Building a DNA barcode library for the freshwater fishes of Bangladesh

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.

The emerging vertebrate model species for neurophysiological studies is Danionella cerebrum, new species (Teleostei: Cyprinidae)

“…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 serperaster 15 , the significance of which is unknown. Interestingly, we were also able to identify two adenin insertions in the coxI gene in the whole genome sequence of D. cerebrum provided by Kadobianskyi et al 16 (GenBank accession SRMA00000000 as D. translucida ) as well as the expected mt DNA tRNAs flanking the coxI, hundreds of base pairs up and downstream of the coxI region sequenced in our study, suggesting a genuine mitochondrial origin of our coxI sequences rather than a nuclear pseudogene (NUMT).…”

Revisiting the Diversity of Barbonymus (Cypriniformes, Cyprinidae) in Sundaland Using DNA-Based Species Delimitation Methods

“…Most sequences of BOLD:ADD1940 from mainland Asia were attributed to B. gonionotus [29,32,33,36], while sequences from Sundaland were called B. balleroides [9,16]. Sequences from BOLD:AAU0688 from Java were assigned to B. gonionotus, while previously published and newly generated sequences from Sumatra and Borneo were assigned to B. schwanefeldii.…”

“…DNA barcoding, the use of cytochrome oxidase I (COI) as a species tag for automated identification, opened new perspectives for the characterization of Sundaland's ichthyofauna by helping to clarify taxonomic confusion within several groups [15,21,22], by identifying discrepancies in historical species records [9] and by detecting a substantial amount of morphologically similar, yet highly divergent lineages (i.e., cryptic diversity) within numerous species [9,15,[21][22][23][24][25][26][27][28]. Several molecular studies that aimed at characterizing patterns of genetic diversity in Barbonymus led to conflicting species identities associated with sequences submitted to international repositories [9,16,[29][30][31][32][33][34][35][36].…”

Evidence of cryptic diversity in freshwater Macrobrachium prawns from Indochinese riverine systems revealed by DNA barcode, species delimitation and phylogenetic approaches

“…The barcoding region has also shown significant utility in biodiversity studies that aim to rapidly identify unknown specimens collected from various habitat and sample types such as soil [ 17 , 18 ], water [ 19 ], feces [ 20 , 21 ], and dietary products [ 22 , 23 ]. Moreover, it has been used to construct regional and local DNA barcode libraries for further biodiversity assessment [ 24 , 25 ]. The use of integrative methods in systematics has shown remarkable ability to resolve species identification problems in organismal groups [ 26 , 27 ].…”