NAISS
SUPR
NAISS Projects
SUPR
Nuclear genome of Betadevario ramachandrani
Dnr:

NAISS 2026/4-1655

Type:

NAISS Small

Principal Investigator:

Michael Noren

Affiliation:

Naturhistoriska riksmuseet

Start Date:

2026-09-17

End Date:

2027-10-01

Primary Classification:

10609: Genetics and Genomics (Medical aspects at 30107 and agricultural at 40402)

Webpage:

Allocation

Abstract

Betadevario ramachandrani is a poorly known danionine fish from the Western Ghats of India and may now be extinct. A previous study generated approximately 46 GiB of Illumina paired-end shotgun data from a museum specimen and used these data to assemble and publish the complete mitochondrial genome. The nuclear component of this dataset has not yet been analysed. The aim of this project is to recover as much of the nuclear genome as possible from the existing short-read data. Although the degraded source DNA and short insert size preclude a chromosome-level assembly, the high sequencing depth should permit recovery of a substantial proportion of the unique nuclear genome, including protein-coding genes and other phylogenetically informative regions. The reads will first be characterized using quality-control and k-mer analyses to estimate genome size, heterozygosity, repeat content and effective coverage. De novo assemblies will then be generated using short-read genome assemblers, with alternative assembly strategies and parameters compared. Assembly quality will be assessed using read mapping, k-mer completeness, standard assembly statistics, BUSCO gene-content completeness and taxonomic screening for contamination. The resulting draft genome will provide a genomic resource for an exceptionally rare, and possibly extinct, vertebrate species and may facilitate future studies of danionine evolution, phylogenetics and comparative genomics. Because no additional material may become available, maximizing the information recoverable from the existing sequence data is of particular value.