scholarly journals DNA barcoding of Naididae (Annelida, Oligochaeta), based on cytochrome C oxidase gene and ITS2 region in China

2021 ◽  
Vol 9 ◽  
Author(s):  
Tingting Zhou ◽  
Wei Jiang ◽  
Hongzhu Wang ◽  
Yongde Cui
Keyword(s):  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Species Identification ◽  
Genetic Distances ◽  
Coi Gene ◽  
Tubifex Tubifex ◽  
Its2 Region ◽  
Aquatic Oligochaetes ◽  
Barcode Gap

Exploring the effectiveness of DNA barcoding in species identification is a prerequisite for biodiversity conservation and environmental monitoring. Aquatic oligochaetes could serve as excellent indicators in aquatic monitoring programmes. However, few studies have examined the effectiveness of DNA barcoding in these specific organisms. The mitochondrial cytochrome C oxidase (COI) gene of 83 specimens belonging to 40 species of 18 genera were sequenced in this study. The results showed that there was a barcode gap between species of Naididae and the intraspecific genetic distances of each species were smaller than interspecific genetic distances. The classification results of ABGD (Automatic Barcode Gap Discovery) were consistent with those of morphological identification, except for Tubifex tubifex and Lumbriculus variegatus. All species were successfully distinguished in the phylogenetic tree, based on the ITS2 region, which was coincident with the morphological result. Our results provided evidence that DNA barcoding can be used as an effective and convenient tool for species identification of the family Naididae and even for other aquatic oligochaetes.

scholarly journals DNA barcoding of Naididae (Annelida, Oligochaeta) based on COI and ITS2 genes in China

2021 ◽  
Author(s):  
Tingting Zhou ◽  
Hongzhu Wang ◽  
Yongde Cui
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Genetic Distances ◽  
Coi Gene ◽  
Tubifex Tubifex ◽  
Morphological Identification ◽  
Lumbriculus Variegatus ◽  
Mitochondrial Coi ◽  
Aquatic Oligochaete ◽  
Barcode Gap

Exploring the effectiveness of DNA barcoding in species identification is prerequisite for biodiversity conservation and environmental monitoring. Aquatic oligochaete could serve as an excellent indicator in aquatic monitoring programs. However, few studies have examined the effectiveness of DNA barcoding in these specific organisms. The mitochondrial COI gene and nuclear ITS2 gene of 83 specimens belonging to 36 species of 18 genera were sequenced in this study. The results showed that there was a barcode gap between species of Naididae, and the intraspecific genetic distances of each species were smaller than interspecific genetic distances. The classification results of ABGD (Automatic Barcode Gap Discovery) were consistent with those of morphological identification except for Tubifex tubifex and Lumbriculus variegatus. All species were successfully distinguished in the phylogenetic tree based on ITS2 gene, which was coincident with morphological result. Our results provided evidence that DNA barcoding can be used as an effective and convenient tool for species identification of the family Naididae and even aquatic oligochaete.

DNA barcoding of bats (Chiroptera) from the Colombian northern region

Mammalia ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Álvaro J. Benítez ◽  
Dina Ricardo-Caldera ◽  
María Atencia-Pineda ◽  
Jesús Ballesteros-Correa ◽  
Julio Chacón-Pacheco ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequences ◽  
Genetic Distances ◽  
Northern Region ◽  
Coi Gene ◽  
Individual Species ◽  
Species Variation ◽  
Molossus Molossus ◽  
Artibeus Lituratus

Abstract Bats are mammals of great ecological and medical importance, which have associations with different pathogenic microorganisms. DNA barcoding is a tool that can expedite species identification using short DNA sequences. In this study, we assess the DNA barcoding methodology in bats from the Colombian Northern region, specifically in the Córdoba department. Cytochrome oxidase subunit I (COI) gene sequences of nine bat species were typified, and their comparison with other Neotropic samples revealed that this marker is suitable for individual species identification, with ranges of intra-species variation from 0.1 to 0.9%. Bat species clusters are well supported and differentiated, showing average genetic distances ranging from 3% between Artibeus lituratus and Artibeus planirostris, up to 27% between Carollia castanea and Molossus molossus. C. castanea and Glossophaga soricina show geographical structuring in the Neotropic. The findings reported in this study confirm DNA barcoding usefulness for fast species identification of bats in the region.

scholarly journals First results of Central Asiatic Euchalcia DNA-studies: comparison of nucleotide sequence differences in COI between Euchalcia herrichi and Euchalcia gyulai (Lepidoptera: Noctuidae)

2020 ◽  
Vol 6 ◽  
pp. 1-4
Author(s):  
Stanislav K Korb
Keyword(s):  
Nucleotide Sequence ◽  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Coi Gene ◽  
First Results ◽  
The Difference ◽  
Coi Sequences ◽  
Lepidoptera Noctuidae ◽  
Two Populations

We submitted first results of the DNA studies of the Central Asiatic owlet moths of the genus Euchalcia. Standard cytochrome C oxidase subunit I (COI) gene fragments were sequenced for DNA barcoding of six specimens belonging to Euchalcia herrichi and Euchalcia gyulai. We compared the received sequences between discussed species and with two European Euchalcia species (E. variabilis and E. consona). We found no variability within the COI sequences of the samples collected in the same locality (Alai Mts., Kyrgyzstan), whereas the difference in COI sequences between two populations (Ketmen Mts., Kazakhstan and Alai Mts., Kyrgyzstan) was 0.005.

scholarly journals First results of Central Asiatic Euchalcia DNA-studies: comparison of nucleotide sequence differences in COI between Euchalcia herrichi and Euchalcia gyulai (Lepidoptera: Noctuidae)

2020 ◽  
Vol 6 ◽  
pp. 1-4
Author(s):  
Stanislav Korb
Keyword(s):  
Nucleotide Sequence ◽  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Coi Gene ◽  
First Results ◽  
The Difference ◽  
Coi Sequences ◽  
Lepidoptera Noctuidae ◽  
Two Populations

We submitted first results of the DNA studies of the Central Asiatic owlet moths of the genus Euchalcia. Standard cytochrome C oxidase subunit I (COI) gene fragments were sequenced for DNA barcoding of six specimens belonging to Euchalcia herrichi and Euchalcia gyulai. We compared the received sequences between discussed species and with two European Euchalcia species (E. variabilis and E. consona). We found no variability within the COI sequences of the samples collected in the same locality (Alai Mts., Kyrgyzstan), whereas the difference in COI sequences between two populations (Ketmen Mts., Kazakhstan and Alai Mts., Kyrgyzstan) was 0.005.

Sequencing of COI gene in four rodent pests for species identification

DNA Barcodes ◽  
2015 ◽  
Vol 3 (1) ◽  
Author(s):  
Rengarajan Rengasamy Lakshminarayanan ◽  
Achiraman Shanmugam ◽  
Archunan Govindaraju
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Species Identification ◽  
Crop Production ◽  
Morphometric Parameters ◽  
Coi Gene ◽  
Pest Species ◽  
Important Group

AbstractAmong mammals, rodents are the most important group since they influence the crop production and protection. Species identification of rodents on morphometric parameters is cumbersome and often misleading. However, DNA based identification would enable accurate species identification. For this purpose, we examined 650 bp of Cytochrome c oxidase subunit1 (COI) in four rodent pest species namely

scholarly journals Cytochrome c oxidase barcodes for aquatic oligochaete identification: development of a Swiss reference database

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4122 ◽  
Author(s):  
Régis Vivien ◽  
Maria Holzmann ◽  
Inge Werner ◽  
Jan Pawlowski ◽  
Michel Lafont ◽  
...  
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Morphological Data ◽  
Reference Database ◽  
Its2 Region ◽  
Aquatic Oligochaete ◽  
Aquatic Oligochaetes ◽  
Morphological Criteria ◽  
Unidentified Species ◽  
Coi Sequences

Introduction Aquatic oligochaetes represent valuable indicators of the quality of sediments of watercourses and lakes, but their difficult identification based on morphological criteria compromises their more common use for eco-diagnostic analyses. This issue could be overcome by using DNA barcodes for species identification. A 10% threshold of cytochrome c oxidase (COI) divergence was proposed for differentiating between oligochaete species based on molecular and morphological data. A Swiss database of COI sequences of aquatic oligochaetes was initiated in 2012. The aim of this study is to complement the Swiss oligochaete database of COI sequences and to confirm the relevance of this threshold for species delimitation. Methods We sequenced the COI sequence of 216 specimens collected in different regions of Switzerland and ITS2 region of some lineages whose delimitation with COI data was doubtful. Results We distinguished 53 lineages, among which 34 were new for Switzerland and 17 sequenced for the first time. All the lineages were separated by more than 10% of COI variation, with the exception of some species within Nais and Uncinais. In these two genera, the threshold was lowered to 8% to be congruent with the morphological analysis. The total number of lineages reported so far for Switzerland is 75, including 59 morphospecies or unidentified species and 16 cryptic species. Discussion Our study shows that the threshold of 10% of COI divergence is generally appropriate to distinguish aquatic oligochaete lineages, but that it must be adjusted for some species. The database reported here will be complemented in the future in parallel to the development of genetic oligochaete indices.

scholarly journals Identifikasi ikan gabus, Channa spp. (Scopoli 1777) stok liar dan generasi I hasil domestikasi berdasarkan gen Cytochrome C Oxidase Subunit I (COI)

2018 ◽  
Vol 17 (2) ◽  
pp. 165 ◽  
Author(s):  
Irmawati Irmawati ◽  
Joeharnani Tresnati ◽  
Liestiaty Fachruddin ◽  
Nur Rahmawaty Arma ◽  
Andi Haerul
Keyword(s):  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Native Species ◽  
First Generation ◽  
Coi Gene ◽  
Oxidase Subunit ◽  
South Sulawesi ◽  
Phylogenetic Resolution ◽  
Channa Striata

The snakehead fish (Channidae) is widely distributed in inland water of Indonesia. This fish is native species in Suma-tera, Java and Kalimantan, but non-native species in Sulawesi and Papua. Study on molecular identification and phylo-geny of this fish using cytochrome c oxidase subunit I (COI) gene has only been conducted on snakehead fish origin from Tasikmalaya, Ambarawa, Bali, Aceh, Pontianak, and Banjarmasin waters, but none is available in South Sulawesi waters. The objectives of this research are to identify species of snakehead fish from Towuti Lake Sorowako and the first generation (F1) of domesticated snakehead fish from Bantaeng waters of South Sulawesi using COI gene for DNA barcoding, and to analyze the phylogenetic resolution of the fish. Partial sequences of the COI gene of the snakehead fish were aligned with sequences of snakehead fish deposited in GenBank. The phylogenetic tree was constructed using MEGA 7.0.20 program. The result indicated that COI gene nucleotides of snakehead fish from Towuti Lake Sorowako showed 99% homology with Channa striata acc no. KU692418 and KU692421, and showed 98% homology with those of acc no. KU852443. Therefore it can be conclude that Channa striata exist in Towuti Lake Sorowako. Nucleotide sequences of the first generation (F1) of domesticated snakehead fish from Bantaeng waters showed 65% homology with Channa pleurophthalma (acc no. KJ937390) origins from Banjarmasin waters and Channa gachua (acc no. KX389277). Based on this result, it assumed that snakehead fish from Towuti Lake Sorowako are distantly in gene to those from Bantaeng waters, and further analyses are required to identify the population of snakehead fish from Bantaeng waters. Abstrak Populasi ikan gabus (famili Channidae) tersebar luas di wilayah perairan tawar Indonesia. Ikan gabus merupakan ikan asli di Sumatera, Jawa, dan Kalimantan) tetapi merupakan ikan introduksi di Sulawesi dan Papua. Identifikasi berdasar-kan gen cytochrome c oxidase subunit I (COI) telah dilakukan terhadap ikan gabus dari perairan di Tasikmalaya, Amba-rawa, Bali, Aceh, Pontianak dan Banjarmasin, tetapi ikan gabus dari perairan Sulawesi Selatan belum dilakukan. Tuju-an penelitian adalah untuk mengidentifikasi species ikan gabus dari Danau Towuti Sorowako dan ikan gabus generasi I (F1) hasil domestikasi dari induk yang berasal dari perairan tawar Kabupaten Bantaeng Sulawesi Selatan menggunakan gen COI untuk DNA barcoding, dan untuk menganalisis filogeni ikan gabus tersebut. Sekuen gen COI ikan gabus terse-but disejajarkan dengan sekuen nukleotida ikan gabus yang terdeposit di GenBank. Pohon filogenetik dikonstruksi de-ngan menggunakan program MEGA 7.0.20. Hasil penelitian menunjukkan bahwa nukleotida gen COI sampel ikan gabus dari Danau Towuti Sorowako memiliki kemiripan 99% dengan Channa striata nomor aksesi KU692418 dan KU692421 dan 98% dengan Channa striata nomor aksesi KU852443 sehingga dapat disimpulkan bahwa di Danau To-wuti terdapat ikan gabus jenis Channa striata. Tingkat kemiripan sekuen nukleotida ikan gabus F1dari perairan Kabu-paten Bantaeng adalah 65% dengan ikan gabus Channa pleurophthalma (KJ937390) asal perairan Banjarmasin dan ikan gabus Channa gachua (KX389277). Berdasarkan hasil tersebut maka diduga bahwa ikan gabus dari Danau Towu-ti Sorowako berkerabat jauh dengan ikan gabus dari perairan Bantaeng, dan diperlukan analisis yang lebih lanjut untuk menentukan jenis populasi ikan gabus F1 asal perairan tawar Kabupaten Bantaeng tersebut.

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