Biology subjects

Minhas, B. F.

Publications and source records attributed to Minhas, B. F..

5 recordsLinked to original sources

bioRxiv2024

The genome of the cryopelagic Antarctic bald notothen, Trematomus borchgrevinki

The Antarctic bald notothen, Trematomus borchgrevinki (Notothenioidae) occupies a high latitude, ice-laden environment and represents an extreme example of cold-specialization among fishes. We present the first, high quality, long-read genome of a female T. borchgrevinki individual comprised of 23 putative chromosomes, the largest of which is 65 megabasepairs (Mbp) in length. The total length of the genome 935.13 Mbp, composed of 2,095 scaffolds, with a scaffold N50 of 42.80 Mbp. Annotation yielded 22,567 protein coding genes while 54.75% of the genome was occupied by repetitive elements; an analysis of repeats demonstrated that an expansion occurred in recent time. Conserved synteny analysis revealed that the genome architecture of T. borchgrevinki is largely maintained with other members of the notothenioid clade, although several significant translocations and inversions are present, including the fusion of orthologous chromosomes 8 and 11 into a single element. This genome will serve as a cold-specialized model for comparisons to other members of the notothenioid adaptive radiation.

genomics↗

bioRxiv2024

Klumpy: A tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs

The improvement and decreasing costs of third-generation sequencing technologies has widened the scope of biological questions researchers can address with de novo genome assemblies. With the increasing number of reference genomes, validating their integrity with minimal overhead is vital for establishing confident results in their applications. Here, we present Klumpy, a tool for detecting and visualizing both misassembled regions in a genome assembly and genetic elements (e.g., genes, promotors, or transposable elements) of interest in a set of sequences. By leveraging the initial raw reads in combination with their respective genome assembly, we illustrate Klumpys utility by investigating antifreeze glycoprotein (afgp) loci across two icefishes, by searching for a reported absent gene in the northern snakehead fish, and by scanning the reference genomes of a mudskipper and bumblebee for misassembled regions. In the two former cases, we were able to provide support for the noncanonical placement of an afgp locus in the icefishes and locate the missing snakehead gene. Furthermore, our genome scans were able to identify an cryptic locus in the mudskipper reference genome, and identify a putative repetitive element shared amongst several species of bees.

bioinformatics↗

bioRxiv2023

Chromosome-Level Genome Assembly and Circadian Gene Repertoire of the Patagonia blennie Eleginops maclovinus - the closest ancestral proxy of Antarctic cryonotothenioids

The basal S. American notothenioid Eleginops maclovinus (Patagonia blennie) occupies a uniquely important phylogenetic position in Notothenioidei as the singular closest sister species to the Antarctic cryonotothenioid fishes. Its genome and the traits encoded therein would be nearest representatives of the temperate ancestor from which the Antarctic clade arose, providing an ancestral reference for deducing polar derived changes. In this study, we generated a gene- and chromosome-complete assembly of E. maclovinus genome using long read sequencing and HiC scaffolding. We compared its genome architecture with the more basally divergent Cottoperca gobio and the derived genomes of nine cryonotothenioids representing all five Antarctic families. We additionally curated its repertoire of circadian rhythm genes, ascertained their functionality by transcriptome sequencing, and compared its pattern of gene retention with C. gobio and the derived cryonotothenioids. Both analyses found E. maclovinus to share greater conservation with the Antarctic clade, solidifying its evolutionary status as direct sister and best suited ancestral proxy of cryonotothenioids. The high quality genome of E. maclovinus will facilitate inquiries into cold derived traits in temperate to polar evolution, as well as inform on the paths of readaptation to non-freezing habitats in various secondarily temperate cryonotothenioids through comparative genomic analyses.

genomics↗

bioRxiv2022

Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy in Antarctic Notothenioid Fishes

Mitochondrial genomes are known for their compact size and conserved gene order, however, recent studies employing long-read sequencing technologies have revealed the presence of atypical mitogenomes in some species. In this study, we assembled and annotated the mitogenomes of five Antarctic notothenioids, including four icefishes (Champsocephalus gunnari, C. esox, Chaenocephalus aceratus, and Pseudochaenuchthys georgianus) and the cold-specialized Trematomus borchgrevinki. Antarctic notothenioids are known to harbor some rearrangements in their mt genomes, however the extensive duplications in icefishes observed in our study have never been reported before. In the icefishes, we observed duplications of the protein coding gene ND6, two transfer RNAs, and the control region with different copy number variants present within the same individuals and with some ND6 duplications appearing to follow the canonical Duplication-Degeneration-Complementation (DDC) model in C. esox and C. gunnari. In addition, using long-read sequencing and k-mer analysis, we were able to detect extensive heteroplasmy in C. aceratus and C. esox. We also observed a large inversion in the mitogenome of T. borchgrevinki, along with the presence of tandem repeats in its control region. This study is the first in using long-read sequencing to assemble and identify structural variants and heteroplasmy in notothenioid mitogenomes and signifies the importance of long-reads in resolving complex mitochondrial architectures. Identification of such wide-ranging structural variants in the mitogenomes of these fishes could provide insight into the genetic basis of the atypical icefish mitochondrial physiology and more generally may provide insights about their potential role in cold adaptation.

evolutionary biology↗

bioRxiv2022

Genomics of secondarily temperate adaptation in the only non-Antarctic icefish

AO_SCPLOWBSTRACTC_SCPLOWWhite-blooded Antarctic icefishes, a family within the adaptive radiation of Antarctic notothenioid fishes, are an example of extreme biological specialization to both the chronic cold of the Southern Ocean and life without hemoglobin. As a result, icefishes display derived physiology that limits them to the cold and highly oxygenated Antarctic waters. Against these constraints, remarkably one species, the pike icefish Champsocephalus esox, successfully colonized temperate South American waters. To study the genetic mechanisms underlying secondarily temperate adaptation in icefishes, we generated chromosome-level genome assemblies of both C. esox and its Antarctic sister species, Champsocephalus gunnari. The C. esox genome is similar in structure and organization to that of its Antarctic congener; however, we observe evidence of chromosomal rearrangements coinciding with regions of elevated genetic divergence in pike icefish populations. We also find several key biological pathways under selection, including genes related to mitochondria and vision, highlighting candidates behind temperate adaptation in C. esox. Substantial antifreeze glycoprotein (AFGP) pseudogenization has occurred in the pike icefish, likely due to relaxed selection following ancestral escape from Antarctica. The canonical AFGP locus organization is conserved in C. esox and C. gunnari, but both show a translocation of two AFGP copies to a separate locus, previously unobserved in cryonotothenioids. Altogether, the study of this secondarily temperate species provides an insight into the mechanisms underlying adaptation to ecologically disparate environments in this otherwise highly specialized group.

genomics↗