DNA Barcoding of the Family: Leiognathidae in the Water of Bay of Bengal, Odisha Coast, India Based on 16s rRNA and COI Gene Sequences

Seth, Jaya Kishor; Barik, Tapan Kumar

doi:10.1007/s41208-021-00324-1

Cited by 9 publications

(5 citation statements)

References 19 publications

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“…Accurate identi cation of organisms based on partial sequence of COI gene. However, the success of species identi cation using DNA barcoding is dependent on the accuracy of species identi cation in DNA barcode libraries, speci cally GenBank and the BOLD System (Nur et al 2022) and ABGD analysis (Seth and Barik 2021). DNA barcoding clearly distinguish Echinoderm species with barcodes on Australia, Canada, India, Thailand, Germany, and Indonesia (Ward et al 2005, Hubert et al 2008).…”

Section: Introductionmentioning

confidence: 99%

New Record of Echinoderms from Gili Ketapang Island by Combining DNA Barcoding and Morphology: A Baseline Report

Nugroho

Ardiansyah

Kurniawan

et al. 2022

Preprint

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Echinoderms are marine water invertebrates that are showing diverse morphologies and grouped in five classes, however the reports on this species from Gili Ketapang Island, East Java is currently limited. DNA barcodes (DNA fragments of the 5' end of the cytochrome c oxidase subunit I gene, COI) have been used to support the morphological examination in identifying evolutionary lineages. This study aims to identify the morphology and supplement of COI sequence and phylogenetic of Echinoderms from Gili Ketapang Island. A total of sixteen samples of Echinoderms were collected from Gili Ketapang, Probolinggo, Indonesia, then identified based on morphological characters, and supports identification was confirmed using molecular data. Subsequently, molecular characterization and identification was conducted based on 503 bp of COI gene similarity, sequence variation, genetic distance, phylogenetic topology, and BOLD System. According to the results, sixteen sample were identified as Diadema setosum; Macrophiothrix longipeda; Archaster typicus; Echinometra mathaei, Holothuria atra; Linckia laevigata, Bohadschia argus, and Ophiactis savignyi. Each species was associated with a specific DNA barcode cluster and the relationship among these species was clearly revealed. Each species based on morphological identification and COI sequence clusters were congruent. The median joining network and Automatic Barcode Gap Discovery (ABGD) analysis showed this Echinoderms population from Probolinggo had relatives of 14 haplotypes and divided into eight haplogroups. Furthermore, the population belonged to the same haplogroup but had different haplotypes. This newly records established sequence reference library for the Gili Ketapang Island.

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Section: Introductionmentioning

confidence: 99%

New Record of Echinoderms from Gili Ketapang Island by Combining DNA Barcoding and Morphology: A Baseline Report

Nugroho

Ardiansyah

Kurniawan

et al. 2022

Preprint

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“…Total genomic DNA was extracted from ethanol‐fixed tissues followed by proteinase K digestion, phenol–chloroform extraction, and ethanol precipitation. Mitochondrial DNA (mtDNA) regions (e.g., 16S rRNA, COI , and Cytb ) have been useful and cost‐effective phylogenetic markers in vertebrates (Bernt et al, 2019; Seth & Barik, 2021). We amplified mtDNA fragments of 16S rRNA, COI, Cytb , and D‐loop with primers designed from the Rhizomys pruinosus mitochondrial genome, downloaded from NCBI (NC_021478.1) (Table ).…”

Section: Methodsmentioning

confidence: 99%

Fragmented habitats and Pleistocene climate shaped diversification of the hoary bamboo rat (Rhizomys pruinosus) in the mountainous plateau of SW China

Gao

Yan

Yin

et al. 2022

J of Systematics Evolution

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The southwest mountainous region of China has been characterized as one of the worldwide biodiversity hotspots, but mechanisms underlying diversification of organisms in this region are still not clear. We assessed whether fragmented mountainous habitats and Pleistocene climate changes impacted the genetic diversity and diversification patterns of the hoary bamboo rat (Rhizomys pruinosus Blyth), a widely distributed species of rodent in SW China. Genetic diversity analyses were undertaken based on four mitochondrial DNA regions and 12 nuclear microsatellite loci (simple sequence repeats), representing 153 individuals from 24 populations across SW China. Moreover, we investigated correlations between genotype and geographical components, and predicted species distribution models for R. pruinosus under the historical and present climate conditions. Both mitochondrial DNA and simple sequence repeat markers revealed substantial genetic diversity and strong differentiation between populations. Phylogeographical analyses revealed two phylogenetic clades that were consistent with their geographical distributions (eastern and western clades). We inferred that the divergence of R. pruinosus was largely driven by Quaternary climatic oscillations and regionally fragmented mountainous habitats with environmental and geographical heterogeneity. Overall, our study revealed diversification patterns of R. pruinosus-patterns that may be shared by small alpine vertebrates in SW China.

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“…Furthermore, still using the older chemistry, we could demonstrate that the main pollen resources of bumble bees can be identified by MinION nanopore sequencing to mostly similar extent as with Illumina sequencing (Leidenfrost et al, 2020). ONT provides a protocol for sequencing short reads, called Amplicons by Ligation (SQK-LSK109), that can be used for metabarcoding (Knot et al, 2020;Seth and Barik, 2021).…”

Section: Hands-on …mentioning

confidence: 99%

A primer on pollen assignment by nanopore-based DNA sequencing

Prudnikow

Pannicke²,

Wünschiers³

2023

Front. Ecol. Evol.

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The possibility to identify plants based on the taxonomic information coming from their pollen grains offers many applications within various biological disciplines. In the past and depending on the application or research in question, pollen origin was analyzed by microscopy, usually preceded by chemical treatment methods. This procedure for identification of pollen grains is both time-consuming and requires expert knowledge of morphological features. Additionally, these microscopically recognizable features usually have a low resolution at species-level. Since a few decades, DNA has been used for the identification of pollen taxa, as sequencing technologies evolved both in their handling and affordability. We discuss advantages and challenges of pollen DNA analyses compared to traditional methods. With readers with little experience in this field in mind, we present a hands-on primer for genetic pollen analysis by nanopore sequencing. As our lab mainly works with pollen collected within agroecological research projects, we focus on pollen collected by pollinating insects. We briefly consider sample collection, storage and processing in the laboratory as well as bioinformatic aspects. Currently, pollen metabarcoding is mostly conducted with next-generation sequencing methods that generate short sequence reads (<1 kb). Increasingly, however, pollen DNA analysis is carried out using the long-read generating (several kb), low-budget and mobile MinION nanopore sequencing platform by Oxford Nanopore Technologies. Therefore, we are focusing on aspects for palynology with the MinION DNA sequencing device.

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DNA Barcoding of the Family: Leiognathidae in the Water of Bay of Bengal, Odisha Coast, India Based on 16s rRNA and COI Gene Sequences

Cited by 9 publications

References 19 publications

New Record of Echinoderms from Gili Ketapang Island by Combining DNA Barcoding and Morphology: A Baseline Report

New Record of Echinoderms from Gili Ketapang Island by Combining DNA Barcoding and Morphology: A Baseline Report

Fragmented habitats and Pleistocene climate shaped diversification of the hoary bamboo rat (Rhizomys pruinosus) in the mountainous plateau of SW China

A primer on pollen assignment by nanopore-based DNA sequencing

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