scholarly journals Molecular classification and comparative phylogeographic study of insectivorous bat species (Pipisitrellus coromandra) from Punjab, Pakistan

2022 ◽  
Vol 82 ◽  
Author(s):  
Z. Ahmad ◽  
M. H. Abbasi ◽  
S. R. Ahmad ◽  
N. Sheikh
Keyword(s):  
Molecular Classification ◽  
Genetic Distances ◽  
Coi Gene ◽  
Local Alignment ◽  
Identity Match ◽  
Gene Coi ◽  
Search Tool ◽  
Identity Score ◽  
First Time

Abstract Molecular based identification of bat fauna in Pakistan has been relatively less explored. The current study was therefore planned to report for the first time the molecular classification of insectivorous bats (Pipistrellus coromandra) based on mitochondrion gene (COI) from Punjab, Pakistan. Specimens were collected from five different locations followed by DNA extraction with subsequent gene amplification and sequencing. All samples in the study had shown close identity matches with species (Pipistrellus coromandra) from India and (Pipistrellus tenuis) from Vietnam with percentage identity score of 96.11 and 95.58 respectively except one sequence which only revealed 86.78% identity match on Basic Local Alignment Search Tool (BLAST) and could only be assigned to genus level Pipistrellus sp. The results indicated negligible intra-population genetic distance among collected samples whereas the comparison with species from other countries had shown high intraspecific (P. coromandra) and interspecific (P. tenuis) mean genetic distances. The current study hence successfully proved the efficiency of COI gene as a molecular marker for species identification and in analyzing the patterns of genetic variation with species from other countries.

scholarly journals Fish Identification based on Partial Fragments of The Mitochondrial COI Subunit I Gene

2021 ◽  
Vol 322 ◽  
pp. 01038
Author(s):  
Tuah N. M. Wulandari
Keyword(s):  
Phylogenetic Tree ◽  
Coi Gene ◽  
Local Alignment ◽  
Mtdna Sequences ◽  
Mitochondrial Coi ◽  
Search Tool ◽  
Very High ◽  
I Gene

The mtDNA sequences revealed that several of the fish studied were Hampala macrolepidota and Barbonymus gonionotus. The objective of this research was to learn the pattern of COI gene in mtDNA and establish a phylogenetic tree. Basic Local Alignment Search Tool-nucleotide (BLASTn) confirmed that Barbonymus gonionotus froma the Ranau Lake, South Sumatera has 100% matching ranges to the species from Memberamo River (Indonesia), India, Bangladesh, Thailand (Mae Khlong), Indo-Myanmar, and Malaysia_1. The lowest closeness (98.76%) is related to species from Thailand (Lower Ing). The Blast investigation appears us that the level of familiarity was very high, it is coming to 98-100% in Barbonymus gonionotus. Hampala macrolepidota had 100% matching ranges to the species from Indonesia (SouthaSumatera_1) and Vietnam. They had 99.05%-99.84% closeness from Malaysia_1,2&3, Indonesia (South Sumatera_2&3, Java and Bali_1,2&3).

The Cochlostoma (Holcopoma) westerlundi group in Italy (Caenogastropoda: Cochlostomatidae)

Biologia ◽  
2014 ◽  
Vol 69 (6) ◽  
Author(s):  
Mariastella Colomba ◽  
Fabio Liberto ◽  
Armando Gregorini ◽  
Walter Renda ◽  
Agatino Reitano ◽  
...  
Keyword(s):  
16S Rdna ◽  
Southern Italy ◽  
Genetic Distances ◽  
Morphological Data ◽  
Molecular Evidence ◽  
Systematic Classification ◽  
Phylogenetic Status ◽  
First Time ◽  
Reproductive Apparatus

AbstractCurrently, the Cochlostoma (Holcopoma) westerlundi (Paulucci, 1879) group includes three subspecies inhabiting southern Italy up to southeastern Sicily. C. w. westerlundi (Paulucci, 1879) is limited to southern Calabria, C. w. yapigium (Westerlund, 1885) is widespread across the Salento (the southeastern extremity of the Apulia region) and C. w. dionysii (Paulucci, 1879) is endemic to the environs of Siracusa (SE Sicily). There is also a fourth taxon, C. paganum (Westerlund, 1885) described for Otranto (LE, Apulia), considered a synonym of C. w. yapigium. Up to now, the molecular genetics of C. westerlundi s.l. have been unknown and the morphological data of several populations are still lacking. Hence, the systematic classification of the group is tentative. Aiming at filling this gap, mtDNA (16S rDNA and COI) partial sequences were investigated and, in addition, the reproductive apparatus of C. w. westerlundi was described for the first time. Molecular sequences and anatomical data were used to test the taxonomic and phylogenetic status of the examined populations. Maximum Likelihood and Bayesian analysis revealed three clusters, strongly supported, corresponding to the three taxa. For the first time, synonymy between paganum and yapigium was confirmed by molecular evidence. Genetic distances between groups (DxyJC) ranged from 2.6% to 5% (16S rDNA) and from 6.3% to 8.3% (COI). Molecular and morphological data led us to suggest elevating the three subspecies to the species rank.

scholarly journals DNA Barcoding of Fish in Mischief Reef—Fish Diversity of a Reef Fish Community From Nansha Islands

2021 ◽  
Vol 7 ◽  
Author(s):  
Binbin Shan ◽  
Yan Liu ◽  
Changping Yang ◽  
Yu Zhao ◽  
Gongjun Zhang ◽  
...  
Keyword(s):  
Reef Fish ◽  
Management Strategies ◽  
Genetic Distances ◽  
Coi Gene ◽  
Fish Diversity ◽  
Nansha Islands ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
First Time ◽  
Effective Conservation

Development of effective conservation and management strategies requires assessments of ecosystem biodiversity status, especially in understudied hotspots of global fish diversity. Coral reefs are important habitats for fishes, with biodiversity hotspots known globally. We present the first data on molecular diversity of fishes of Mischief Reef, the largest atoll in the Nansha Islands. Partial sequences (650 bp) of mitochondrial COI gene (Cytochrome c oxidase subunit I) are used to identify 209 individuals, representing 101 species, referable to 62 genera, 27 families, 8 orders, and 1 class. The most abundant orders are the Perciformes (176 specimens, 84.21%), Tetraodontiformes (13 specimens, 6.22%), and Beryciformes (13 specimens, 6.22%). Mean Kimura 2-Parameter genetic distances within genera, families, and orders are 4.51, 13.90, and 17.63%, respectively. We record Monotaxis heterodon from this region for the first time—a species that may previously have been misidentified as M. grandoculis. In addition, we recognized possible cryptic species of Lethrinus olivaceus based on significantly diverging barcode sequences. Barcode data provide new insights into fish diversity of Mischief Reef, important for developing further researches on this fauna, and for its conservation.

scholarly journals Karyotype and COI gene sequence of Chironomus heteropilicornis Wülker, 1996 (Diptera, Chironomidae) from the Gydan Peninsula, Russia

2021 ◽  
Vol 15 (4) ◽  
pp. 447-458
Author(s):  
Viktor V. Bolshakov ◽  
Alexander A. Prokin ◽  
Sergey V. Artemenko
Keyword(s):  
Phylogenetic Tree ◽  
Gene Sequence ◽  
Genetic Distances ◽  
Coi Gene ◽  
Gene Sequences ◽  
South Caucasus ◽  
Homozygous State ◽  
Banding Sequence ◽  
First Time ◽  
Georgian Population

The karyotype features and gene COI sequence of Chironomus heteropilicornis Wülker, 1996 from the Gydan Peninsula are presented for the first time. Nine banding sequences were determined, eight of them hpiA2, hpiB1, hpiC1, hpiC2, hpiD1, hpiE1, hpiF3 and hpiG1 were previously known from European, Georgian (South Caucasus) and Siberian populations. One new banding sequence for Ch. heteropilicornis, hpiB2, was found. The hpiA2 banding sequence was found in all individuals, and this is its second finding after the Georgian population (Karmokov 2019). The hpiF3 banding sequence was found only in the homozygous state. Additional B-chromosomes are absent. The genetic distances (K2P) between Ch. heteropilicornis COI gene sequence from Gydan Peninsula and Norway are 1.1­–1.3%, and Georgia – 1.8%, much lower than the commonly accepted threshold of 3% for species of genus Chironomus Meigen, 1803. The phylogenetic tree for COI gene sequences estimated by Bayesian inference showed geographically determined clusters of Norway and Gydan and a separate lineage of the Georgian population of Ch. heteropilicornis. The analysis of karyotype and COI gene sequences shows that the population of Ch. heteropilicornis from the Gydan Peninsula has an intermediate position within the Ch. pilicornis group between Georgian, Yakutian and Norwegian populations. The position of Ch. pilicornis Fabricius, 1787 from Canada and Greenland on the phylogenetic tree is discussed.

Not endemic after all: Imparipecten Freeman, 1961 (Diptera: Chironomidae) described from the Neotropical Region

Zootaxa ◽  
2018 ◽  
Vol 4532 (3) ◽  
pp. 396 ◽  
Author(s):  
LÍVIA MARIA FUSARI ◽  
GALILEU P.S. DANTAS ◽  
NEUSA HAMADA ◽  
VANDERLY ANDRADE-SOUZA ◽  
KÁTIA M. LIMA ◽  
...  
Keyword(s):  
Nuclear Protein ◽  
Mitochondrial Protein ◽  
Neotropical Region ◽  
Genetic Distances ◽  
Ribosomal Gene ◽  
Monotypic Genus ◽  
Bayesian Phylogenetics ◽  
Protein Coding ◽  
Gene Coi ◽  
First Time

Imparipecten, a previously monotypic genus, was considered endemic to Australia. Here, we report Imparipecten from the Neotropical region for the first time and describe Imparipecten sychnacanthus sp. n. from Brazil. The association between larvae and adults was established by sequencing a fragment of one ribosomal gene (28S), two fragments of a nuclear protein-coding gene (CAD1 and CAD4), and one mitochondrial protein-coding gene (COI). We also show the close molecular proximity with Imparipecten pictipes through analyses of genetic distances and Bayesian phylogenetics. 

scholarly journals BARKODING DNA BURUNG ELANG (FAMILI ACCIPITRIDAE) DI INDONESIA

2018 ◽  
Vol 17 (2) ◽  
Author(s):  
Moch Syamsul Arifin Zein
Keyword(s):  
Animal Species ◽  
Distance Matrix ◽  
Pairwise Distance ◽  
Coi Gene ◽  
Local Alignment ◽  
Protein Coding ◽  
Genetic Distance Matrix ◽  
The Family ◽  
Search Tool ◽  
Identification Tool

The cytochrome c oxidase subunit I (COI) gene is a reprensentative of all the protein-coding genes of the mitochondrial DNA genome that has been widely used as an animal species identification tool. In this study, 86 sequences of DNA barcodes of members of the family Accipitridae in Indonesia including Nisaetus bartelsi, Nisaetus cirrhatus, Haliaeetus leucogaster, Spilornis cheela, Haliastur indus, and 11 sequences from Genbank were examined. Each species was confirmed through the Basic Local Alignment Search Tool (BLAST). The construction of phylogeny trees based on COI gene sequences was performed by the Neighbors-joining method where the calculation of the genetic distance matrix with the Kimura 2-parameter model was implemented in pairwise distance calculation in the Mega version 6.05 programe. The results of the analysis showed that the divergence within species ranged from 0 to 0.3% (0.13 ± 0.12%), between species ranged from 1.6 to 18.5% (12.8 ± 3.73%), between genera ranged from 13 to 18.6%, and the average in the Accipitridae Family was 11.8%. Therefore, it could form clusters in each species cohesively and clearly separated between the taxa analyzed.

scholarly journals Phylogenetic of Marble Goby (Oxyeleotris marmorata Blkr.) in South Sumatra Based on Cytochrome C Oxidase Subunit I (COI) Gene

10.4194/ga433 ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Mochamad Syaifudin ◽  
Dade Jubaedah ◽  
Ferdinand Hukama Taqwa ◽  
Ria Octaviani
Keyword(s):  
Genetic Distance ◽  
Coi Gene ◽  
Local Alignment ◽  
Coi Mtdna ◽  
Oxidase Subunit ◽  
Three Samples ◽  
Search Tool ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Musi River

Marble goby (Oxyeleotris marmorata) in Indonesia, spread across Sumatra, Kalimantan and Papua. The purpose of this study was to utilize a sequence of mitochondrial DNA Cytochrome Oxidase Subunit I gene, to analyze the phylogenetic tree and genetic distance between cultured and captured populations. This research was conducted on March-August 2020. The methods used in barcoding species were DNA isolation, amplification using PCR (Polymerase Chain Reaction) and sequencing of the COI mtDNA gene. The domesticated samples (n=3) were collected from Gandus Fish Seed Center (GFSC), while the wild samples (n=3) were captured from the Musi River in Beruge Village, Babat Toman District, both in Musi Banyuasin Regency. The sequenced COI mtDNA gene fragments were obtained from the PCR method. Three samples performed good PCR results, while the other three didn’t amplify properly. After the editing process, the COI gene sequencing produced a nucleotide length of 610 bp. Based on the BLAST (Basic Local Alignment Search Tool), domesticated marble goby (OMD2, OMD3) was in the same cluster with marble goby from the Musi River (OMS3). The genetic distance indicated that two specimens of domesticated marble goby were 100% identical, while the wild (OMS3) indicated a genetic distance of 0.0066 to domesticated species.

scholarly journals The genus Syntozyga Lower (Lepidoptera, Tortricidae) in China, with descriptions of two new species

ZooKeys ◽  
2021 ◽  
Vol 1028 ◽  
pp. 95-111
Author(s):  
Wenxu Yang ◽  
Ruiqin Dong ◽  
Xueling Song ◽  
Haili Yu
Keyword(s):  
New Species ◽  
Sequence Data ◽  
Chinese Mainland ◽  
Coi Gene ◽  
Neighbor Joining ◽  
Distribution Map ◽  
Two New Species ◽  
Gene Coi ◽  
Coi Sequences ◽  
First Time

Species of the genus Syntozyga Lower, 1901 (Lepidoptera, Tortricidae, Olethreutinae) from China are studied. Syntozyga apicispinatasp. nov. and S. similispirographasp. nov. are described, S. pedias (Meyrick, 1920) is recorded for the first time from China, and S. spirographa (Diakonoff, 1968) is newly recorded from the Chinese mainland. Adults and genitalia are illustrated, and a distribution map of the Chinese species is given. Keys to identify the Chinese species of Syntozyga are provided. Species of the genus are well clustered in a neighbor-joining tree based on the sequence data of the COI gene. COI sequences corresponding to the new species and S. spirographa (Diakonoff, 1968) are submitted to BOLD.

scholarly journals Cytogenomics of Deschampsia P. Beauv. (Poaceae) Species Based on Sequence Analyses and FISH Mapping of CON/COM Satellite DNA Families

Plants ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1105
Author(s):  
Alexandra V. Amosova ◽  
Lilit Ghukasyan ◽  
Olga Yu. Yurkevich ◽  
Nadezhda L. Bolsheva ◽  
Tatiana E. Samatadze ◽  
...  
Keyword(s):  
Chromosomal Rearrangements ◽  
5S Rdna ◽  
Chromosome Mapping ◽  
Local Alignment ◽  
Multiple Sequence ◽  
Satellite Dnas ◽  
Phylogenetic Studies ◽  
Search Tool ◽  
Main Components ◽  
First Time

The genus Deschampsia P. Beauv. (Poaceae) involves a group of widespread polymorphic species, and many of them are highly tolerant to stressful environmental conditions. Genome diversity and chromosomal phylogeny within the genus are still insufficiently studied. Satellite DNAs, including CON/COM families, are the main components of the plant repeatome, which contribute to chromosome organization. For the first time, using PCR-based (Polymerase Chain Reaction) techniques and sequential BLAST (Basic Local Alignment Search Tool) and MSA (Multiple Sequence Alignment) analyses, we identified and classified CON/COM repeats in genomes of eleven Deschampsia accessions and three accessions from related genera. High homology of CON/COM sequences were revealed in the studied species though differences in single-nucleotide alteration profiles detected in homologous CON/COM regions indicated that they tended to diverge independently. The performed chromosome mapping of 45S rDNA, 5S rDNA, and CON/COM repeats in six Deschampsia species demonstrated interspecific variability in localization of these cytogenetic markers and facilitated the identification of different chromosomal rearrangements. Based on the obtained data, the studied Deschampsia species were distinguished into karyological groups, and MSA-based schematic trees were built, which could clarify the relationships within the genus. Our findings can be useful for further genetic and phylogenetic studies.

scholarly journals Karyotype characteristics, chromosomal polymorphism and gene COI sequences of Chironomus heteropilicornis Wülker, 1996 (Diptera, Chironomidae) from the South Caucasus

2019 ◽  
Vol 13 (4) ◽  
pp. 339-357
Author(s):  
Mukhamed Kh. Karmokov
Keyword(s):  
Chromosomal Polymorphism ◽  
Genetic Distances ◽  
Caucasian Population ◽  
Coi Gene ◽  
The South ◽  
South Caucasus ◽  
Gene Coi ◽  
Banding Sequence ◽  
Separate Line ◽  
Coi Sequences

The study presents data on the karyotype characteristics, features of chromosomal polymorphism and the gene COI sequences of Chironomus heteropilicornis Wülker, 1996 (Diptera, Chironomidae) from the South Caucasus. We found 8 banding sequences in the Caucasian population. Overall, The Caucasian population of the species can be characterized as having a low level of polymorphism. We found one new banding sequence hpiA2 in the banding sequence pool of Ch. heteropilicornis. We observed inversion polymorphism only in the arm F. The dendrogram of genetic distances by Nei criteria (1972) shows a clear separation of the Caucasian population from populations of Siberia. At the same time, the distance between populations of Siberia and the population of South Caucasus (0.379–0.445) almost reach the mean distance (0.474 ± 0.314) between subspecies (Gunderina 2001). Due to this, we can assume that the population of South Caucasus separated from Siberian populations at the level of subspecies. Constructed on data for COI gene sequences the phylogenetic tree estimated by the Bayesian inference shows that the sequences of Ch. heteropilicornis from the South Caucasus form a separate line in the general branch of Ch. heteropilicornis sequences. At the same time, calculated K2P genetic distances between Ch. heteropilicornis sequences from Norway and Caucasus (2.0–2.2%) do not exceed the 3% threshold for the genus Chironomus.

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