Yuanyuan Cheng

Transcript- and annotation-guided genome assembly of the European starling

The paper presents two genome assemblies for the European starling, using long-read transcript data and homology-based annotation to improve assembly quality and provide a reference for population genetics.

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.

Genomes of Symbiodiniaceae reveal extensive sequence divergence but conserved functions at family and genus levels

The paper presents whole-genome comparisons of Symbiodiniaceae isolates, revealing extensive sequence divergence but conserved gene functions across species and genera.

Illuminating the dark side of the human transcriptome with TAMA Iso-Seq analysis

The paper uses TAMA to analyze long-read RNA sequencing data and identifies thousands of potential novel genes while highlighting challenges in RNA preparation and data processing.

Circadian clock mechanism driving mammalian photoperiodism

This study identifies the circadian clock mechanism in mammals that drives seasonal responses to photoperiod changes through BMAL2 and EYA3/TSH pathways.

Polarella glacialis genomes encode tandem repeats of single-exon genes with functions critical to adaptation of dinoflagellates

This study presents genome assemblies of Polarella glacialis, revealing a high proportion of single-exon genes and their role in cold adaptation.

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.

Structural rearrangements drive extensive genome divergence between symbiotic and free-living Symbiodinium

This study compares genome structures of symbiotic and free-living Symbiodinium species, finding extensive divergence and suggesting structural rearrangements contribute to lifestyle differences.