DNA barcoding allows identification of undescribed crab megalopas from the open sea

AbstractMegalopas of 15 brachyuran crab species collected in the open sea plankton, and unknown until now, were identified using DNA barcodes (COI and 16S rRNA). Specimens belonging to the families Portunidae, Pseudorhombilidae and Xanthidae (Crustacea, Decapoda, Brachyura), and corresponding to the species Achelous floridanus, Arenaeus mexicanus, Callinectes amnicola, C. arcuatus, C. ornatus, C. toxones, Charybdis (Charybdis) hellerii, Portunus hastatus, Thalamita admete, Scopolius nuttingi, Etisus odhneri, Liomera cinctimanus, Neoliomera cerasinus, Pseudoliomera variolosa, and Williamstimpsonia stimpsoni, are described and illustrated, and compared with other congeneric species previously described. We also provide a new geographical record for N. cerasinus and the most remarkable features for each species.

Download Full-text

Diversity, phylogeny and DNA barcoding of brachyuran crabs in artificially created mangrove environments

10.1101/2020.09.07.286823 ◽

2020 ◽

Cited By ~ 4

Author(s):

Ganesh Manikantan ◽

Chinnamani PrasannaKumar ◽

J. Vijaylaxmi ◽

S. R. Pugazhvendan ◽

Narra Prasanthi

Keyword(s):

Dna Barcoding ◽

High Throughput Sequencing ◽

Species Abundance ◽

Mangrove Ecosystem ◽

Crab Species ◽

Vegetative Cover ◽

Mangrove Species ◽

Association Index ◽

Brachyuran Crab ◽

Brachyuran Crabs

AbstractGlobally, at the rate of 1-2 percent per annum, mangrove coverings are disappearing and 35 percent have been lost in the last 20 years due to changes in climate and human activities. No mangrove-associated crabs were found when the mangroves were artificially transplanted 25 years ago in the Vellar estuary. This mangrove ecosystem was sampled for brachyuran biodiversity estimation, species abundance, composition and evaluation of the effectiveness of DNA barcoding in brachyuran crabs species identification. A total of 2844 crabs were collected, representing 35 species within 8 families belonging to 20 genera. Four brachyuran crab species, that is, Uca lactae, U. Triangularis, Selatium brockii, and Neosarmatium asiaticum account for >70% of the total abundance. An approximate 87.5% of crab species estimated to occur by various species estimator were recovered in the present study. Between Uca lactea and U. triangularis, the maximum association index value was observed (97.7%). Cluster analysis grouped the sampled stations according to the types of mangrove species, clearly influencing the structure and composition of the brachyuran crabs. In general, vegetative cover composed of multiple species of mangroves is preferred for the abundance of all collected crabs species, and particularly Neosarmatium asiaticum. Analysis of DNA barcoding indicates that 40% of the brachyuran species gathered in this sample were first barcoded. The advent of new high-throughput sequencing technologies will change biomonitoring applications and surveys drastically in the near future, making reference datasets like ours relevant.

Download Full-text

New Geographical Record of Three Cumacean Species Eudorella nana, Leucon affinis, Leucon siphonatus and One Rare Amphipod Presence Confirmation, Stenothoe bosphorana, in Adriatic Sea, Italy

Thalassas An International Journal of Marine Sciences ◽

10.1007/s41208-021-00294-4 ◽

2021 ◽

Author(s):

P. Strafella ◽

V. Salvalaggio ◽

C. Cuicchi ◽

E. Punzo ◽

A. Santelli ◽

...

Keyword(s):

Adriatic Sea ◽

Geographical Record ◽

New Geographical Record ◽

First Time ◽

Adriatic Basin

AbstractThree cumacean species, Eudorella nana Sars, 1879, Leucon affinis Fage, 1951, Leucon siphonatus Calman, 1905, were recorded for the first time and one rare amphipod presence, Stenothoe bosphorana Sowinsky, 1898, was confirmed in the Adriatic basin.

Download Full-text

A new geographical record ofPolycera hedgpethiEr. Marcus, 1964 (Nudibranchia: Polyceridae) and evidence of its established presence in the Mediterranean Sea, with a review of its geographical distribution

Marine Biology Research ◽

10.1080/17451000.2012.706306 ◽

2012 ◽

Vol 8 (10) ◽

pp. 969-981 ◽

Cited By ~ 10

Author(s):

Erica Keppel ◽

Marco Sigovini ◽

Davide Tagliapietra

Keyword(s):

Mediterranean Sea ◽

Geographical Distribution ◽

Geographical Record ◽

The Mediterranean ◽

New Geographical Record

Download Full-text

Benchmarking DNA barcodes: an assessment using available primate sequences

Genome ◽

10.1139/g06-025 ◽

2006 ◽

Vol 49 (7) ◽

pp. 851-854 ◽

Cited By ~ 48

Author(s):

Mehrdad Hajibabaei ◽

Gregory AC Singer ◽

Donal A Hickey

Keyword(s):

New Species ◽

Cryptic Species ◽

Dna Barcoding ◽

Species Identification ◽

Dna Sequences ◽

Phylogenetic Relationships ◽

Primate Species ◽

Dna Barcodes ◽

Global Biodiversity ◽

Efficient Sequence

DNA barcoding has been recently promoted as a method for both assigning specimens to known species and for discovering new and cryptic species. Here we test both the potential and the limitations of DNA barcodes by analysing a group of well-studied organisms—the primates. Our results show that DNA barcodes provide enough information to efficiently identify and delineate primate species, but that they cannot reliably uncover many of the deeper phylogenetic relationships. Our conclusion is that these short DNA sequences do not contain enough information to build reliable molecular phylogenies or define new species, but that they can provide efficient sequence tags for assigning unknown specimens to known species. As such, DNA barcoding provides enormous potential for use in global biodiversity studies.Key words: DNA barcoding, species identification, primate, biodiversity.

Download Full-text

Species Validation of Mole Crabs Based on Molecular Marker of 16s rRNA from Bantul and Purworejo waters

Tropical Fisheries Management Journal ◽

10.29244/jppt.v3i2.30434 ◽

2019 ◽

Vol 3 (2) ◽

pp. 28-35

Author(s):

Nurlisa A Butet ◽

Inge Anggraeni Bela Putri Dewi ◽

Zairion Zairion ◽

Agus Alim Hakim

Keyword(s):

16S Rrna ◽

Molecular Marker ◽

Dna Barcoding

Undur-undur laut hidup pada habitat intertidal pantai berpasir. Identifikasi spesies akuatik sering mengalami kesalahan yang diakibatkan oleh fenomena cryptic spesies, sehingga diperlukan teknik identifikasi dengan pendekatan molekuler yaitu DNA barcoding. Penelitian ini bertujuan untuk menvalidasi dan menganalisis hubungan kekerabatan dari undur-undur laut berdasarkan marka molekuler gen 16S rRNA dari perairan Bantul dan Purworejo. Kit komersil berupa Gene Aid digunakan untuk isolasi dan ekstraksi DNA dan dihasilkan tiga DNA total dari setiap lokasi. DNA total dengan kualitas baik dilanjutkan pada proses amplifikasi menggunakan teknik PCR dengan primer 16S rRNA. Hasil sekuen gen 16S rRNA sampel undur-undur laut disejajarkan dengan beberapa sekuen dengan spesies lain dari genus Emerita, Scylla, dan Portunus yang berasal dari GeneBank. Validasi spesies dilakukan dengan mengunakan BLASTn. Jarak genetik dan pohon filogenik didapatkan dari program MEGA 5.0. Sampel undur-undur laut yang berasal dari Bantul dan Purworejo tidak berbeda nyata dan sampel berasal dari sumber genetik yang sama.

Download Full-text

Parasitic wasps as natural enemies of aphid populations in the Mashhad region of Iran: New data from DNA barcodes and SEM

Archives of Biological Sciences ◽

10.2298/abs1104225d ◽

2011 ◽

Vol 63 (4) ◽

pp. 1225-1234 ◽

Cited By ~ 1

Author(s):

Reyhaneh Darsouei ◽

Javad Karimi ◽

Mehdi Modarres-Awal

Keyword(s):

Dna Barcoding ◽

Modern Method ◽

Diaeretiella Rapae ◽

Coi Gene ◽

Dna Barcodes ◽

Parasitic Wasps ◽

Pome Fruit ◽

Initial Attempt ◽

Morphometric Characters ◽

Preliminary Identification

DNA barcoding is a modern method for the identification of different species, including insects. Among animals, the major emphasis of DNA barcoding is on insects. Due to this global trend we addressed this approach for surveying a group of insects. The parasitic wasps (including primary and hyperparasitoids) of pome fruit orchard aphids were collected from Iran-Mashhad during 2009-2010. Preliminary identification of this group was performed by using morphological and morphometric characters and SEM. The COI gene in the specimens was amplified and sequenced. In this survey, Aphidius matricariae, Binodoxys angelicae, Diaeretiella rapae, Ephedrus persicae, Lysiphlebus fabarum and Praon volucre parasitoids and Alloxysta sp., Asaphes suspensus, Dendrocerus carpenteri, Pachyneuron aphidis, Syrphophagus aphidivorus hyperparasitoids were studied. Based on intra-interspecies distances and phylogenetic analysis using NJ, all species possess diagnostic barcode sequences. The results of this study show that the COI sequence could be useful in identification study of this group of insects. Here we have provided the first GenBank data for the COI gene of the above-mentioned hyperparasitoids as well as an initial attempt toward preparing DNA barcodes for Iranian parasitoid and hyperparasitoid aphids.

Download Full-text

Investigating leaf beetles (Coleoptera, Chrysomelidae) on the west coast islands of Sabah via checklist-taking and DNA barcoding

10.7287/peerj.preprints.26801 ◽

2018 ◽

Author(s):

Kam-Cheng Yeong ◽

Haruo Takizawa ◽

Thor-Seng Liew

Keyword(s):

Dna Barcoding ◽

West Coast ◽

Leaf Beetle ◽

Coi Gene ◽

Beetle Species ◽

Dna Barcodes ◽

The West ◽

Leaf Beetles ◽

Baseline Knowledge ◽

Island Habitats

Sabah, northern Borneo is one of the world’s most well-recognized biodiversity hotspots famous for the incredible diversity of its flora and fauna. Plenty of studies of leaf beetle fauna from this region have been conducted over the past 30 years. Yet, our knowledge of the leaf beetle fauna from island habitats remains scarce despite Sabah having the highest number of islands in Malaysia (ca. 500 islands). In this study, we collected leaf beetle fauna from 13 islands off the west coast of Sabah between January 2016 and March 2017. All specimens were identified to species level. Species names were assigned when the specimens fitted the description of species in the literature and morpho-species were assigned when the species names could not be determined. In addition, DNA barcodes – mitochondarial COI gene – of the species were sequenced. A total of 68 species from 31 genera and 5 subfamilies were collected with 12 species name being determined. From the data it was established that Pulau Gaya has the highest species richness (42 species), followed by Pulau Tiga (22 species) and Pulau Sapangar (18 species). Furthermore, a total of 64 Barcode Index Numbers consisting of 101 DNA barcodes were obtained from 60 leaf beetle species. The mean intraspecific and interspecific distances were determined as 0.77 % and 16.11 %, respectively. In addition, DNA barcoding also reveals phenotypic variation in leaf beetle species, particularly in the case of the subfamily Galerucinae. This study provides baseline knowledge and information about the DNA barcodes of leaf beetle species on Sabah’s island habitats for use in future studies.

Download Full-text

A Review of Recent Phytomedicinal Investigations and the Need for DNA Barcoding of Endemic Plants of Northern Cyprus

Journal of Pharmaceutical Research International ◽

10.9734/jpri/2020/v32i930483 ◽

2020 ◽

pp. 61-70

Author(s):

Dudu Özkum Yavuz ◽

Mustapha Bulama- Modu

Keyword(s):

Quality Control ◽

Dna Barcoding ◽

Dna Sequences ◽

Pharmacological Properties ◽

Endemic Plants ◽

Dna Barcodes ◽

Inclusion Criteria ◽

Ovid Medline ◽

Northern Cyprus ◽

Medicinal Properties

Aims: To review the phytomedicinal researches on endemic plants of Northern Cyprus and to assess the plants of their DNA barcoding status. Study Design: A review. Methodology: This work reviewed available and accessible original articles in EBSCO, Ovid MEDLINE®, PubMed®, ScienceDirectTM, Scopus® and Web of ScienceTM databases on phytomedicinal investigations and BOLD System, MMDBD version 1.5 and GenBank® on DNA barcodes of the endemic plants of Northern Cyprus until May, 2020. Using keywords searches related to phytochemistry, biological activity and DNA barcoding, DNA Sequences and the data obtain evaluated and the information that does not meet the inclusion criteria were excluded. We believe that this information would tentatively help researchers to ethically explore these plants for their Medicinal and Aromatic potentials. Results: Only 6 of the 20 endemic plants of Northern Cyprus were phytopharmaceutically investigated, while DNA sequences of 5 were found to be deposited in the publicly accessible databases accounting for 30% and 25% of the total plants respectively. Conclusion: Endemism is related to uniqueness in features including the phytomedicinal features, thus Northern Cyprus endemic plants hold ample of such. However the results of this review showed that only few were harnessed for their medicinal properties and hence the need for their pharmacological properties and comprehensive barcoding for proper authentication, detection of adulteration, and quality control.

Download Full-text

Description of new apterous winter species of Leuctra (Plecoptera: Leuctridae) based morphology and DNA barcoding and further records to stonefly fauna of the Caucasus, Georgia

Zootaxa ◽

10.11646/zootaxa.4585.3.9 ◽

2019 ◽

Vol 4585 (3) ◽

pp. 547

Author(s):

VALENTINA A. TESLENKO ◽

DMITRY M. PALATOV ◽

ALEXANDER A. SEMENCHENKO

Keyword(s):

New Species ◽

Dna Barcoding ◽

Interspecific Variation ◽

Genetic Distances ◽

Dna Barcodes ◽

The Caucasus ◽

Diagnostic Characters ◽

Males And Females ◽

Lesser Caucasus ◽

First Time

Leuctra adjariae sp. n. and Leuctra georgiae sp. n. (Plecoptera: Leuctridae) are described as two new apterous stonefly species from the Meskheti Range (Lesser Caucasus) in southwestern Georgia. Descriptions and illustrations are provided for both sexes and diagnostic characters are discussed. Males and females of the two species are associated by DNA barcodes. Comparisons with corresponding regions of COI between L. adjariae sp. n. and L. georgiae sp. n. produced K2P genetic distances of 8.38%, values well associated with interspecific variation. The well-supported monophyly as well as results of an ABGD analysis confirms the validity of both new species. Capnioneura gouanerae Vinçon & Sivec, 2011, previously described and known only from Turkey, is reported for the first time for the Caucasus.

Download Full-text