The impact of local genomic properties on the evolutionary fate of genes

Intragenomic mutational heterogeneity: structural and functional insights from gene evolution

Variation of mutation rates between species has been documented over decades, but the variation between different regions of a genome has been less often discussed. Recent studies using high-quality sequence data have revealed previously unknown levels of intragenomic heterogeneity of mutation rates and their association with other structural and functional features of DNA sequences. This article reviews accumulating evidence of this intragenomic heterogeneity and speculates its cause and influence on organismal phenotypes.

An Extensive Survey of Vertebrate-specific, Nonvisual Opsins Identifies a Novel Subfamily, Q113-Bistable Opsin

A group of nonvisual opsins specific to vertebrates is essential to understand evolution of lateral eyes, one of the most prominent innovations in this lineage. Nevertheless, our knowledge of their evolutionary history remains limited. To develop an integrated view of their evolution, we surveyed these non-visual opsins (VA opsin, pinopsin, parapinopsin, parietopsin, and parapinopsin-like) in 451 vertebrate genomes. Through extensive manual curation, we completed a high-quality catalog. We could not find them in 202 mammals, supporting previous reports of their loss. VA opsins are highly conserved among nonmammals. In contrast, other opsin subfamilies experienced more dynamic molecular evolution with many secondary losses. In addition, we found a previously unreported opsin subfamily that we named Q113-Bistable (QB) opsin. We found its orthologs only in several lizards and the tuatara. Nevertheless, QB opsin pseudogenes were discovered in diverse taxa, including ray-finned fishes, indicating its ancient origin. QB opsin, parapinopsin, and parietopsin are extremely prone to be lost in the course of evolution, and loss events involving these opsins seem to occur concomitantly. Furthermore, we demonstrated the spectral properties of QB opsin as a UV-sensitive, bistable photo-pigment. This study provides the first integrated view of the entire evolutionary history of this group of opsins.

A comprehensive Thai pharmacogenomics database (TPGxD-1): Phenotype prediction and variants identification in 942 whole-genome sequencing data

Computational methods analyze genomic data to identify genetic variants linked to drug responses, thereby guiding personalized medicine. This study analyzed 942 whole-genome sequences from the Electricity Generating Authority of Thailand (EGAT) cohort to establish a population-specific pharmacogenomic database (TPGxD-1) in the Thai population. Sentieon (version 201808.08) implemented the GATK best workflow practice for variant calling. We then annotated variant call format (VCF) files using Golden Helix VarSeq 2.5.0 and employed Stargazer v2.0.2 for star allele analysis. The analysis of 63 very important pharmacogenes (VIPGx) reveals 85,566 variants, including 13,532 novel discoveries. Notably, we identified 464 known PGx variants and 275 clinically relevant novel variants. The phenotypic prediction of 15 VIPGx demonstrated a varied metabolic profile for the Thai population. Genes like CYP2C9 (9%), CYP3A5 (45.2%), CYP2B6 (9.4%), NUDT15 (15%), CYP2D6 (47%) and CYP2C19 (43%) showed a high number of intermediate metabolizers; CYP3A5 (41%), and CYP2C19 (9.9%) showed more poor metabolizers. CYP1A2 (52.7%) and CYP2B6 (7.6%) were found to have a higher number of ultra-metabolizers. The functional prediction of the remaining 10 VIPGx genes reveals a high frequency of decreased functional alleles in SULT1A1 (12%), NAT2 (84%), and G6PD (12%). SLCO1B1 reports 20% poor functional alleles, while PTGIS (42%), SLCO1B1 (4%), and TPMT (5.96%) showed increased functional alleles. This study discovered new variants and alleles in the 63 VIPGx genes among the Thai population, offering insights into advancing clinical pharmacogenomics (PGx). However, further validation is needed using other computational and genotyping methods.

Enigmatic Nodal and Lefty gene repertoire discrepancy: Latent evolutionary history revealed by vertebrate-wide phylogeny

Homology in vertebrate body plans is traditionally ascribed to the high-level conservation of regulatory components within the genetic programs governing them, particularly during the "phylotypic stage." However, advancements in embryology and molecular phylogeny have unveiled the dynamic nature of gene repertoires responsible for early development. Notably, the Nodal and Lefty genes, members of the transforming growth factor-beta superfamily producing intercellular signaling molecules and crucial for left-right (L-R) symmetry breaking, exhibit distinctive features within their gene repertoires. These features encompass among-species gene repertoire variations resulting from gene gain and loss, as well as gene conversion. Despite their significance, these features have been largely unexplored in a phylogenetic context, but accumulating genome-wide sequence information is allowing the scrutiny of these features. It has exposed hidden paralogy between Nodal1 and Nodal2 genes resulting from differential gene loss in amniotes. In parallel, the tandem cluster of Lefty1 and Lefty2 genes, which was thought to be confined to mammals, is observed in sharks and rays, with an unexpected phylogenetic pattern. This article provides a comprehensive review of the current understanding of the origins of these vertebrate gene repertoires and proposes a revised nomenclature based on the elucidated history of vertebrate genome evolution.