Biology subjects

Uthanumallian, K.

Publications and source records attributed to Uthanumallian, K..

3 recordsLinked to original sources

bioRxiv2026

Dynamic genomes uncover opposite sex determination in the invasive quagga and zebra mussels

Sex determination is a fundamental developmental switch, yet the genetic architectures that underlie transitions between sex-determining systems remain poorly understood, especially in non-model animals with homomorphic sex chromosomes. Here, we combine chromosome-scale genomes, whole-genome resequencing of 80 sexed individuals, sex-specific k-mer analyses, and developmental transcriptomics to resolve and compare sex determination in zebra and quagga mussels, two closely related and globally invasive freshwater bivalves. We find that these species have evolved sharply contrasting sex-determining architectures since their divergence. Zebra mussels show signatures of a polygenic ZZ/ZW system, with sex-linked regions on multiple chromosomes, including signal at the conserved ovarian regulator FoxL2. In contrast, quagga mussels possess a localized [~]800 kb XX/XY sex-determining region containing FoxL2-Y, a duplicated and structurally modified FoxL2 paralog and candidate male-determining locus. In quagga mussels, SNP-based differentiation, model-based inference, sex-biased read coverage, and male-specific k-mers independently converge on this Y-linked region, while diagnostic k-mer screening of staged embryonic transcriptomes reveals rare, early developmental expression of FoxL2-Y, consistent with a transient regulatory role. The quagga sex-determining region is enriched for C-type lectins and other genes implicated in reproductive interactions, suggesting that haploid selection may have contributed to the stabilization of this region. Together, these findings show that closely related species can rapidly evolve different genetic solutions to sex determination and identify gene duplication, genome dynamism, and reproductive selection as potential contributors to sex-determining system turnover. Because zebra and quagga mussels are major freshwater invaders, resolving their divergent reproductive architectures also provides essential genomic context for assessing the future feasibility of sex-ratio-based biocontrol strategies.

genomics↗

bioRxiv2024

Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems

Brown seaweeds are keystone species of coastal ecosystems, often forming extensive underwater forests, that are under considerable threat from climate change. Despite their ecological and evolutionary importance, this phylogenetic group, which is very distantly related to animals and land plants, is still poorly characterised at the genome level. Here we analyse 60 new genomes that include species from all the major brown algal orders. Comparative analysis of these genomes indicated the occurrence of several major events coinciding approximately with the emergence of the brown algal lineage. These included marked gain of new orthologous gene families, enhanced protein domain rearrangement, horizontal gene transfer events and the acquisition of novel signalling molecules and metabolic pathways. The latter include enzymes implicated in processes emblematic of the brown algae such as biosynthesis of the alginate-based extracellular matrix, and halogen and phlorotannin biosynthesis. These early genomic innovations enabled the adaptation of brown algae to their intertidal habitats. The subsequent diversification of the brown algal orders tended to involve loss of gene families, and genomic features were identified that correlated with the emergence of differences in life cycle strategy, flagellar structure and halogen metabolism. Analysis of microevolutionary patterns within the genus Ectocarpus indicated that deep gene flow between species may be an important factor in genome evolution on more recent timescales. Finally, we show that integration of large viral genomes has had a significant impact on brown algal genome content and propose that this process has persisted throughout the evolutionary history of the lineage.

genomics↗

bioRxiv2021

Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae

The genomic diversity underpinning high ecological and species diversity in the green algae (Chlorophyta) remains little known. Here, we aimed to track genome evolution in the Chlorophyta, focusing on loss and gain of homologous genes, and lineage-specific innovations of the Core Chlorophyta. We generated a high-quality nuclear genome for pedinophyte YPF701, a sister lineage to others in the Core Chlorophyta, and incorporated this genome in a comparative analysis with 25 other genomes from diverse Viridiplantae taxa. The nuclear genome of pedinophyte YPF701 has an intermediate size and gene number between those of most early-diverging prasinophytes and the remainder of the Core Chlorophyta. Our results suggest positive selection for genome streamlining in Pedinophyceae, independent from genome minimisation observed among prasinophyte lineages. Genome expansion was predicted along the branch leading to the UTC clade (classes Ulvophyceae, Trebouxiophyceae and Chlorophyceae) after divergence from their common ancestor with pedinophytes, with genomic novelty implicated in a range of basic biological functions. These results emphasise multiple independent signals of genome minimisation within the Chlorophyta, as well as the genomic novelty arising prior to diversification in the UTC clade, which may underpin the success of this species-rich clade in a diversity of habitats.

evolutionary biology↗