Gene expression is regulated by chromatin architecture and epigenetic remodeling in cell homeostasis and pathologies.Histone modifications act as the key factors to modulate the chromatin accessibility.Different histone modifications are strongly associated with the localization of chromatin.Heterochromatin primarily localizes at the nuclear periphery,where it interacts with lamina proteins to suppress gene expression.In this review,we summarize the potential bridges that have regulatory functions of histone modifications in chromatin organization and transcriptional regulation at the nuclear periphery.We use lamina-associated domains(LADs)as examples to elucidate the biological roles of the interactions between histone modifications and nuclear lamina in cell differentiation and development.In the end,we highlight the technologies that are currently used to identify and visualize histone modifications and LADs,which could provide spatiotemporal information for understanding their regulatory functions in gene expression and discovering new targets for diseases.
Chicken(Gallus gallus)is a vital living organism and plays a crucial role in food requirements.Complete and accurate chicken genomes are critical for insights into chicken breeding,avian evolution,and comparative genomics(Bravo et al.,2021).Pan-genomes possess more power to capture complete gene sets,thus presenting more comprehensive genomic information within species.
Sechium edule(chayote)is an important vegetable crop belonging to the Cucurbitaceae family.To decipher the chayote genome,a highquality chromosome-level chayote genome was obtained by genome sequencing and bioinformatic analysis.The total length was612.91 Mb,and 25755 genes were detected in the chayote genome.The contig N50 was more than 20.01 Mb,and the scaffold N50 was over47.11 Mb.Of the genome,60.35%were composed of repetitive sequences,and 31.18%of genome sequences belonged to long-terminal repeats.A global alignment of homologous regions in chayote and other Cucurbitaceae plant genomes was constructed using grape as a reference.Based on this genome-wide and global alignment map,researchers can easily identify homologous collinear genes of the studied genomes in most Cucurbitaceae species.Twenty-five chayote accessions were divided into two subgroups based on phylogenetic tree,population structure analysis,and principal component analysis using genome re-sequencing data.The chayote genome,re-sequencing dataset,and comprehensive genomic analysis will accelerate comparative and functional genomic analysis of chayote and other Cucurbitaceae species in the future.
Xiaojing WangShaoqin ShenYanhong FuRui CaoYunfeng WeiXiaoming Song
Background Unveiling genetic diversity features and understanding the genetic mechanisms of diverse goat pheno-types are pivotal in facilitating the preservation and utilization of these genetic resources.However,the total genetic diversity within a species can’t be captured by the reference genome of a single individual.The pan-genome is a col-lection of all the DNA sequences that occur in a species,and it is expected to capture the total genomic diversity of the specific species.Results We constructed a goat pan-genome using map-to-pan assemble based on 813 individuals,including 723 domestic goats and 90 samples from their wild relatives,which presented a broad regional and global represen-tation.In total,146 Mb sequences and 974 genes were identified as absent from the reference genome(ARS1.2;GCF_001704415.2).We identified 3,190 novel single nucleotide polymorphisms(SNPs)using the pan-genome analysis.These novel SNPs could properly reveal the population structure of domestic goats and their wild relatives.Presence/absence variation(PAV)analysis revealed gene loss and intense negative selection during domestication and improvement.Conclusions Our research highlights the importance of the goat pan-genome in capturing the missing genetic variations.It reveals the changes in genomic architecture during goat domestication and improvement,such as gene loss.This improves our understanding of the evolutionary and breeding history of goats.
Cimex species are ectoparasites that exclusively feed on warm-blooded animals such as birds and mammals.Three cimicid species are known to be persistent pests for humans,including the tropical bed bug Cimex hemipterus,common bed bug Cimex lectularius,and Eastern bat bug Leptocimex boueti.To date,genomic information is restricted to the common bed bug C.lectularius,which limits understanding their biology and to provide controls of bed bug infestations.Here,a chromosomal-level genome assembly of C.hemipterus(495 Mb[megabase pairs])contained on 16 pseudochromosomes(scaffold N50=34 Mb),together with 9 messenger RNA and small RNA transcriptomes were obtained.In comparison between hemipteran genomes,we found that the tetraspanin superfamily was expanded in the Cimex ancestor.This study provides the first genome assembly for the tropical bed bug C.hemipterus,and offers an unprecedented opportunity to address questions relating to bed bug infestations,as well as genomic evolution to hemipterans more widely.
Sean Tsz Sum LawWenyan NongChade LiTze Kiu ChongHo Yin YipThomas SwaleSiu Wai ChiuRoger Yat-Nork ChungHon-Ming LamSamuel Y.S.WongHung WongJerome H.L.Hui
The donkey is an important livestock species that can provide milk,meat,and skin and belongs to the family Equus.The first genome of a male donkey was sequenced and de novo assembled using a whole-genome shotgun strategy(Huang et al.,2015).Subsequently,the donkey genome showed greater improvement in continuity and chromosome length than a previous assembly(Renaud et al.,2018).
Ge YangMian GongQi-Meng YangYi-Dan LiHalima JafariChu-Zhao LeiYu JiangRui-Hua Dang
Coconut(Cocos nucifera L.)is a key tropical economic tree valued for its fruit flavor,particularly 2-acetyl-1-pyrroline(2AP),a vital aroma metabolite.To enhance high-aromatic coconut breeding efforts,it is essential to deeply understand the hereditary factors governing the production of 2AP.In this study,a genome-wide association analysis identifies 32 loci that exhibit significant associations with 2AP content based on single nucleotide polymorphism(SNP)variations from 168 aromatic coconut germplasm resources.Transcriptome analysis then pinpoints 22 candidate genes near significant loci involved in 2AP metabolism.Proteins encoded by these genes are involved in amino acid metabolism,glycolysis,and secondary metabolism.Among these,Asparagine synthetase coding gene ASN1,Gamma-glutamylcysteine synthetase coding gene GSH1,and UbiA prenyltransferase coding gene UBIA are enriched in the linkage region constructed by significant locus Chr04_61490504.In particular,the SNP mutation of CnASN1 leads to amino acid changes in the functional region of the coding protein,potentially resulting in differences in 2AP content among haplotype populations.Identifying variations in related candidate genes,particularly the gene CnASN1,provides molecular markers closely associated with 2AP synthesis for coconut breeding and offers further insights into the metabolic mechanisms of 2AP.
Hao DingXiang LvGuangzhen ZhouXiaomei LiuXiwei SunJing LiAmjad IqbalYaodong Yang
