scholarly journals Genetic identification of bat species for pathogen surveillance across France

PLoS ONE ◽  
2022 ◽  
Vol 17 (1) ◽  
pp. e0261344
Author(s):  
Youssef Arnaout ◽  
Zouheira Djelouadji ◽  
Emmanuelle Robardet ◽  
Julien Cappelle ◽  
Florence Cliquet ◽  
...  

With more than 1400 chiropteran species identified to date, bats comprise one-fifth of all mammalian species worldwide. Many studies have associated viral zoonoses with 45 different species of bats in the EU, which cluster within 5 families of bats. For example, the Serotine bats are infected by European Bat 1 Lyssavirus throughout Europe while Myotis bats are shown infected by coronavirus, herpesvirus and paramyxovirus. Correct host species identification is important to increase our knowledge of the ecology and evolutionary pattern of bat viruses in the EU. Bat species identification is commonly determined using morphological keys. Morphological determination of bat species from bat carcasses can be limited in some cases, due to the state of decomposition or nearly indistinguishable morphological features in juvenile bats and can lead to misidentifications. The overall objective of our study was to identify insectivorous bat species using molecular biology tools with the amplification of the partial cytochrome b gene of mitochondrial DNA. Two types of samples were tested in this study, bat wing punches and bat faeces. A total of 163 bat wing punches representing 22 species, and 31 faecal pellets representing 7 species were included in the study. From the 163 bat wing punches tested, a total of 159 were genetically identified from amplification of the partial cyt b gene. All 31 faecal pellets were genetically identified based on the cyt b gene. A comparison between morphological and genetic determination showed 21 misidentifications from the 163 wing punches, representing ~12.5% of misidentifications of morphological determination compared with the genetic method, across 11 species. In addition, genetic determination allowed the identification of 24 out of 25 morphologically non-determined bat samples. Our findings demonstrate the importance of a genetic approach as an efficient and reliable method to identify bat species precisely.

2021 ◽  
Vol 104 (2) ◽  
pp. 003685042110261
Author(s):  
Wannapimol Kriangwanich ◽  
Korakot Nganvongpanit ◽  
Kittisak Buddhachat ◽  
Puntita Siengdee ◽  
Siriwadee Chomdej ◽  
...  

Wildlife trading and the illegal hunting of wildlife are contributing factors to the biodiversity crisis that is presently unfolding across the world. The inability to control the trade of animal body parts or available biological materials is a major challenge for those who investigate wildlife crime. The effective management of this illegal trade is an important facet of wildlife forensic sciences and can be a key factor in the enforcement of effective legislation surrounding the illegal trade of protected and endangered species. However, the science of wildlife forensics is limited by the absence of a comprehensive database for wildlife investigations. Inter-simple sequence repeat markers (ISSR) coupled with high resolution melting analysis (HRM) have been effectively used for species identification of 38 mammalian species. Six primers of the ISSR markers were chosen for species identification analysis. From six ISSR primers resulting in a range of accuracy of 33.3%–100% and 100% in terms of precision in every primer. Furthermore, 161 mammalian samples were 100% distinguished to the correct species using these six ISSR primers. ISSR-HRM analysis was successfully employed in determining mammal identification among varying mammalian species, and thus could serve as an effective alternative tool or technique in the species identification process. This option would offer researchers a heightened level of convenience in terms of its performance and the ease with which researchers or field practice veterinarians would be able to interpret results in effectively identifying animal parts at wildlife investigation crime scenes.


2020 ◽  
Vol 13 (1) ◽  
pp. 96-103
Author(s):  
Dorothea Vera Megarani ◽  
Herjuno Ari Nugroho ◽  
Zahrah Prawita Andarini ◽  
Yura Dwi Risa B. R. Surbakti ◽  
Rini Widayanti

Aim: This study aimed to determine the genetic characterization and phylogenetic structure of Indonesian indigenous catfish using cytochrome B (Cyt B) sequences. Materials and Methods: The genomes of 26 catfishes caught from nine rivers from nine different geographical locations around Indonesia were analyzed. The tissue isolation method was used to isolate the total genome of the fishes. Furthermore, polymerase chain reaction was done to amplify the mtDNA Cyt B using the CytBF and CytBR primers. Following sequencing, the analysis of genetic variation and the phylogenetic relationship was performed using MEGA version X software. Results: Cyt B gene sequencing attained a total of 1139 nucleotides encrypting 379 amino acids for all samples. The ClustalW alignment program using MEGA X software revealed 395 substituted nucleotides, which then translated into 63 amino acid variation sites among all 26 samples. No amino acids in catfish BB were different compared to catfish PM, MP, and KR2,3. Catfish MS had one modified amino acid; KR1 and KS had two different amino acids; BF had 38 different amino acids; EM had 31 different amino acids; and BSBJ had 26 different amino acids compared to catfish BB. The most significant alteration of amino acids was between catfish EM and BF (49 amino acids). Conclusion: Indonesian catfish were divided into five clades based on the Cyt B gene. Samples KR and MP (Sumatra); MS and BB (Kalimantan); and PM (Java) were clustered with Hemibagrus nemurus and Hemibagrus wyckioides (Bagridae family). Samples from Kalimantan (KS) and one sample of KR (KR1) from Sumatra were clustered with Sperata seenghala and Hemibagrus spilopterus (Bagridae family). Samples from Java (BSBJ) were clustered with Pseudolais pleurotaenia (Pangasiidae family). Samples EM (Java) were together with Mystus cavasius (Bagridae family). Samples from West Papua were clustered with Potamosilurus latirostris (Ariidae family).


2018 ◽  
Vol 10 (1) ◽  
pp. 6
Author(s):  
Roza Elvyra ◽  
Dedy Duryadi Solihin

The mitochondrial cytochrome b (cyt-b) gene as a phylogenetic marker of lais fish Kryptopterus schilbeides from Kampar River in Riau has been studied. This is a prelimininary research on the utility of cyt-b gene as a molecular marker to obtain species diversity and phylogenetic relationship among Kryptopterus fishes from Kampar River. The primers of L14841 and H15149 were used to amplify the cyt-b gene. The results showed that K. schilbeides has isoleusine at site-81 and metionine at site-114; K. schilbeides from Kampar River and K. schilbeides from GenBank form a phylogeny cluster at 45% value.


2020 ◽  
Vol 52 (1) ◽  
pp. 71-75
Author(s):  
Maurizio Cornalba ◽  
Paolo Biella ◽  
Andrea Galimberti

DNA barcoding is well-known to support morphological species identification and it can be helpful for unveiling unexpected populations divergence patterns, especially in the context of the impacts on species posed by global change. In this note, we provided the first Italian record of the alpine mining bee Andrena allosa Warncke, 1975, confirmed with DNA barcoding. In addition, genetic identification of a specimen of Andrena praecox (Scopoli 1753) from western Italy pointed to an unexpected intraspecific genetic structuring at COI DNA barcoding region, with sequences from the Italian and the western sector of its global distribution differing 2.22% (p-dist) from populations of the eastern sector. Given the relevance of these records and of the genetic identity of bee populations from Italy, we argue that implementing molecular surveys in bee monitoring would surely contribute to the conservation of these important pollinators.


Author(s):  
RA Begum ◽  
MT Alam ◽  
H Jahan ◽  
MS Alam

Labeo calbasu (Family Cyprinidae) was studied at DNA level to know genetic diversity within and between species. The mitochondrial cytochrome b (cyt-b) gene of L. calbasu was sequenced and compared to the corresponding sequences of other Labeo species. DNA was isolated from the tissue sample of L. calbasu using phenol: chloroform extraction method. Forward and reverse primers were designed to amplify the target region of cytochrome b gene. A standard PCR protocol was used for the amplification of the desired region. Then, the forward and reverse sequences obtained were aligned and edited to finalize a length of 510 nucleotides which was submitted to NCBI genbank database. Nucleotide BLAST of this sequence at NCBI resulted 100% sequence similarity with L. calbasu sequence of the same region of cyt-b gene. Multiple sequence alignment of the sequence with seven more Labeo species sequences revealed 120 polymorphic sites, which have been mark of diversity among the species and might be used in molecular identification of the Labeo species. A constructed phylogenetic tree has shown relationship among the Labeo species. This research demonstrated the usefulness of mitochondrial DNA-based approach in species identification. Further, the data will provide appropriate background for studying genetic diversity within-species of the Labeo species in general and of L. calbasu in particular. J. Biodivers. Conserv. Bioresour. Manag. 2019, 5(1): 25-30


2017 ◽  
Vol 25 (1) ◽  
pp. 469-478
Author(s):  
Adrian Duba ◽  
Klaudia Goriewa ◽  
Urszula Wachowska ◽  
Marian Wiwart

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