Dynamic patterns of the translatome in a hybrid triplet show translational fractionation of the maize subgenomes

Heterosis,the phenomenon in which hybrids outperform their parents,has been utilized in maize(Zea mays L.)for over 100 years.To provide a more complete understanding of heterosis,we collected a comprehensive transcriptome and translatome dataset on seedling leaves for B73,Mo17,and their F1 hybrid,which provided a dynamic landscape of transcriptomic and translatomic variation in maize.Although additivity accounted for a large proportion of variation at two omics-levels,an elevated nonadditive effect was observed in the translatome,especially in the translated subgenome maize1 genes,and the genes that switched from additivity in the transcriptome to nonadditivity in the translatome were significantly enriched in the subgenome maize1.Many genes with allele-specific expression and translation show dramatic regulatory switches between the transcriptome and translatome,and partial genes with allele-specific translation underlying regulatory mechanism also exhibited subgenome bias.Interestingly,we found the translated isoforms show different expression patterns compared with transcriptome and more genes changed their dominant isoforms during the genetic flow from parents to the hybrid at the translatome level.The translated genes with switched dominant isoforms significantly biased to the subgenome maize2 while genes with conserved dominant isoforms significantly enriched in subgenome maize1.Together,the dynamic changed patterns in translatome across hybrid and parental lines show translational fractionation of the maize subgenomes,which may be associated with heterosis in maize and provides a potential theoretical basis for breeding.

Investigation on Evolutionary Relationships of the Subgenomes in Interspecific Triploid Cotton via Meiotic FISH

We report in this paper primary studies on interspecific species of cotton vis GISH(genomic in situ hybridization).We use interspecific triploid hybrids(F1 from hybridization of allotetraploid cultivated species with diploid A,D,or C genome species) and two cultivated tetraploids to study

Evolutionary divergence of subgenomes in common carp provides insights into speciation and allopolyploid success

Hybridization and polyploidization have made great contributions to speciation,heterosis,and agricultural production within plants,but there is still limited understanding and utilization in animals.Subgenome structure and expression reorganization and cooperation post hybridization and polyploidization are essential for speciation and allopolyploid success.However,the mechanisms have not yet been comprehensively assessed in animals.Here,we produced a high-fidelity reference genome sequence for common carp,a typical allotetraploid fish species cultured worldwide.This genome enabled in-depth analysis of the evolution of subgenome architecture and expression responses.Most genes were expressed with subgenome biases,with a trend of transition from the expression of subgenome A during the early stages to that of subgenome B during the late stages of embryonic development.While subgenome A evolved more rapidly,subgenome B contributed to a greater level of expression during development and under stressful conditions.Stable dominant patterns for homoeologous gene pairs both during development and under thermal stress suggest a potential fixed heterosis in the allotetraploid genome.Preferentially expressing either copy of a homoeologous gene at higher levels to confer development and response to stress indicates the dominant effect of heterosis.The plasticity of subgenomes and their shifting of dominant expression during early development,and in response to stressful conditions,provide novel insights into the molecular basis of the successful speciation,evolution,and heterosis of the allotetraploid common carp.

Functional Divergence between Subgenomes anc Gene Pairs after Whole Genome Duplications

Gene loss following whole genome duplication （WGD） is often biased, with one subgenome retaining more ancestral genes and the other sustaining more gene deletions. While bias toward the greater expression of gene copies on one subgenome can explain bias in gene loss, this raises the question to what drives differences in gene expression levels between subgenomes. Differences in chromatin modifications and epigenetic markers between subgenomes in several model species are now being identified, providing an explanation for bias in gene expression between subgenomes. WGDs can be classified into duplications with higher, biased gene loss and bias in gene expression between subgenomes versus those with lower, unbiased rates of gene loss and an absence of detectable bias between subgenomes; however, the origi- nally proposed link between these two classes and whether WGD results from an allo- or autopolyploid event is inconsistent with recent data from the allopolyploid Capsella bursa-pastoris. The gene balance hypothesis can explain bias in the functional categories of genes retained following WGD, the difference in gene loss rates between unbiased and biased WGDs, and how plant genomes have avoided being overrun with genes encoding dose-sensitive subunits of multiprotein complexes. Comparisons of gene expression patterns between retained transcription factor pairs in maize suggest the high degree of retention for WGD-derived pairs of transcription factors may instead be explained by the older duplication-degeneration-complementation model.

Construction of a chimeric hepatitis C virus replicon based on a strain isolated from a chronic hepatitis C patient

Subgenomic replicons of hepatitis C virus （HCV） have been widely used for studying HCV replication.Here,we report a new subgenomic replicon based on a strain isolated from a chronically infected patient.The coding sequence of HCV was recovered from a Chinese chronic hepatitis C patient displaying high serum HCV copy numbers.A consensus sequence designated as CCH strain was constructed based on the sequences of five clones and this was classified by sequence alignment as belonging to genotype 2a.The subgenomic replicon of CCH was replication-deficient in cell culture,due to dysfunctions in NS3 and NS5B.Various JFH1/CCH chimeric replicons were constructed,and specific mutations were introduced.The introduction of mutations could partially restore the replication of chimeric replicons.A replication-competent chimeric construct was finally obtained by the introduction of NS3 from JFH1 into the backbone of the CCH strain.

Mapping subgenomic promoter of coat protein gene of Cucumber green mottle mosaic virus

Many plant viruses utilize subgenomic RNA as gene expression strategy, therefore mapping subgenomic promoter(SGP) is extremely important for constructing viral vectors. Although Cucumber green mottle mosaic virus(CGMMV)-based virus vectors have been constructed, SGP of the coat protein(CP) has not yet mapped. To this end, we firstly presumed 13 nucleotides upstream of the start codon as the transcription starting site(TSS) as previous study identified by random amplification of c DNA ends(RACE). Secondly, the region from nucleotides –110 to +175 is the putative CP SGP, as predicted, a long stem loop structure by the secondary structure of RNA covering movement protein(MP) and CP. To map the CGMMV CP SGP, we further constructed a series of deletion mutants according to RNA secondary structure prediction. The deletion of TSS upstream significantly enhanced CP transcription when 105 nucleotides were retained before the CP TSS. For the downstream of CP TSS, we analyzed the expression of enhanced green fluorescent protein(EGFP) in a series of vectors with partial deletion of the CGMMV CP and found that the nucleotides from +71 to +91 played a key role in the EGFP expression at the transcription level, while EGFP showed the highest expression level when 160 nucleotides were retained downstream of the CP TSS. To confirm these results, we applied online software MEME to predict the motifs and cis-acting elements in the 466 nucleotides covering the sequences of deletion analysis. Conserved motifs and relative acting elements were in regions in which transcription levels were the highest or enhanced. To our best knowledge, this is the first mapping of CGMMV SGP.

Quantitative and qualitative subgenomic RNA profiles of SARS-CoV-2 in respiratory samples: A comparison between Omicron BA.2 and non-VOC-D614G

The SARS-CoV-2 Omicron variants are notorious for their transmissibility,but little is known about their subgenomic RNA(sgRNA)expression.This study applied RNA-seq to delineate the quantitative and qualitative profiles of canonical sgRNA of 118 respiratory samples collected from patients infected with Omicron BA.2 and compared with 338 patients infected with non-variant of concern(non-VOC)-D614G.A unique characteristic profile depicted by the relative abundance of 9 canonical sgRNAs was reproduced by both BA.2 and non-VOCD614G regardless of host gender,age and presence of pneumonia.Remarkably,such profile was lost in samples with low viral load,suggesting a potential application of sgRNA pattern to indicate viral activity of individual patient at a specific time point.A characteristic qualitative profile of canonical sgRNAs was also reproduced by both BA.2 and non-VOC-D614G.The presence of a full set of canonical sgRNAs carried a coherent correlation with crude viral load(AUC¼0.91,95%CI 0.88–0.94),and sgRNA ORF7b was identified to be the best surrogate marker allowing feasible routine application in characterizing the infection status of individual patient.Further potentials in using sgRNA as a target for vaccine and antiviral development are worth pursuing.

A chromosome-scale genome assembly of Artemisia argyi reveals unbiased subgenome evolution and key contributions of gene duplication to volatile terpenoid diversity

Artemisia argyi Le´vl.et Vant.,a perennial Artemisia herb with an intense fragrance,is widely used in traditional medicine in China and many other Asian countries.Here,we present a chromosome-scale genome assembly of A.argyi comprising 3.89 Gb assembled into 17 pseudochromosomes.Phylogenetic and comparative genomic analyses revealed that A.argyi underwent a recent lineage-specificwhole-genomeduplication(WGD)event after divergence fromArtemisia annua,resulting in two subgenomes.Wedeciphered the diploid ancestral genome of A.argyi,and unbiased subgenome evolution was observed.The recent WGD led to a large number of duplicated genes in the A.argyi genome.Expansion of the terpene synthase(TPS)gene family through various types of gene duplication may have greatly contributed to the diversity of volatile terpenoids in A.argyi.In particular,we identified a typical germacrene D synthase gene cluster within the expanded TPS gene family.The entire biosynthetic pathways of germacrenes,(+)-borneol,and(+)-camphor were elucidated in A.argyi.In addition,partial deletion of the amorpha-4,11-diene synthase(ADS)gene and loss of function of ADS homologs may have resulted in the lack of artemisinin production in A.argyi.Our study provides newinsights into the genome evolution of Artemisia and lays a foundation for further improvement of the quality of this important medicinal plant.

Genome resources for the elite bread wheat cultivar Aikang 58 and mining of elite homeologous haplotypes for accelerating wheat improvement

Despite recent progress in crop genomics studies,the genomic changes brought about by modern breeding selection are still poorly understood,thus hampering genomics-assisted breeding,especially in polyploid crops with compound genomes such as common wheat(Triticum aestivum).In this work,we constructed genome resources for the modern elite common wheat variety Aikang 58(AK58).Comparative genomics between AK58 and the landrace cultivar Chinese Spring(CS)shed light on genomic changes that occurred through recent varietal improvement.We also explored subgenome diploidization and divergence in common wheat and developed a homoeologous locus-based genome-wide association study(HGWAS)approach,which was more effective than single homoeolog-based GWAS in unraveling agronomic trait-associated loci.A total of 123 major HGWAs loci were detected using a genetic population derived from AK58 and cs.Elite homoeologous haplotypes(HHs),formed by combinations of subgenomic homoeologs of the associated loci,were found in both parents and progeny,and many could substantially improve wheat yield and related traits.We built a website where users can download genome assembly sequence and annotation data for AK58,perform blast analysis,and run JBrowse.Our work enriches genome resources for wheat,provides new insights into genomic changes during modern wheat improve-.ment,and suggests that efficientmining of elite HHs can make a substantial contribuutionto genomics-assisted breeding in common wheat and other polyploid crops.

Differential Transcriptomic Landscapes of SARS-CoV-2 Variants in Multiple Organs from Infected Rhesus Macaques

Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)caused the persistent coronavirus disease 2019(COVID-19)pandemic,which has resulted in millions of deaths worldwide and brought an enormous public health and global economic burden.The recurring global wave of infections has been exacerbated by growing variants of SARS-CoV-2.In this study,the virological characteristics of the original SARS-CoV-2 strain and its variants of concern(VOCs;including Alpha,Beta,and Delta)in vitro,as well as differential transcriptomic landscapes in multiple organs(lung,right ventricle,blood,cerebral cortex,and cerebellum)from the infected rhesus macaques,were elucidated.The original strain of SARS-CoV-2 caused a stronger innate immune response in host cells,and its VOCs markedly increased the levels of subgenomic RNAs,such as N,Orf9b,Orf6,and Orf7ab,which are known as the innate immune antagonists and the inhibitors of antiviral factors.Intriguingly,the original SARS-CoV-2 strain and Alpha variant induced larger alteration of RNA abundance in tissues of rhesus monkeys than Beta and Delta variants did.Moreover,a hyperinflammatory state and active immune response were shown in the right ventricles of rhesus monkeys by the up-regulation of inflammation-and immune-related RNAs.Furthermore,peripheral blood may mediate signaling transmission among tissues to coordinate the molecular changes in the infected individuals.Collectively,these data provide insights into the pathogenesis of COVID-19 at the early stage of infection by the original SARS-CoV-2 strain and its VOCs.

Genome sequencing of Sitopsis species provides insights into their contribution to the B subgenome of bread wheat

Wheat(Triticum aestivum,BBAADD)is an allohexaploid species that originated from two polyploidization events.The progenitors of the A and D subgenomes have been identified as Triticum urartu and Aegilops tauschii,respectively.Current research suggests that Aegilops speltoides is the closest but not the direct ancestor of the B subgenome.However,whether Ae.speltoides has contributed genomically to the wheat B subgenome and which chromosome regions are conserved between Ae.speltoides and the B subgenome remain unclear.Here,we assembled a high-quality reference genome for Ae.speltoides,resequenced 53 accessions from seven species(Aegilops bicornis,Aegilops longissima,Aegilops searsii,Aegilops sharonensis,Ae.speltoides,Aegilops mutica[syn.Amblyopyrum muticum],and Triticumdicoccoides)and revealed their genomic contributions to the wheat B subgenome.Our results showed that centromeric regions were particularly conserved between Aegilops and Triticum and revealed 0.17 Gb of conserved blocks between Ae.speltoides and the B subgenome.We classified five groups of conserved and non-conserved genes between Aegilops and Triticum,revealing their biological characteristics,differentiation in gene expression patterns,and collinear relationships between Ae.speltoides and the wheat B subgenome.We also identified gene families that expanded in Ae.speltoides during its evolution and 789 genes specific to Ae.speltoides.These genes can serve as genetic resources for improvement of adaptability to biotic and abiotic stress.The newly constructed reference genome and large-scale resequencing data for Sitopsis species will provide a valuable genomic resource for wheat genetic improvement and genomic studies.

The genome of Orychophragmus violaceus provides genomic insights into the evolution of Brassicaceaepolyploidizationandits distinct traits

Orychophragmus violaceus,referred to as‘‘eryuelan’’(February orchid)in China,is an early-flowering ornamental plant.The high oil content and abundance of unsaturated fatty acids in O.violaceus seeds make it a potential high-quality oilseed crop.Here,we generated a whole-genome assembly for O.violaceus using Nanopore and Hi-C sequencing technologies.The assembled genome of O.violaceus was~1.3 Gb in size,with 12 pairs of chromosomes.Through investigation of ancestral genome evolution,we determined that the genome of O.violaceus experienced a tetraploidization event from a diploid progenitor with the translocated proto-Calepineae karyotype.Comparisons between the reconstructed subgenomes of O.violaceus identified indicators of subgenome dominance,indicating that subgenomes likely originated via allotetraploidy.O.violaceus was phylogenetically close to the Brassica genus,and tetraploidy in O.violaceus occurred approximately 8.57 million years ago,close in time to the whole-genome triplication of Brassica that likely arose via an intermediate tetraploid lineage.However,the tetraploidization in Orychophragmus was independent of the hexaploidization in Brassica,as evidenced by the results from detailed phylogenetic analyses and comparisons of the break and fusion points of ancestral genomic blocks.Moreover,identification of multi-copy genes regulating the production of high-quality oil highlighted the contributions of both tetraploidization and tandem duplication to functional innovation in O.violaceus.These findings provide novel insights into the polyploidization evolution of plant species and will promote both functional genomic studies and domestication/breeding efforts in O.violaceus.

Genome Sequences Provide Insights into the Reticulate Origin and Unique Traits of Woody Bamboos

Polyploidization is a major driver of speciation and its importance to plant evolution has been well recognized.Bamboos comprise one diploid herbaceous and three polyploid woody lineages,and are members of the only major subfamily in grasses that diversified in forests,with the woody members having a tree-like lignified culm.In this study,we generated four draft genome assemblies of major bamboo lineages with three different ploidy levels(diploid,tetraploid,and hexaploid).We also constructed a high-density genetic linkage map for a hexaploid species of bamboo,and used a linkage-map-based strategy for genome assembly and identification of subgenomes in polyploids.Further phylogenomic analyses using a large dataset of syntenic genes with expected copies based on ploidy levels revealed that woody bamboos originated subsequent to the divergence of the herbaceous bamboo lineage,and experienced complex reticulate evolution through three independent allopolyploid events involving four extinct diploid ancestors.A shared but distinct subgenome was identified in all polyploid forms,and the progenitor of this subgenome could have been critical in ancient polyploidizations and the origin of woody bamboos.Important genetic clues to the unique flowering behavior and woody trait in bamboos were also found.Taken together,our study provides significant insights into ancient reticulate evolution at the subgenome level in the absence of extant donor species,and offers a potential model scenario for broad-scale study of angiosperm origination by allopolyploidization.

Translation landscape of SARS-CoV-2 noncanonical subgenomic RNAs

The ongoing COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)with a positive-stranded RNA genome. Current proteomic studies of SARS-CoV-2 mainly focus on the proteins encoded by its genomic RNA(gRNA) or canonical subgenomic RNAs(sgRNAs). Here, we systematically investigated the translation landscape of SARS-CoV-2, especially its noncanonical sgRNAs. We first constructed a strict pipeline, named vipep, for identifying reliable peptides derived from RNA viruses using RNA-seq and mass spectrometry data. We applied vipep to analyze 24 sets of mass spectrometry data related to SARS-CoV-2infection. In addition to known canonical proteins, we identified many noncanonical sgRNA-derived peptides,which stably increase after viral infection. Furthermore, we explored the potential functions of those proteins encoded by noncanonical sgRNAs and found that they can bind to viral RNAs and may have immunogenic activity. The generalized vipep pipeline is applicable to any RNA viruses and these results have expanded the SARSCoV-2 translation map, providing new insights for understanding the functions of SARS-CoV-2 sgRNAs.

Characterization of two SARS-CoV-2 subgenomic RNA dynamics in severe COVID-19 patients

Little is known about Subgenomic RNA(sgRNA)dynamics in patients with Coronavirus diseases 2019(COVID-19).We collected 147 throat swabs,74 gut swabs and 46 plasma samples from 117 COVID-19 patients recruited in the LOTUS China trial(ChiCTR2000029308)and compared E and orf7a sgRNA load in patients with different illness duration,outcome,and comorbidities.Both sgRNAs were detected in all the three types of samples,with longest duration of 25,13,and 17 days for E sgRNA,and 32,28,and 17 days for orf7a sgRNA in throat,gut,and plasma,respectively.A total of 95%(57/60)of patients had no E sgRNA detected after 10 days post treatment,though 86%of them were still E RNA positive.High correlation on titer was observed between sgRNA encoding E and orf7a gene.sgRNA showed similar variation in the standard care and Lopinavir-Ritonavir group.Patients with diabetes and heart diseases showed higher pharyngeal E sgRNA at the first day(P=0.016 and 0.013,respectively)but no difference at five days after treatment,compared with patients without such commodities.Patients with hypertension and cerebrovascular diseases showed no difference in the pharyngeal sgRNA levels at both one and five days after treatment,compared with patients without these two commodities.E sgRNA levels in the initial infection showed no correlation with the serum antibody against spike,nucleoprotein,and receptor binding domains at ten days later.sgRNA lasted a long period in COVID-19 patients and might have little effect on humoral response.