Genome size estimation and its associations with body length, chromosome number and evolution in teleost fishes.

Precise estimation of genome size (GS) is vital for various genomic studies, such as deciding genome sequencing depth, genome assembly, biodiversity documentation, evolution, genetic disorders studies, duplication events etc. Animal Genome Size Database provides GS of over 2050 fish species, which ranges from 0.35 pg in pufferfish (Tetraodon nigroviridis) to 132.83 pg in marbled lungfish (Protopterus aethiopicus). The GS of majority of the fishes inhabiting waters of Indian subcontinent are still missing. In present study, we estimated GS of 51 freshwater teleost (31 commercially important, 7 vulnerable and 13 ornamental species) that ranged from 0.58 pg in banded gourami (Trichogaster fasciata) to 1.92 pg in scribbled goby (Awaous grammepomus). Substantial variation in GS was observed within the same fish orders (0.64-1.45 pg in cypriniformes, 0.70-1.41 pg in siluriformes and 0.58-1.92 pg in perciformes). We examined the relationship between the GS, chromosome number and body length across all the fishes. Body length was found to be associated with GS, whereas no relationship was noticed between the GS and the chromosome number. The analysis using ancestral information revealed haploid chromosome number 25, 27 and 24 for the most recent common ancestor of cypriniformes, siluriformes and perciformes, respectively. The study led to generation of new records on GS of 43 fish species and revalidated records for 8 species. The finding is valuable resource for further research in the areas of fish genomics, molecular ecology and evolutionary conservation genetics.

The identity of Rasbora neilgherriensis (Teleostei: Danionidae), with a re-description.

Rasbora neilgherriensis Day, long considered a synonym of Rasbora daniconius or Rasbora dandia, is re-described and shown to be a valid species based on an examination of type and recently-acquired topotypical specimens from the Western Ghats of India. The species is characterised by a complete lateral line with 32-34 pored scales on body, ½5-6/1/2½ scales in transverse line on body, a mid-lateral stripe that is 2½ scales wide anterior to the pelvic fin and 1-1½ scales wide on the caudal peduncle, and a caudal fin that is emarginate to forked with broadly rounded lobes. The species was recorded from the Cauvery River Basin in Kerala and Tamil Nadu, India, at elevations ranging from 710 m to 2015 m above sea level, in stream stretches with relatively denser riparian canopy cover.

Characterization of the complete mitochondrial genome of Barilius malabaricus and its phylogenetic implications.

Bariliine fishes are important components of the ornamental as well as subsistence fishery sectors in India. Many of the species in the genus Barilius are threatened by habitat loss and therefore need to be met with conservation initiatives. Effective conservation measures, however, require clarification of species identities and resolution of the validity of many species currently treated as synonymous or sub-species. The complete mitochondrial genome data provide better insight into phylogenetic information than the short fragment or single gene based analysis. Thus, we have sequenced the complete mitochondrial genome of Barilius malabaricus, one of the important fish species in the fresh water ornamental sector, for better understanding its phylogenetic status. The 16,519 bp mitochondrial genome consists of 37 genes which classifies as 22 tRNA, 13 protein coding and 2 ribosomal RNA genes and a control region. Overall, the mitochondrial genome bears the typical gene order and composition as in other fishes. Further, the COI, cytochrome b and 16S rRNA gene sequences revealed that, B. malabaricus is genetically closer to B. canarensis and B. bakeri compared to other Barilius species. Also, the Barilius species of west flowing rivers in Western Ghats were consistently recovered as a clade distinct from other species. We therefore suggest to retain the genus name Barilius for the species from the Western Ghats until a comprehensive analysis based on both morphological and molecular markers reveals the relationship between species now variously placed in the genera Barilius and Opsarius in greater detail.

Aenigmachanna mahabali, a new species of troglophilic snakehead (Pisces: Channidae) from Kerala, India.

Aenigmachanna mahabali, a new species of troglophilic snakehead is described on the basis of a single specimen recovered from a well in Kerala, India, over 200km south of the type locality for the only known species in the genus. The new species can be distinguished from its congener in possessing fewer dorsal fin rays (53 vs 56-57), fewer total vertebrae (61 vs 64), fewer scales in lateral series (76 vs 83-85) and in the pectoral-fin rays being extended beyond the margin of the membrane into filaments.

Resurrection and Re-description of Pampus candidus (Cuvier), Silver Pomfret from the Northern Indian Ocean.

Pomfrets (Genus Pampus) are commercially important fish in the Indo-Pacific region. The systematics of this genus is complicated because of morphological similarities between species. The silver pomfret from Indian waters has long been considered to be Pampus argenteus. Morphological and molecular examination of specimens from the Arabian Sea and Bay of Bengal regions suggested the silver pomfret from the region represents two species that are distinct both from each other and from P. argenteus from the South China Sea. Based on detailed morphological, meristic and molecular examinations, the most common species from the Indian Ocean was found to correspond with the descriptions of Stromateus candidus (Cuvier), which is resurrected from the synonymy of P. argenteus and redescribed here as Pampus candidus (new combination). The second species, which has restricted distribution in Indian waters needs further studies to arrive at taxonomic conclusions and is hence not described in the current study. Lectotypes are also designated for Pampus candidus.

Molecular and morphological evidences resolve taxonomic ambiguity between Systomus sarana sarana (Hamilton, 1822) and S. sarana subnasutus (Valenciennes) and suggest elevating them into distinct species.

Taxonomic ambiguity exists in genus Systomus and recently many new species were described under this genus. Systomus sarana subnasutus is considered a valid subspecies of S. sarana sarana although revisions have been done by some researchers. We employed a combination of morpho-meristics and molecular tools (Cytochrome c oxidase I, 16S and Cytochrome b genes of mitochondrial genome) to resolve the two species. Three morpho-meristic characters, head length/maxillary barbel length (HL/MxBL), Lateral Line Scales (LLSs) as well as two truss-based characters, had discernible variation between the two taxa. The sequence analysis (2353 nucleotides) depicted a separate clad of S. sarana subnasutus with high bootstrap support. The findings from combined use of morphology, meristics and mitogenes were concordant. The corroborative results suggest the possibility of two different species. The results suggest to adopt suitable management measures, accordingly.

Mitochondrial signatures for identification of grouper species from Indian waters.

Groupers are important commercial fish in many parts of the world. Accurate identification is critical for effective conservation assessment and fisheries management. Genetic barcodes provide a simple and reproducible method for the identification of species even in the absence of taxonomic expertise. The generation of reference barcodes from properly identified specimens is an important first step in this direction. Here, 36 species belonging to the subfamily Epinephelinae (Family: Serranidae) were collected from landings on the west coast of India and Port Blair, Andaman, and partial nucleotide sequence data of the mitochondrial cytochrome C oxidase subunit I (COI) gene was generated. Barcodes for 13 species were developed from Indian waters for the first time. Analysis using the COI gene produced phylogenetic trees in concurrence with other multi-gene studies. Epinephelus fasciatus and E. areolatus were found to be a species complex, as hypothesized in other studies. The DNA barcodes developed in the study can be used for identifying species within Epinehelinae, where taxonomic ambiguity still exists.

Mass mortality in ornamental fish, Cyprinus carpio koi caused by a bacterial pathogen, Proteus hauseri.

Moribund koi carp, Cyprinus carpio koi, from a farm with 50% cumulative mortality were sampled with the aim of isolating and detecting the causative agent. Three bacterial species viz., Citrobacter freundii (NSCF-1), Klebsiella pneumoniae (NSKP-1) and Proteus hauseri [genomospecies 3 of Proteus vulgaris Bio group 3] (NSPH-1) were isolated, identified and characterized on the basis of biochemical tests and sequencing of the 16S rDNA gene using universal bacterial primers. Challenge experiments with these isolates using healthy koi carp showed that P. hauseri induced identical clinical and pathological states within 3 d of intramuscular injection. The results suggest P. hauseri (NSPH-1) was the causative agent. In phylogenetic analysis, strain NSPH-1 formed a distinct cluster with other P. hauseri reference strains with ≥99% sequence similarity. P. hauseri isolates were found sensitive to Ampicillin, Cefalexin, Ciprofloxacin and Cefixime and resistant to Gentamycin, Oxytetracycline, Chloramphenicol, and Kanamycin. The affected fish recovered from the infection after ciprofloxacin treatment.

A review of the species of Oreichthys (Teleostei: Cyprinidae) in the Western Ghats, India.

Fishes currently assigned to Oreichthys cosuatis from the Western Ghats are shown to belong to a closely-related group of three valid species: Puntius coorgensis, which is raised from synonymy, and two new species, O. duospilus and O. incognito. Oreichthys coorgensis can be distinguished from its congeners by a combination of characters that include 22-23+1-2 scales in the longitudinal series with 5-8 pored scales; ½3/1/2½ scales in the transverse row; 6-7 predorsal scales and usually a faint blackish spot on the caudal-fin base. Oreichthys duospilus,  sp. nov., can be distinguished by possessing an almost complete lateral line with 11-21 pored scales and two black spots: one on the dorsal fin and the other on the anal fin. Oreichthys incognito,  sp. nov., can be distinguished by a lateral line with 5 pored scales; ½3/1/1½ scales in the transverse row; 8 predorsal scales and a vertical black bar on the dorsal fin.