A telomere-to-telomere genome assembly of Hongyingzi,a sorghum cultivar used for Chinese Baijiu production

Sorghum(Sorghum bicolor(L.)Moench)is a world cereal crop used in China for producing Baijiu,a distilled spirit.We report a telomere-to-telomere genome assembly of the Baijiu cultivar Hongyingzi,HYZ-T2T,using ultralong reads.The 10 chromosome pairs contained 33,462 genes,of which 93%were functionally annotated.The 20 telomeres and 10 centromeric regions on the HYZ-T2T chromosomes were predicted and two consecutive large inversions on chromosome 2 were characterized.A 65-gene reconstruction of the metabolic pathway of tannins,the flavor substances in Baijiu,was performed and may advance the breeding of sorghum cultivars for Baijiu production.

A chromosome-level genome assembly of rugged rose (Rosa rugosa) provides insights into its evolution, ecology, and floral characteristics

Rosa rugosa,commonly known as rugged rose,is a perennial ornamental shrub.It produces beautiful flowers with a mild fragrance and colorful seed pods.Unlike many other cultivated roses,R.rugosa adapts to a wide range of habitat types and harsh environmental conditions such as salinity,alkaline,shade,drought,high humidity,and frigid temperatures.Here,we produced and analyzed a high-quality genome sequence for R.rugosa to understand its ecology,floral characteristics and evolution.PacBio HiFi reads were initially used to construct the draft genome of R.rugosa,and then Hi-C sequencing was applied to assemble the contigs into 7 chromosomes.We obtained a 382.6Mb genome encoding 39,704 protein-coding genes.The genome of R.rugosa appears to be conserved with no additional whole-genome duplication after the gamma whole-genome triplication(WGT),which occurred~100 million years ago in the ancestor of core eudicots.Based on a comparative analysis of the high-quality genome assembly of R.rugosa and other high-quality Rosaceae genomes,we found a unique large inverted segment in the Chinese rose R.chinensis and a retroposition in strawberry caused by post-WGT events.We also found that floral development-and stress response signaling-related gene modules were retained after the WGT.Two MADS-box genes involved in floral development and the stress-related transcription factors DREB2A-INTERACTING PROTEIN 2(DRIP2)and PEPTIDE TRANSPORTER 3(PTR3)were found to be positively selected in evolution,which may have contributed to the unique ability of this plant to adapt to harsh environments.In summary,the high-quality genome sequence of R.rugosa provides a map for genetic studies and molecular breeding of this plant and enables comparative genomic studies of Rosa in the near future.

NextPolish2:A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads

The high-fidelity(HiFi)long-read sequencing technology developed by PacBio has greatly improved the base-level accuracy of genome assemblies.However,these assemblies still contain base-level errors,particularly within the error-prone regions of HiFi long reads.Existing genome polishing tools usually introduce overcorrections and haplotype switch errors when correcting errors in genomes assembled from HiFi long reads.Here,we describe an upgraded genome polishing tool-NextPolish2,which can fix base errors remaining in those“highly accurate”genomes assembled from HiFi long reads without introducing excessive overcorrections and haplotype switch errors.We believe that NextPolish2 has a great significance to further improve the accuracy of telomere-to-telomere(T2T)genomes.NextPolish2 is freely available at https://github.com/Nextomics/NextPolish2.

T2T-YAO: A Telomere-to-telomere Assembled Diploid Reference Genome for Han Chinese

Since its initial release in 2001,the human reference genome has undergone continuous improvement in quality,and the recently released telomere-to-telomere(T2T)version-T2T-CHM13—reaches its highest level of continuity and accuracy after 20 years of effort by working on a simplified,nearly homozygous genome of a hydatidiform mole cell line.Here,to provide an authentic complete diploid human genome reference for the Han Chinese,the largest population in the world,we assembled the genome of a male Han Chinese individual,T2T-YAO,which includes T2T assemblies of all the 22+X+M and 22+Y chromosomes in both haploids.The quality of T2T-YAO is much better than those of all currently available diploid assemblies,and its haploid version,T2T-YAO-hp,generated by selecting the better assembly for each autosome,reaches the top quality of fewer than one error per 29.5 Mb,even higher than that of T2T-CHM13.Derived from an individual living in the aboriginal region of the Han population,T2T-YAO shows clear ancestry and potential genetic continuity from the ancient ancestors.Each haplotype of T2TYAO possesses330-Mb exclusive sequences,3100 unique genes,and tens of thousands of nucleotide and structural variations as compared with CHM13,highlighting the necessity of a population-stratified reference genome.The construction of T2T-YAO,an accurate and authentic representative of the Chinese population,would enable precise delineation of genomic variations and advance our understandings in the hereditability of diseases and phenotypes,especially within the context of the unique variations of the Chinese population.

Genome-wide DNA methylation landscape of four Chinese populations and epigenetic variation linked to Tibetan high-altitude adaptation

DNA methylation(DNAm)is one of the major epigenetic mechanisms in humans and is important in diverse cellular processes.The variation of DNAm in the human population is related to both genetic and environmental factors.However,the DNAm profiles have not been investigated in the Chinese population of diverse ethnicities.Here,we performed double-strand bisulfite sequencing(DSBS)for 32 Chinese individuals representing four major ethnic groups including Han Chinese,Tibetan,Zhuang,and Mongolian.We identified a total of 604,649 SNPs and quantified DNAm at more than 14 million Cp Gs in the population.We found global DNAm-based epigenetic structure is different from the genetic structure of the population,and ethnic difference only partially explains the variation of DNAm.Surprisingly,non-ethnic-specific DNAm variations showed stronger correlation with the global genetic divergence than these ethnic-specific DNAm.Differentially methylated regions(DMRs)among these ethnic groups were found around genes in diverse biological processes.Especially,these DMR-genes between Tibetan and nonTibetans were enriched around high-altitude genes including EPAS1 and EGLN1,suggesting DNAm alteration plays an important role in high-altitude adaptation.Our results provide the first batch of epigenetic maps for Chinese populations and the first evidence of the association of epigenetic changes with Tibetans'high-altitude adaptation.

The N^6-adenine methylation in yeast genome profiled by single-molecule technology

The most common and abundant DNA modification is 5-methylcytosine（5mC）,which has been well-established as an epigenetic mark regulating gene expression in eukaryotes（Jones,2012）.Another DNA modification N^6-methyldeoxyadenosine（6mA）,previously reported as a widespread DNA methylation in prokaryotes.

Multi-omics analyses of 398 foxtail millet accessions reveal genomic regions associated with domestication,metabolite traits,and antiinflammatory effects

Foxtail millet(Setaria italica),which was domesticatedfromthewild speciesgreenfoxtail(Setaria viridis),isa richsource of phytonutrientsfor humans.To evaluate how breeding changed themetabolome offoxtail millet grains,we generated and analyzed the datasets encompassing the genomes,transcriptomes,metabolomes,and anti-inflammatory indices from 398 foxtail millet accessions.We identified hundreds of common variants that influence numerous secondary metabolites.We observed tremendous differences in natural variations of the metabolites and their underlying genetic architectures between distinct sub-groups of foxtail millet.Furthermore,we found that the selection of the gene alleles associated with yellow grains led to altered profiles of metabolites such as carotenoids and endogenous phytohormones.Using CRiSPR-mediated genome editing wevalidated the function of PHYTOENE SYNTHASE1(PSY1)gene in affecting milletgrain colorand quality.Interestingly,our in vitro cell inflammation assays showed that 83 metabolites in millet grains have anti-inflammatory effects.Taken together,ourmulti-omics study illustrates how the breeding history of foxtail millet has shaped its metabolite profile.The datasets we generated in this study also provide important resources for further understanding how millet grain quality is affected by different metabolites,laying the foundations for future millet genetic research and metabolome-assisted improvement.

Digital Noah's Ark:last chance to save the endangered species

Global biodiversity is undergoing dramatic loss,mostly due to anthropogenic actions and climate change.Around 2.3seed plants died out each year in the past 2.5 centuries(Humphreys et al.,2019).Current species extinction rates are about 1,000 times the likely background rate of extinction(Pimm et al.,2014).

Nanopore sequencing of African swine fever virus

Dear Editor,African swine fever(ASF)is one of the most pathogenic viral diseases in pigs caused by African swine fever virus(ASFV).The fatality rate is almost 100%,which brings huge economic losses to the hog industry in countries with epiepidemics(Galindo and Alonso,2017).China was the first Asian country to have an ASF epidemic,and it spread quickly across the country after the first epidemic was re・ported in August 2018(Ge et al.,2018).After that,Mongolia,Vietnam,Cambodia and North Korea also reported on the ASF epidemic in succession(OIE,2019).

Noncarrier embryo selection and transfer in preimplantation genetic testing cycles for reciprocal translocation by Oxford Nanopore Technologies

Balanced reciprocal translocation is one of the most common chromosome abnormalities,with an incidence of approximately 1in every 500 newborns(Mackie Ogilvie and Scriven,2002).Most balanced reciprocal translocation carriers have no observable phenotype because there is no loss or gain of genetic material(Ogilvie et al.,2001).However,the carriers have a risk of infertility.

Rapid Acquisition of High-Quality SARS-CoV-2 Genome via Amplicon-Oxford Nanopore Sequencing

Genome sequencing has shown strong capabilities in the initial stages of the COVID-19 pandemic such as pathogen identification and virus preliminary tracing.While the rapid acquisition of SARS-Co V-2 genome from clinical specimens is limited by their low nucleic acid load and the complexity of the nucleic acid background.To address this issue,we modified and evaluated an approach by utilizing SARS-Co V-2-specific amplicon amplification and Oxford Nanopore Prometh ION platform.This workflow started with the throat swab of the COVID-19 patient,combined reverse transcript PCR,and multi-amplification in one-step to shorten the experiment time,then can quickly and steadily obtain high-quality SARS-Co V-2 genome within 24 h.A comprehensive evaluation of the method was conducted in 42 samples:the sequencing quality of the method was correlated well with the viral load of the samples;high-quality SARS-Co V-2 genome could be obtained stably in the samples with Ct value up to 39.14;data yielding for different Ct values were assessed and the recommended sequencing time was 8 h for samples with Ct value of less than 20;variation analysis indicated that the method can detect the existing and emerging genomic mutations as well;Illumina sequencing verified that ultra-deep sequencing can greatly improve the single read error rate of Nanopore sequencing,making it as low as 0.4/10,000 bp.In summary,high-quality SARS-Co V-2 genome can be acquired by utilizing the amplicon amplification and it is an effective method in accelerating the acquisition of genetic resources and tracking the genome diversity of SARSCo V-2.

Robust Benchmark Structural Variant Calls of An Asian Using State-of-the-art Long-read Sequencing Technologies

The importance of structural variants(SVs)for human phenotypes and diseases is now recognized.Although a variety of SV detection platforms and strategies that vary in sensitivity and specificity have been developed,few benchmarking procedures are available to confidently assess their performances in biological and clinical research.To facilitate the validation and application of these SV detection approaches,we established an Asian reference material by characterizing the genome of an Epstein-Barr virus(EBV)-immortalized B lymphocyte line along with identified benchmark regions and high-confidence SV calls.We established a high-confidence SV callset with 8938 SVs by integrating four alignment-based SV callers,including 109×Pacific Bio sciences(PacBio)continuous long reads(CLRs),22×PacBio circular consensus sequencing(CCS)reads,104×Oxford Nanopore Technologies(ONT)long reads,and 114×Bionano optical mapping platform,and one de novo assembly-based SV caller using CCS reads.A total of 544 randomly selected SVs were validated by PCR amplification and Sanger sequencing,demonstrating the robustness of our SV calls.Combining trio-binning-based haplotype assemblies,we established an SV benchmark for identifying false negatives and false positives by constructing the continuous high-confidence regions(CHCRs),which covered 1.46 gigabase pairs(Gb)and 6882 SVs supported by at least one diploid haplotype assembly.Establishing high-confidence SV calls for a benchmark sample that has been characterized by multiple technologies provides a valuable resource for investigating SVs in human biology,disease,and clinical research.

Correction to: Rapid Acquisition of High-Quality SARS-CoV-2 Genome via Amplicon-Oxford Nanopore Sequencing

Correction to:Virologica Sinica(2021)36:901-912 https://doi.Org/10.1007/sl 2250-021-00378-8 The original version of article contains errors in Figure 4,Supplementary Figure S2,Supplementary Table S2,and the corresponding description in part 3 of“Results”section.