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Cited by 36Environmental DNA in Biodiversity StudiesFish Biology and Ecology StudiesInvertebrate Taxonomy and Ecology

Building a DNA barcode library for the freshwater fishes of Bangladesh

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Rahman, Md. Mizanur, Norén, Michael, Mollah, Abdur Rob, Kullander, Sven O.·2019·Scientific Reports
DOI 10.1038/s41598-019-45379-6PMC PMC6599201
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Abstract

We sequenced the standard DNA barcode gene fragment in 694 newly collected specimens, representing 243 species level Operational Barcode Units (OBUs) of freshwater fishes from Bangladesh. We produced coi sequences for 149 out of the 237 species already recorded from Bangladesh. Another 83 species sequenced were not previously recorded for the country, and include about 30 undescribed or potentially undescribed species. Several of the taxa that we could not sample represent erroneous records for the country, or sporadic occurrences. Species identifications were classified at confidence levels 1(best) to 3 (worst). We propose the new term Operational Barcode Unit (OBU) to simplify references to would-be DNA barcode sequences and sequence clusters. We found one case where there were two mitochondrial lineages present in the same species, several cases of cryptic species, one case of introgression, one species yielding a pseudogene to standard barcoding primers, and several cases of taxonomic uncertainty and need for taxonomic revision. Large scale national level DNA barcode prospecting in high diversity regions may suffer from lack of taxonomic expertise that cripples the result. Consequently, DNA barcoding should be performed in the context of taxonomic revision, and have a defined, competent end-user.

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  • The 12 individuals of D. cerebrum and D. mirifica sequenced for coxI had unique adenin insertions at positions 95 and 624 of the coxI alignment leading to frame shifts and premature stop codons.

    “The 12 individuals of Danionella cerebrum and D. mirifica sequenced for the cytochrome coxidase subunit I (coxI) gene had unique adenin insertions at positions 95 and 624 of the coxI alignment leading to frame shifts and premature stop codons as previously reported for the gobioid Parapocryptes serperaster15, the significance of which is unknown.”

    From The emerging vertebrate model species for neurophysiological studies is Danionella cerebrum, new species (Teleostei: Cyprinidae) (2021) · cites this paper as [15]

    The citation is attached to the comparison with Parapocryptes serperaster, not to the finding about Danionella. The Discussion reports a frameshift and stop codon in Pseudapocryptes elongatus; it mentions P. serperaster only as the reference genome used to locate the corresponding position. It does not report the insertion in P. serperaster. (LLM, conf=0.86)

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Cited by

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Authors
Rahman, M. M., Norén, M., Mollah, A. R., & Kullander, S. O.
Affiliations
  • Swedish Museum of Natural History (SE)
  • University of Dhaka (BD)
Corresponding author
Kullander, Sven O.
ORCID
Venue
Scientific Reports
Publisher
Springer Science and Business Media LLC
Published
2019-06-28
Volume
9
Issue
1
Pages
9382-9382
ISSN
2045-2322 (ISSN-L)
DOI
10.1038/s41598-019-45379-6
PMC
PMC6599201
OpenAlex
W2954678766
Cited by
36
References
0
Citations by year
2026: 6 · 2025: 4 · 2024: 6 · 2023: 5 · 2022: 8 · 2021: 5 · 2020: 2
FWCI
2.34
Type
journal article
Language
en
Update notices
correction (2020-01-29)
Open access
Licence
Locations
  • Scientific Reports (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
Vetenskapsrådet (D0674001)
Topics
  • Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
  • Life Sciences › Agricultural and Biological Sciences › Aquatic Science › Fish Biology and Ecology Studies
  • Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Invertebrate Taxonomy and Ecology
Keywords
DNA barcoding, freshwater fish, Bangladesh, COI sequences, cryptic species, mitochondrial lineages, introgression, pseudogenes, taxonomic revision, species identification, new records

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