Toward the generation of pure coral genomes with experimental and bioinformatic improvements

Stony corals,the primary architects of coral reef ecosystems,are largely underrepresented in omics studies despite their importance.The presence of endosymbiotic Symbiodiniaceae algae complicates the extraction of pure coral DNA,posing a challenge for genomic research.Here,we devised a comprehensive methodological framework that incorporates various experimental treatments to achieve 99%purity in coral DNA extraction and a robust bioinformatics pipeline to guarantee the assembly of high-quality,contamination-free coral genomes.Validation of our framework using Acropora millepora samples demonstrated its efficacy and superiority in obtaining high-quality pure coral genomes using easily accessible adult colony.This integrated framework serves as a critical foundation for largescale genome-enabled research on stony corals,providing insight into coral evolution and conservation.

Exploring marine endosymbiosis systems with omics techniques

Endosymbiosis is the phenomenon where one organism lives inside another,usually in a mutualistic way.In this system,the hosts provide shelter and nutrients to the endosymbionts,who could affect the hosts in a physiological(Sommer and B?ckhed,2013),behavioral(Ezenwa et al.,2012),and evolutionary(Perlmutter and Bordenstein,2020)way.

Comparative analysis reveals epigenomic evolution related to species traits and genomic imprinting in mammals

DNA methylation is an epigenetic modification that plays a crucial role in various regulatory processes,including gene expression regulation,transposable element repression,and genomic imprinting.However,most studies on DNA methylation have been conducted in humans and other model species,whereas the dynamics of DNA methylation across mammals remain poorly explored,limiting our understanding of epigenomic evolution in mammals and the evolutionary impacts of conserved and lineage-specific DNA methylation.Here,we generated and gathered comparative epigenomic data from 13 mammalian species,including two marsupial species,to demonstrate that DNA methylation plays critical roles in several aspects of gene evolution and species trait evolution.We found that the species-specific DNA methylation of promoters and noncoding elements correlates with species-specific traits such as body patterning,indicating that DNA methylation might help establish or maintain interspecies differences in gene regulation that shape phenotypes.For a broader view,we investigated the evolutionary histories of 88 known imprinting control regions across mammals to identify their evolutionary origins.By analyzing the features of known and newly identified potential imprints in all studied mammals,we found that genomic imprinting may function in embryonic development through the binding of specific transcription factors.Our findings show that DNA methylation and the complex interaction between the genome and epigenome have a significant impact on mammalian evolution,suggesting that evolutionary epigenomics should be incorporated to develop a unified evolutionary theory.

The metabolic adaptation in wild vertebrates via omics approaches

Metabolism is the basis for sustaining life and essential to the adaptive evolution of organisms.With the development of high-throughput sequencing technology,genetic mechanisms of adaptive evolution,including metabolic adaptation,have been extensively resolved by omics approaches,but a deep understanding of genetic and epigenetic metabolic adaptation is still lacking.Exploring metabolic adaptations from genetic and epigenetic perspectives in wild vertebrates is vital to understanding species evolution,especially for the early stages of adaptative evolution.Herein,we summarize the advances in our understanding of metabolic adaptations via omics approaches in wild vertebrates based on three types of cases:extreme environment,periodically changing environment,and changes of species characteristics.We conclude that the understanding of the formation of metabolic adaptations at the genetic level alone can well identify the adaptive genetic variation that has developed during evolution,but cannot resolve the potential impact of metabolic adaptations on the adaptative evolution in the future.Thus,it seems imperative to include epigenomics and metabolomics in the study of adaptation,and that in the future genomic and epigenetic data should be integrated to understand the formation of metabolic adaptation of wild vertebrate organisms.