chironomus Meigen, 1803. Our results show that the accepted cytogenetic criteria of species level in the genus Chironomus are more in accordance with morphological ones of the same level, than with molecular-genetic criteria accepted for species COI genetic distance.

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Identification of Single Nucleotide Polymorphism in Y-chromosome Specific DDX3Y Gene in Murrah Buffalo Bulls

Indian Journal of Animal Research ◽

10.18805/ijar.b-4692 ◽

2022 ◽

Author(s):

P. Ramajayan ◽

S.N. Sivaselvam ◽

S.M.K. Karthickeyan ◽

A. Gopinathan ◽

S. Poobitha

Keyword(s):

Single Nucleotide Polymorphism ◽

Phylogenetic Tree ◽

Y Chromosome ◽

Bos Taurus ◽

Production Performance ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Murrah Buffalo ◽

Frozen Semen ◽

Single Nucleotide Variations

Background: Molecular markers based approaches are essential to select fertile bulls for frozen semen production at an early age. The present investigation was undertaken to perform the molecular characterization and identify single nucleotide polymorphisms (SNP) in Y-chromosome specific DDX3Y gene in Murrah buffalo bulls. Methods: The genomic DNA isolated from the blood samples of 70 Murrah buffalo bulls, covering bulls with normal seminal traits and poor production performance (poor semen quality, freezability, libido), were subjected to PCR amplification. The sequences of DDX3Y gene were analyzed for single nucleotide polymorphism using the seqman module of DNASTAR LASERGENE software. The single nucleotide variations in the sequences with reference to the Bos taurus sequence were determined using Clustal W. The phylogenetic tree and genetic distance were constructed using the MegAlign module. Result: The analysis of sequences revealed that the exons and their adjacent intronic regions of the DDX3Y gene are monomorphic in nature without any variations indicating that the sequences are highly conserved in the studied population of Murrah buffalo bulls. However, a considerable number of single nucleotide variations were observed in the sequences of Murrah buffalo compared with Bos taurus sequences. Furthermore, the phylogenetic tree analysis revealed less divergence and close genetic association between the sequences of Murrah buffalo and other species in the bovinae family than the caprinea species. Further studies on DDX3Y gene in a more extensive and diverse population of Murrah buffalo bulls distributed in different regions could aid to discover substantial SNPs.

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Uncovering phylogenetic relationships and genetic diversity of water dropwort using phenotypic traits and SNP markers

PLoS ONE ◽

10.1371/journal.pone.0249825 ◽

2021 ◽

Vol 16 (7) ◽

pp. e0249825

Author(s):

Qun Ji ◽

Honglian Zhu ◽

Xinfang Huang ◽

Kai Zhou ◽

Zhengwei Liu ◽

...

Keyword(s):

Genetic Diversity ◽

Single Nucleotide Polymorphism ◽

Phylogenetic Tree ◽

Phylogenetic Relationships ◽

Morphological Characteristics ◽

Phenotypic Traits ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Linear Leaf ◽

Water Dropwort

The water dropworts Oenanthe linearis Wall. ex DC. and O. javanica (Blume) DC. are aquatic perennial herbs that have been used in China as vegetables and traditional medicines. However, their phylogenetic relationships and genetic diversity are poorly understood. Here, we presented the phenotypic traits and genome-wide DNA marker-based analysis of 158 water dropwort accessions representing both species. The analysis revealed that Oenanthe linearis was readily segregated into linear-leaf and deep-cleft leaf water dropworts according to their leaf shapes at flowering. Oenanthe javanica was classified by clustering analysis into two clusters based mainly on the morphological characteristics of their ultimate segments (leaflets). A set of 11 493 high-quality single-nucleotide polymorphisms was identified and used to construct a phylogenetic tree. There was strong discrimination between O. linearis and O. javanica, which was consistent with their phenotype diversification. The population structure and phylogenetic tree analyses suggested that the O. linearis accessions formed two major groups, corresponding to the linear-leaf and deep-cleft leaf types. The most obvious phenotypic differences between them were fully expressed at the reproductive growth stage. A single-nucleotide polymorphism-based analysis revealed that the O. javanica accessions could be categorized into groups I andII. However, this finding did not entirely align with the clusters revealed by morphological classification. Landraces were clustered into one group along with the remaining wild accessions. Hence, water dropwort domestication was short in duration. The level of genetic diversity for O. linearis (π = 0.1902) was slightly lower than that which was estimated for O. javanica (π = 0.2174). There was a low level of genetic differentiation between O. linearis and O. javanica (Fst = 0.0471). The mean genetic diversity among accessions ranged from 0.1818 for the linear-leaf types to 0.2318 for the groupII accessions. The phenotypic traits and the single-nucleotide polymorphism markers identified here lay empirical foundation for future genomic studies on water dropwort.

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Short communication: Population structure of the South African Bonsmara beef breed using high density single nucleotide polymorphism genotypes

Livestock Science ◽

10.1016/j.livsci.2017.01.012 ◽

2017 ◽

Vol 197 ◽

pp. 102-105 ◽

Cited By ~ 1

Author(s):

L. Bosman ◽

E. van Marle-Köster ◽

R.R. van der Westhuizen ◽

C. Visser ◽

D.P. Berry

Keyword(s):

Single Nucleotide Polymorphism ◽

Population Structure ◽

South African ◽

Short Communication ◽

High Density ◽

Nucleotide Polymorphism ◽

The South ◽

Single Nucleotide ◽

Beef Breed

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Development of Single Nucleotide Polymorphism (SNP) Markers for Analysis of Population Structure and Invasion Pathway in the Coconut Leaf Beetle Brontispa longissima (Gestro) Using Restriction Site-Associated DNA (RAD) Genotyping in Southern China

Insects ◽

10.3390/insects11040230 ◽

2020 ◽

Vol 11 (4) ◽

pp. 230

Author(s):

Zhiming Chen ◽

Guihua Wang ◽

Min Li ◽

Zhengqiang Peng ◽

Habib Ali ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Population Structure ◽

Phylogenetic Tree ◽

Structure Analysis ◽

Restriction Site ◽

Southern China ◽

Leaf Beetle ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Invasion Pathway

To determine population genomic structure through high-throughput sequencing techniques has revolutionized research on non-model organisms. The coconut leaf beetle, Brontispa longissima (Gestro), is a widely distributed pest in Southern China. Here, we used restriction site-associated DNA (RAD) genotyping to assess the invasion pathway by detecting and estimating the degree of genetic differentiation among 51 B. longissima accessions collected from Southern China. A total of 10,127 SNPs were obtained, the screened single nucleotide polymorphism (SNP) information was used to construct the phylogenetic tree, FST analysis, principal component analysis, and population structure analysis. Genetic structure analysis was used to infer the population structure; the result showed that all accessions were divided into Hainan population and non-Hainan population. The Hainan population remained stable, only the Sansha population differentiated, and the non-Hainan populations have gradually differentiated into smaller sub-populations. We concluded that there are two sources of invasion of B. longissima into mainland China: Taiwan and Hainan. With the increase of the invasion time, the Hainan population was relatively stable, and the Taiwan population was differentiated into three sub-populations. Based on the unrooted phylogenetic tree, we infer that Taiwan and Hainan are the two invasive base points. The Taiwan population invaded Fujian, Guangdong, and Guangxi, while the Hainan population invaded Yunnan and Sansha. Our results provide strong evidence for the utility of RAD sequencing (RAD-seq) in population genetics studies, and our generated SNP resource could provide a valuable tool for population genomics studies of B. longissima in the future.

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Karyotype and COI sequences of Chironomus sokolovae Istomina, Kiknadze et Siirin, 1999 (Diptera,Chironomidae) from the bay of Orkhon River, Mongolia

Comparative Cytogenetics ◽

10.3897/compcytogen.v15i2.66549 ◽

2021 ◽

Vol 15 (2) ◽

pp. 149-157

Author(s):

Viktor V. Bolshakov ◽

Alexander A. Prokin

Keyword(s):

Bayesian Inference ◽

Phylogenetic Tree ◽

Genetic Distance ◽

Dna Barcoding ◽

Molecular Genetic ◽

Species Level ◽

Coi Gene ◽

High Similarity ◽

Coi Sequences ◽

First Time

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Phylogenetic tree of Kuantan cattle by DNA barcoding

Jurnal Ilmu Ternak dan Veteriner ◽

10.14334/jitv.v21i1.1351 ◽

2016 ◽

Vol 21 (1) ◽

pp. 41

Author(s):

. Hidayati ◽

R. Misrianti ◽

A. Ali

Keyword(s):

Beef Cattle ◽

Phylogenetic Tree ◽

Genetic Distance ◽

Gene Segment ◽

Bos Indicus ◽

Dna Barcode ◽

Cattle Breed ◽

Coi Gene ◽

Blood Samples ◽

Primer Sequence

Kuantan cattle is one of local beef cattle breed of Riau Province which its origin was unknown. Kuantan cattle are commonly found in Indragiri Hulu and Kuantan Singingi Regency. Based on phenotype characterizations, kuantan cattles are similar with pesisir cattle (West Sumatera beef cattle). Historically, kuantan cattle were pesisir cattle brought by “minang” immigrants (Immigrant from West Sumatera) to this region. The purpose of this study was to analyze the origin of the kuantan cattle through genetic diversity analysis using DNA barcode. DNA barcode used was Cytochrome oxidase subunit I gene which was found in the mtDNA. DNA isolation was done on 25 kuantan’s blood samples and 18 pesisir blood samples. Amplification of COI gene segment used Polymerase Chain Reaction technique. The forward primer sequence used in this study was F’5 TTCTCAACCAACCATAAAGATATTGG-3’ and the reverse primer sequence used was reverse 5’-TAGACTTCGGGGTGTCCAAAGAATCA-3. It squeezed kuantan and pesisir sequence 5711 - 6420 base (GeneBank accession number NC_005971) with length by 710 bp. Analysis result of sequence using MEGA 5.2 Program showed that there were 6 polymorphic sites establishing 7 haplotypes on kuantan cattle and 9 polymorphic sites establishing 12 haplotypes on pesisir cattle. Based on genetic distance and phylogeney tree, kuantan and pesisir cattle were in same group with Bos indicus. Mutation in the COI gene segment in this study was too small and was not able to distinguish the difference of those breeds. The result of neighbor joining analyze indicated that kuantan cattle origin was from Bos indicus just like pesisir cattle.Key Words: COI Gene, Polymorphic, Kuantan Cattle, Genetic Distance, Phylogenetic Tree

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Morphological and Molecular Characterization of Several Neogastropod Species (Mollusca: Gastropoda) From Coastal Waters of Bangladesh With One New Record

Journal of Bio-Science ◽

10.3329/jbs.v29i0.54824 ◽

2021 ◽

pp. 79-91

Author(s):

KS Sultana ◽

PS Brishti ◽

S Ahmed ◽

MB Billah ◽

KA Habib

Keyword(s):

Molecular Characterization ◽

New Record ◽

Gc Content ◽

Coi Gene ◽

The South ◽

First Time ◽

Mitochondrial Cytochrome Oxidase ◽

Two Parameter ◽

Morphological And Molecular Characterization

The present study reports the morphological and molecular characterization of marine neogastropods collected from the South-East to the South-West coasts of Bangladesh. A total of 21 species under 13 families were identified morphologically, of which 7 species were barcoded successfully using partial sequence of mitochondrial cytochrome oxidase subunit-I (COI) gene. The average nucleotide frequencies of these species were G (guanine) = 20.57%, C (cytosine) = 18.44%, A (adenine) = 23.65%, T (thymine) = 37.35% and the GC content was 39.01%. The average Kimura two-parameter (K2P) distances of the COI barcode sequences within species, genera, and families were 20.7%, 22.0%, and 22.0%, respectively. The average inter-species genetic divergence was calculated as 21.0%. In addition, the COI barcode sequence of Nassarius stolatus was identified and submitted to the GenBank for the first time. The study also reports the new record of a species, Indothais rufotincta Tan & Sigurdsson, 1996 from Bangladesh. This finding greatly extends the distributional range of this species from the West coast to the East coast of the Bay of Bengal. J. Bio-Sci. 29(1): 79-91, 2021 (June)

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