John H. Postlethwait

A non-invasive method to genotype cephalopod sex by quantitative PCR

This paper develops a non-invasive method to genotype cephalopod sex using quantitative PCR, validated across multiple species and sequencing data.

Complete de novo assembly and re-annotation of the zebrafish genome

The paper presents a new zebrafish genome assembly with increased sequence coverage and improved annotation, along with a pangenome resource for variant analysis.

Genomic and genetic insights into speciation and pigment pattern diversification in Danio fishes

This study investigates the genomic and genetic factors underlying speciation and pigment pattern diversification in Danio fishes, revealing introgression, functional divergence of specific genes, and evolutionary changes in protein and regulatory sequences.

Projected warming disrupts embryonic development and hatch timing in Antarctic fish

This study shows that projected warming disrupts embryonic development and hatch timing in Antarctic fish, leading to morphological abnormalities, accelerated development, and molecular stress.

THE HYBRID HISTORY OF ZEBRAFISH

The paper uses exome sequencing of Danio species to show zebrafish has an ancient hybrid origin and recent gene flow, with genomic regions supporting different evolutionary relationships.

Inter-individual gene expression variability implies stable regulation of brain-biased genes across organs in three ray-finned fishes

The paper examines gene expression variability across organs in three ray-finned fish species, finding that brain-biased genes show stable regulation despite inter-individual differences.

A maternal-to-zygotic-transition gene block on the zebrafish sex chromosome

The paper identifies a unique region on the zebrafish sex chromosome that contains genes expressed in testes and embryos but silenced in ovaries, suggesting a maternal-to-zygotic transition gene regulatory block.

Direct Male Development in Chromosomally ZZ Zebrafish

The paper investigates sex determination in zebrafish by comparing chromosomal systems in different strains, showing that NA zebrafish develop testes directly without a juvenile ovary phase when lacking the W chromosome.

Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis

The paper introduces a method to identify eQTLs and improve transcriptome analysis by quantifying differential allelic representation in RNA-sequencing data.

Multi-genome comparisons reveal gain-and-loss evolution of the anti-Mullerian hormone receptor type 2 gene, an old master sex determining gene, in Percidae

The paper compares genomes across multiple fish species to study the evolutionary changes in the amhr2bY gene, a key sex-determining gene, revealing gains and losses in different Percidae species.

Genomics of cold adaptations in the Antarctic notothenioid fish radiation.

The paper generates and analyzes genome assemblies for 24 Antarctic notothenioid fish species to study cold adaptations, identifying genomic changes related to antifreeze proteins and haemoglobin loss.

An ancient truncated duplication of the anti-Mullerian hormone receptor type 2 gene is a potential conserved master sex determinant in the Pangasiidae catfish family

The paper identifies a truncated duplication of the amhr2 gene on the Y chromosome in Pangasiid catfishes as a conserved master sex-determining gene.

Circulating miRNA diversity, origin and response to changing metabolic and reproductive states, new insights from the rainbow trout

The paper identifies circulating miRNAs as biomarkers of metabolic and reproductive states in rainbow trout using small RNA-seq and qPCR, showing fluid-specific miRNAomes and candidate biomarkers for myogenesis and reproductive success.

A complex genetic architecture in zebrafish relatives Danio quagga and D. kyathit underlies development of stripes and spots

This study identifies a complex genetic architecture underlying stripe and spot patterns in zebrafish relatives D. quagga and D. kyathit, revealing multiple loci and epistatic interactions.

RADSex: a computational workflow to study sex determination using Restriction Site-Associated DNA Sequencing data

RADSex is a computational workflow for analyzing RAD-Seq data to identify sex determination systems, uncovering new sex-specific markers in fish species.

An intestinal cell type in zebrafish is the nexus for the SARS-CoV-2 receptor and the Renin-Angiotensin-Aldosterone System that contributes to COVID-19 comorbidities

The paper identifies zebrafish orthologs of the RAAS system and shows they are expressed in a specific intestinal cell type relevant to COVID-19 comorbidities.

Sex chromosome and sex locus characterization in the goldfish, Carassius auratus

This study characterizes the sex determination system and sex chromosomes in goldfish, identifying a large non-recombining region on linkage group 22 as the likely Y chromosome and developing sex-linked genetic markers.

Transgene-mediated skeletal phenotypic variation in zebrafish

The paper investigates how a chromosomally integrated transgene enhances specific phenotypes in fras1 mutant zebrafish, showing genetic partial dominance and locus-specific effects.

Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens

The paper presents a chromosome-scale genome assembly of yellow perch and identifies a Y-specific duplication of the amhr2 gene as a candidate sex determination gene.

Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API

The paper introduces mirGFF3, a standardized format for miRNA/isomiR analysis, and mirtop, a tool to convert outputs into this format, enabling data sharing and comparative analysis.

The roles of Amh in zebrafish gonad development and sex determination

This study investigates the role of Amh in zebrafish gonad development and sex determination by generating amh null mutants, revealing its involvement in germ cell regulation and gonadal soma development.

miRNA analysis with Prost! reveals evolutionary conservation of organ-enriched expression and post-transcriptional modifications in three-spined stickleback and zebrafish

wnt4a Promotes Female Development and Reproductive Duct Elongation in Zebrafish

This paper shows that wnt4a promotes female sex determination and reproductive duct development in zebrafish, similar to its role in mammals.

Epigenetic factors coordinate intestinal development

This paper shows DNA methylation factors are crucial for intestinal development across multiple cell types, including neurons and smooth muscle, and identifies them as potential Hirschsprung disease candidates.