Cross-species single-cell transcriptomics reveals neuronal similarities and heterogeneity in amniote pallium.

The amniote pallium, a vital component of the forebrain, exhibits considerable evolutionary divergence across species and mediates diverse functions, including sensory processing, memory formation, and learning. However, the relationships among pallial subregions in different species remain poorly characterized, particularly regarding the identification of homologous neurons and their transcriptional signatures. In this study, we utilized single-nucleus RNA sequencing to examine over 130 000 nuclei from the macaque ( ) neocortex, complemented by datasets from humans ( ), mice ( ), zebra finches ( ), turtles ( ), and lizards ( s), enabling comprehensive cross-species comparison.

Spatial and single-nucleus transcriptomics decoding the molecular landscape and cellular organization of avian optic tectum.

The avian optic tectum (OT) has been studied for its diverse functions, yet a comprehensive molecular landscape at the cellular level has been lacking. In this study, we applied spatial transcriptome sequencing and single-nucleus RNA sequencing (snRNA-seq) to explore the cellular organization and molecular characteristics of the avian OT from two species: and . We identified precise layer structures and provided comprehensive layer-specific signatures of avian OT.

Tree2GD: a phylogenomic method to detect large-scale gene duplication events.

Motivation: Whole-genome duplication events have long been discovered throughout the evolution of eukaryotes, contributing to genome complexity and biodiversity and leaving traces in the descending organisms. Therefore, an accurate and rapid phylogenomic method is needed to identify the retained duplicated genes on various lineages across the target taxonomy.

Results: Here, we present Tree2GD, an integrated method to identify large-scale gene duplication events by automatically perform multiple procedures, including sequence alignment, recognition of homolog, gene tree/species tree reconciliation, Ks distribution of gene duplicates and synteny analyses.

Parental folate deficiency induces birth defects in mice accompanied with increased de novo mutations.

Dietary folate deficiency (FD) is associated with the occurrence of birth defects. However, the mechanisms underlying this association remain elusive. In particular, how FD affects genome stability is unknown.

Recurrent genome duplication events likely contributed to both the ancient and recent rise of ferns.

Ferns, the second largest group of vascular plants, originated ~400 million years ago (Mya). They became dominant in the ancient Earth landscape before the angiosperms and are still important in current ecosystems. Many ferns have exceptionally high chromosome numbers, possibly resulting from whole-genome duplications (WGDs).

Genome-wide Target Enrichment-aided Chip Design: a 66 K SNP Chip for Cashmere Goat.

Compared with the commercially available single nucleotide polymorphism (SNP) chip based on the Bead Chip technology, the solution hybrid selection (SHS)-based target enrichment SNP chip is not only design-flexible, but also cost-effective for genotype sequencing. In this study, we propose to design an animal SNP chip using the SHS-based target enrichment strategy for the first time. As an update to the international collaboration on goat research, a 66 K SNP chip for cashmere goat was created from the whole-genome sequencing data of 73 individuals.