Abstract:Mitochondrial genome sequences have been widely used for evolutionary and phylogenetic studies. Among vertebrates, fish are an important, diverse group, and their mitogenome sequences are growing rapidly in public repositories. To facilitate mitochondrial genome analysis and to explore the valuable genetic information, we developed the Fish Mitogenome Resource (FMiR) database to provide a workbench for mitogenome annotation, species identification and microsatellite marker mining. The microsatellites are also … Show more
“…This additional tool was also corroborated to update the checklist of ichthyofauna from Ranganadi River in Assam state, and intensification of freshwater fish database from India (Nagpure et al. 2015 ; Kaushik and Bordoloi 2016 ). A significant study was also endeavouring to evaluate the genetic diversity of fishes from Diphlu River inside Kaziranga National Park (Laskar et al.…”
The genetic diversity of freshwater fishes is still anonymous in several drainage systems in northeast India. Moreover, the comparative genetic analysis is largely sporadic to judge their actual diversity and true status. We generated 89 DNA barcodes of 40 morphologically identified fishes collected from two major tributaries of Brahmaputra River. The comparative study revealed that most of the species were clearly discriminated by their estimated genetic distances and monophyletic clustering in Bayesian (BA) tree. Considering the genetic divergence (2%) for species discrimination boundary, the high genetic diversity (2.36–10.73%) was detected in 11 species (
Macrognathus pancalus
,
Channa punctata
,
Puntius terio
,
Bangana ariza
,
Garra arupi
,
Badis badis
,
Mystus vittatus
,
Rita rita
,
Gagata cenia
,
Mastacembelus armatus
, and
Danio dangila
), which signified the occurrence of concealed genetic diversity in this ecozone. However, the insignificant genetic distances were also noticed in few reportedly valid species:
Channa stiktos
and
C. ornatipinnis
(1.43%);
Mystus ngasep
,
M. rufescens
, and
M. carcio
(0.4%);
Glyptothorax trilineatus
,
G. churamanii
, and
G. verrucosus
(0.4%);
Botia almorhae
,
B. histrionica
,
B. lohachata
, and
B. rostrata
(0–0.4%);
Barilius barilia
and
B. vagra
(0.4%);
Batasio merianiensis
and
B. tengana
(1.2%);
Puntius chola
and
P. fraseri
(0%),
Schistura beavani
and
S. paucireticulata
(0%); hence to validate this species, generation of more barcode data was required from their types or topotypes. The present study would help to develop conservation schemes for the native species and collegiate ecosystem, which associated with the livelihoods of millions of ethnic communities in this region.
“…This additional tool was also corroborated to update the checklist of ichthyofauna from Ranganadi River in Assam state, and intensification of freshwater fish database from India (Nagpure et al. 2015 ; Kaushik and Bordoloi 2016 ). A significant study was also endeavouring to evaluate the genetic diversity of fishes from Diphlu River inside Kaziranga National Park (Laskar et al.…”
The genetic diversity of freshwater fishes is still anonymous in several drainage systems in northeast India. Moreover, the comparative genetic analysis is largely sporadic to judge their actual diversity and true status. We generated 89 DNA barcodes of 40 morphologically identified fishes collected from two major tributaries of Brahmaputra River. The comparative study revealed that most of the species were clearly discriminated by their estimated genetic distances and monophyletic clustering in Bayesian (BA) tree. Considering the genetic divergence (2%) for species discrimination boundary, the high genetic diversity (2.36–10.73%) was detected in 11 species (
Macrognathus pancalus
,
Channa punctata
,
Puntius terio
,
Bangana ariza
,
Garra arupi
,
Badis badis
,
Mystus vittatus
,
Rita rita
,
Gagata cenia
,
Mastacembelus armatus
, and
Danio dangila
), which signified the occurrence of concealed genetic diversity in this ecozone. However, the insignificant genetic distances were also noticed in few reportedly valid species:
Channa stiktos
and
C. ornatipinnis
(1.43%);
Mystus ngasep
,
M. rufescens
, and
M. carcio
(0.4%);
Glyptothorax trilineatus
,
G. churamanii
, and
G. verrucosus
(0.4%);
Botia almorhae
,
B. histrionica
,
B. lohachata
, and
B. rostrata
(0–0.4%);
Barilius barilia
and
B. vagra
(0.4%);
Batasio merianiensis
and
B. tengana
(1.2%);
Puntius chola
and
P. fraseri
(0%),
Schistura beavani
and
S. paucireticulata
(0%); hence to validate this species, generation of more barcode data was required from their types or topotypes. The present study would help to develop conservation schemes for the native species and collegiate ecosystem, which associated with the livelihoods of millions of ethnic communities in this region.
“…In continuation, efforts were made to publish databases on certain fish groups like catfishes (Pathak et al 2013), marine ornamental and shell fishes of India (Pathak et al 2011). The application of database technology was further applied in developing different fish genomic databases (Nagpure et al 2012, Nagpure et al 2015, Nagpure et al 2016, Rashid et al 2017.…”
Worldwide, global databases on fishes lack fish diversity information at regional scale of a country, which has fascinated many fishery workers to know the regional scale fish diversity. Databases are essential part of the biodiversity science and have been used widely in the biological research. The present study discusses development, services and utility of the database application (UPFBase) providing information on the freshwater fish biodiversity of Uttar Pradesh. To develop UPFBase, data on the fish biodiversity of this region was compiled from different sources that include primary data generated from different projects and secondary data from published literatures. The collected data were screened and then digitized. Microsoft ACCESS relational database and Visual Basic language technologies were used for designing and implementing the standalone database application with the data management capability. Presently, UPFBase provides taxonomy, synonyms, local name, common name, morphology, biology, distribution, habitat, economic importance, conservation status and other fishery information on 129 fishes belonging to 11 orders and 27 families. UPFBase is user friendly and provides ease in working through search, query and action command button tools. It can easily be deployed on the mobile storages devices like CD-ROM, Pen drive, PCMCIA etc and can be installed on any Windows based Intel x86 machines. This version of UPFBase was built for countries, where computational hardware and software resources are in scare and it is expected that it might play imperious role in knowing and managing the indigenous fish diversity for decision making and posterity.
“…Both types of information displayed in the windows allow the user to generate the report of the displayed information, which can be saved or printed for later use. Moreover, DNA barcode and mitogenome information for species linked with respective public databases FBIS ( 10 ) and FMiR ( 11 ) are presented in Figure 3D . Figure 3.…”
A voluminous information is available on karyological studies of fishes; however, limited efforts were made for compilation and curation of the available karyological data in a digital form. ‘Fish Karyome’ database was the preliminary attempt to compile and digitize the available karyological information on finfishes belonging to the Indian subcontinent. But the database had limitations since it covered data only on Indian finfishes with limited search options. Perceiving the feedbacks from the users and its utility in fish cytogenetic studies, the Fish Karyome database was upgraded by applying Linux, Apache, MySQL and PHP (pre hypertext processor) (LAMP) technologies. In the present version, the scope of the system was increased by compiling and curating the available chromosomal information over the globe on fishes and other aquatic organisms, such as echinoderms, molluscs and arthropods, especially of aquaculture importance. Thus, Fish Karyome version 2.1 presently covers 866 chromosomal records for 726 species supported with 253 published articles and the information is being updated regularly. The database provides information on chromosome number and morphology, sex chromosomes, chromosome banding, molecular cytogenetic markers, etc. supported by fish and karyotype images through interactive tools. It also enables the users to browse and view chromosomal information based on habitat, family, conservation status and chromosome number. The system also displays chromosome number in model organisms, protocol for chromosome preparation and allied techniques and glossary of cytogenetic terms. A data submission facility has also been provided through data submission panel. The database can serve as a unique and useful resource for cytogenetic characterization, sex determination, chromosomal mapping, cytotaxonomy, karyo-evolution and systematics of fishes.Database URL:
http://mail.nbfgr.res.in/Fish_Karyome
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