Alexander Suh

Transposable element activity and polymorphisms drive structural variability within and between individual in bivalves

This study identifies structural variants and transposable element insertions in oysters, showing their role in genomic diversity and adaptation to environmental conditions.

The complete genome of a songbird

This paper presents the first fully phased, diploid, telomere-to-telomere genome of the zebra finch, revealing new genes and structural features.

Evidence of two centromeres in the germline-restricted chromosome (GRC): insights from zebra finch lampbrush chromosomes

This study identifies two centromeres on the zebra finch GRC, suggesting a mechanism for its non-Mendelian inheritance through the maternal germline.

Stable but turbulent: the two faces of the germline-restricted chromosome of passerine birds

The paper presents complete GRC assemblies from passerine birds, revealing their composition, evolution, and dynamic nature despite their stability in the avian karyotype.

The germline-restricted chromosome orchestrates germ cell development in passerine birds

The paper uses RNA-seq and spatial transcriptomics in zebra finches to study the role of the germline-restricted chromosome (GRC) in germ cell development, identifying its involvement in oocyte maturation and gene expression regulation.

Accumulation of a biparentally-inherited Neptune transposable element in natural Killifish hybrids (Fundulus diaphanus X F. heteroclitus)

The paper examines TE accumulation in Killifish hybrids, finding increased levels of bi-parentally inherited Neptune elements due to suboptimal piRNA pathway function.

Retrocopy formation and domestication shape genome evolution in sloths and other xenarthrans

This study presents chromosome-level genomes for sloths and anteaters, revealing retrocopy formation and domestication as key drivers of xenarthran genome evolution and physiological specializations.

Germline-restricted chromosome of songbirds has different centromere compared to regular chromosomes

The paper identifies a centromeric satellite repeat in songbirds and shows it is absent from the germline-restricted chromosome (GRC), suggesting sequence changes underlie its programmed elimination.

Programmed DNA elimination drives rapid genomic innovation in two thirds of all bird species

The paper identifies germline-restricted chromosomes (GRCs) in 6,700 passerine species, showing rapid evolution and functional gene retention despite programmed DNA elimination.

Mechanisms and timing of programmed DNA elimination in songbirds

This study investigates the mechanisms and timing of programmed DNA elimination in songbirds, identifying key cellular and epigenetic processes involved in the removal of the germline-restricted chromosome from somatic cells.

An annotated chromosome-scale reference genome for Eastern Black-eared Wheatear (Oenanthe melanoleuca)

The paper generates and annotates a chromosome-scale reference genome for the Eastern Black-eared Wheatear to support research on adaptation and speciation in wheatears.

Genomic architecture of migration timing in a long-distance migratory songbird

This study identifies a genomic region on chromosome 1 associated with migration timing in purple martins, showing genetic basis and reduced adaptive potential to recent environmental changes.

Differential sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

The paper analyzes genomes of leatherback and green turtles to identify gene family expansions and demographic differences that may influence their ecological adaptations and conservation status.

The swan genome and transcriptome: its not all black and white

The paper generates the first chromosome-length annotated genomes and transcriptomes of black and mute swans, revealing immune system limitations and plumage-related genetic differences.

Transposon- and genome dynamics in the fungal genus Neurospora: insights from nearly gapless genome assemblies

The paper analyzes TE distribution and RIP patterns in 10 Neurospora species using nearly gapless genome assemblies, showing a correlation between TE content, genome size, and RIP signatures.

Occasional paternal inheritance of the germline-restricted chromosome in songbirds

The paper shows that the germline-restricted chromosome (GRC) in zebra finches can be paternally inherited, challenging previous assumptions of strict maternal transmission.

Horizontal transfer and subsequent explosive expansion of a DNA transposon in sea kraits (Laticauda)

The paper describes horizontal transfer of the Harbinger-Snek DNA transposon into sea kraits and its rapid genomic expansion, contributing to adaptation to an amphibious-marine lifestyle.

The Enterprise: A massive transposon carrying Spok meiotic drive genes

The paper describes the discovery of a large transposon, Enterprise, in the fungus Podospora anserina, which carries meiotic drive genes and can transpose, challenging views on TE genome impact.

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise

This study evaluates sequencing technologies and assembly strategies to improve genome completeness in a non-model organism, focusing on resolving dark matter regions like transposable elements and GC-rich areas.

The population genomics of structural variation in a songbird genus

The paper characterizes structural variation in the songbird genus Corvus using multiple sequencing methods and identifies a retrotransposon insertion with evolutionary implications.

Genome Report: De novo genome assembly and annotation for the Taita white-eye (Zosterops silvanus)

The paper presents a high-quality draft genome assembly and annotation for the Taita White-eye, providing a genomic resource for evolutionary and comparative genomics studies.

The tuatara genome: insights into vertebrate evolutionfrom the sole survivor of an ancient reptilian order

The paper presents the tuatara genome, highlighting its evolutionary significance and unique features compared to other vertebrates.

Genome analyses show strong selection on coloration, morphological and behavioral phenotypes in birds-of-paradise

The paper sequenced genomes of birds-of-paradise to identify genomic changes linked to their phenotypic diversity, finding strong selection on coloration, morphology, and sensory systems.

Improved genome assembly and annotation for the rock pigeon (Columba livia)

The paper updates the rock pigeon genome assembly and annotation, improving tools for evolutionary and functional genetic studies.