Balan Ramesh

The University of Texas at Arlington

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Jeffery P. Demuth

The University of Texas at Arlington

Hope M. Healey

University of Oregon

Elyse Barker

University of Idaho

Clayton M. Small

University of Oregon

Mark Currey

University of Oregon

Megean Myers

University of Idaho

Bernadette D. Johnson

University of Idaho

Susan Bassham

University of Oregon

Adam G. Jones

Leipzig University

Jacob M. Luber

The University of Texas at Arlington

Cooperative Institutions

The University of Texas at Arlington

University of Oregon

University of Colorado Denver

University of Northern Colorado

Liverpool School of Tropical Medicine

Denver Health Medical Center

Health and Hospital Corporation

Consejo Superior de Investigaciones Científicas

University of Idaho

Texas A&M University

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Improvements to the Gulf pipefish Syngnathus scovelli genome

Gigabyte (2023)

Balan Ramesh Clayton M. Small Hope M. Healey Bernadette D. Johnson Elyse Barker

The Gulf pipefish Syngnathus scovelli has emerged as an important species for studying sexual selection, development, and physiology. Comparative evolutionary genomics research involving fishes from Syngnathidae depends on having a high-quality genome assembly and annotation. However, the first S. scovelli genome assembled using short-read sequences and a smaller RNA-sequence dataset has limited contiguity and a relatively poor annotation. Here, using PacBio long-read high-fidelity sequences and a proximity ligation library, we generate an improved assembly to obtain 22 chromosome-level scaffolds. Compared to the first assembly, the gaps in the improved assembly are smaller, the N75 is larger, and our genome is ~95% BUSCO complete. Using a large body of RNA-Seq reads from different tissue types and NCBI's Eukaryotic Annotation Pipeline, we discovered 28,162 genes, of which 8,061 are non-coding genes. Our new genome assembly and annotation are tagged as a RefSeq genome by NCBI and provide enhanced resources for research work involving S. scovelli..

Sequence assembly

RefSeq

Comparative Genomics

10.46471/gigabyte.76

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Citations (7)

scRNA-seq reveals novel genetic pathways and sex chromosome regulation inTriboliumspermatogenesis

bioRxiv (Cold Spring Harbor Laboratory) (2023)

Michael Robben Balan Ramesh Shana H. Pau Demetra Meletis Jacob M. Luber

Abstract Insights into single cell expression data are generally collected through well conserved biological markers that separate cells into known and unknown populations. Unfortunately for non-model organisms that lack known markers, it is often impossible to partition cells into biologically relevant clusters which hinders analysis into the species. Tribolium castaneum , the red flour beetle, lacks known markers for spermatogenesis found in insect species like Drosophila melanogaster . Using single cell sequencing data collected from adult beetle testes, we implement a strategy for elucidating biologically meaningful cell populations by using transient expression stage identification markers, weighted principal component leiden clustering. We identify populations that correspond to observable points in sperm differentiation and find species specific markers for each stage. We also develop an innovative method to differentiate diploid from haploid cells based on scRNA-Seq reads and use it to corroborate our predicted demarcation of meiotic cell stages. Our results demonstrate that molecular pathways underlying spermatogenesis in Coleoptera are highly diverged from those in Diptera, relying on several genes with female meiotic pathway annotations. We find that the X chromosome is almost completely silenced throughout pre-meiotic and meiotic cells. Further evidence suggests that machinery homologous to the Drosophila dosage compensation complex (DCC) may mediate escape from meiotic sex chromosome inactivation and postmeiotic reactivation of the X chromosome.

10.1101/2023.07.18.549532

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Divergence time estimation of genus Tribolium by extensive sampling of highly conserved orthologs

Molecular Phylogenetics and Evolution (2021)

Balan Ramesh Thomas J. Firneno Jeffery P. Demuth

Paraphyly

Red flour beetle

Divergence (linguistics)

10.1016/j.ympev.2021.107084

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Citations (6)

Improvements to the Gulf PipefishSyngnathus scovelliGenome

bioRxiv (Cold Spring Harbor Laboratory) (2023)

Balan Ramesh Clayton M. Small Hope M. Healey Bernadette D. Johnson Elyse Barker

Abstract The Gulf pipefish Syngnathus scovelli has emerged as an important species in the study of sexual selection, development, and physiology, among other topics. The fish family Syngnathidae, which includes pipefishes, seahorses, and seadragons, has become an increasingly attractive target for comparative research in ecological and evolutionary genomics. These endeavors depend on having a high-quality genome assembly and annotation. However, the first version of the S. scovelli genome assembly was generated by short-read sequencing and annotated using a small set of RNA-sequence data, resulting in limited contiguity and a relatively poor annotation. Here, we present an improved genome assembly and an enhanced annotation, resulting in a new official gene set for S. scovelli . By using PacBio long-read high-fidelity (Hi-Fi) sequences and a proximity ligation (Hi-C) library, we fill small gaps and join the contigs to obtain 22 chromosome-level scaffolds. Compared to the previously published genome, the gaps in our novel genome assembly are smaller, the N75 is much larger (13.3 Mb), and this new genome is around 95% BUSCO complete. The precision of the gene models in the NCBI’s eukaryotic annotation pipeline was enhanced by using a large body of RNA-Seq reads from different tissue types, leading to the discovery of 28,162 genes, of which 8,061 were non-coding genes. This new genome assembly and the annotation are tagged as a RefSeq genome by NCBI and thus provide substantially enhanced genomic resources for future research involving S. scovelli .

Sequence assembly

RefSeq

Comparative Genomics

Gene Annotation

10.1101/2023.01.23.525209

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Citations (1)

scRNA-seq reveals novel genetic pathways and sex chromosome regulation in Tribolium spermatogenesis

Genome Biology and Evolution (2024)

Michael Robben Balan Ramesh Shana H. Pau Demetra Meletis Jacob M. Luber

Abstract Spermatogenesis is critical to sexual reproduction yet evolves rapidly in many organisms. High-throughput single-cell transcriptomics promises unparalleled insight into this important process but understanding can be impeded in nonmodel systems by a lack of known genes that can reliably demarcate biologically meaningful cell populations. Tribolium castaneum, the red flour beetle, lacks known markers for spermatogenesis found in insect species like Drosophila melanogaster. Using single-cell sequencing data collected from adult beetle testes, we implement a strategy for elucidating biologically meaningful cell populations by using transient expression stage identification markers, weighted principal component clustering, and SNP-based haploid/diploid phasing. We identify populations that correspond to observable points in sperm differentiation and find species specific markers for each stage. Our results indicate that molecular pathways underlying spermatogenesis in Coleoptera are substantially diverged from those in Diptera. We also show that most genes on the X chromosome experience meiotic sex chromosome inactivation. Temporal expression of Drosophila MSL complex homologs coupled with spatial analysis of potential chromatin entry sites further suggests that the dosage compensation machinery may mediate escape from meiotic sex chromosome inactivation and postmeiotic reactivation of the X chromosome.

Dosage compensation

10.1093/gbe/evae059

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The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes

Genome Research (2019)

Drew R. Schield Daren C. Card Nicole R. Hales Blair W. Perry Giulia M. Pasquesi

Here we use a chromosome-level genome assembly of a prairie rattlesnake ( Crotalus viridis ), together with Hi-C, RNA-seq, and whole-genome resequencing data, to study key features of genome biology and evolution in reptiles. We identify the rattlesnake Z Chromosome, including the recombining pseudoautosomal region, and find evidence for partial dosage compensation driven by an evolutionary accumulation of a female-biased up-regulation mechanism. Comparative analyses with other amniotes provide new insight into the origins, structure, and function of reptile microchromosomes, which we demonstrate have markedly different structure and function compared to macrochromosomes. Snake microchromosomes are also enriched for venom genes, which we show have evolved through multiple tandem duplication events in multiple gene families. By overlaying chromatin structure information and gene expression data, we find evidence for venom gene-specific chromatin contact domains and identify how chromatin structure guides precise expression of multiple venom gene families. Further, we find evidence for venom gland-specific transcription factor activity and characterize a complement of mechanisms underlying venom production and regulation. Our findings reveal novel and fundamental features of reptile genome biology, provide insight into the regulation of snake venom, and broadly highlight the biological insight enabled by chromosome-level genome assemblies.

Dosage compensation

Microchromosome

10.1101/gr.240952.118

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Citations (131)

Carbohydrate and Protein are an Attribute to Enhance the Life-History Determinants in Drosophila

Balan Ramesh B.K. Neethu B. P. Harini

Dietary restriction extends life span across a vast diversity of taxa, but the key nutritional components driving this process and how they interact remain uncertain. In Drosophila, while a substantial body of research suggests that protein is the major dietary component affecting longevity, recent studies claim that carbohydrates also play a central role. To clarify how nutritional factors influence longevity, nutrient consumption and lifespan were measured on a series of diets with varying casein and sugar content. Increased dietary carbohydrate or protein concentration does not always result in increased longevity. Our study indicates that the combination of carbohydrate and protein has certainly experiences significant effects with increased values rather than only carbohydrates nor only protein for the life history traits recorded. Thus the media enriched with the rich sources of food composition as resulted with enhanced mating activity, productivity and longevity in Drosophila melanogaster.

Source

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Using Ancestral Reconstruction of Chromosome Expression States (ARChES) to Understand the Evolution of Dosage Compensation

Balan Ramesh Jeff Demuth

Dosage compensation

Expression (computer science)

10.26153/tsw/11486

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Transcriptomic Analysis Reveals Potential Candidate Pathways and Genes Involved in Toxin Biosynthesis in True Toads

Journal of Heredity (2022)

Thomas J. Firneno Balan Ramesh José A. Maldonado Alejandro I Hernandez-Briones Alyson H. Emery

Abstract Synthesized chemical defenses have broadly evolved across countless taxa and are important in shaping evolutionary and ecological interactions within ecosystems. However, the underlying genomic mechanisms by which these organisms synthesize and utilize their toxins are relatively unknown. Herein, we use comparative transcriptomics to uncover potential toxin synthesizing genes and pathways, as well as interspecific patterns of toxin synthesizing genes across 10 species of North American true toads (Bufonidae). Upon assembly and annotation of the 10 transcriptomes, we explored patterns of relative gene expression and possible protein–protein interactions across the species to determine what genes and/or pathways may be responsible for toxin synthesis. We also tested our transcriptome dataset for signatures of positive selection to reveal how selection may be acting upon potential toxin producing genes. We assembled high-quality transcriptomes of the bufonid parotoid gland, a tissue not often investigated in other bufonid-related RNAseq studies. We found several genes involved in metabolic and biosynthetic pathways (e.g., steroid biosynthesis, terpenoid backbone biosynthesis, isoquinoline biosynthesis, and glucosinolate biosynthesis) that were functionally enriched and/or relatively expressed across the 10 focal species that may be involved in the synthesis of alkaloid and steroid toxins, as well as other small metabolic compounds that cause distastefulness in bufonids. We hope that our study lays a foundation for future studies to explore the genomic underpinnings and specific pathways of toxin synthesis in toads, as well as at the macroevolutionary scale across numerous taxa that produce their own defensive toxins.

Metabolic pathway

Steroid biosynthesis

10.1093/jhered/esac015

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Citations (4)

Chromosome-scale genome assemblies for 10 syngnathiform fishes produced using a standardized sequencing and annotation workflow

Authorea (Authorea) (2024)

Balan Ramesh Clayton M. Small Susan Bassham Bernadette D. Johnson Elyse Barker

10.22541/au.172467565.57384610/v1

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