The Physalis floridana genome provides insights into the biochemical and morphological evolution of Physalis fruits

The fruits of Physalis(Solanaceae)have a unique structure,a lantern-like fruiting calyx known as inflated calyx syndrome(ICS)or the Chinese lantern,and are rich in steroid-related compounds.However,the genetic variations underlying the origin of these characteristic traits and diversity in Physalis remain largely unknown.Here,we present a high-quality chromosome-level reference genome assembly of Physalis floridana(~1.40Gb in size)with a contig N50 of~4.87Mb.Through evolutionary genomics and experimental approaches,we found that the loss of the SEP-like MADS-box gene MBP21 subclade is likely a key mutation that,together with the previously revealed mutation affecting floral MPF2 expression,might have contributed to the origination of ICS in Physaleae,suggesting that the origination of a morphological novelty may have resulted from an evolutionary scenario in which one mutation compensated for another deleterious mutation.Moreover,the significant expansion of squalene epoxidase genes is potentially associated with the natural variation of steroid-related compounds in Physalis fruits.The results reveal the importance of gene gains(duplication)and/or subsequent losses as genetic bases of the evolution of distinct fruit traits,and the data serve as a valuable resource for the evolutionary genetics and breeding of solanaceous crops.

Comparative and population genomics of buckwheat species reveal key determinants of flavor and fertility

Common buckwheat(Fagopyrum esculentum)is an ancient crop with a world-wide distribution.Due to its excellent nutritional quality and high economic and ecological value,common buckwheat is becoming increasingly important throughout the world.The availability of a high-quality reference genome sequence and population genomic data will accelerate the breeding of common buckwheat,but the high heterozygosity due to the outcrossing nature has greatly hindered the genome assembly.Here we report the assembly of a chromosome-scale high-quality reference genome of F.esculentum var.homotropicum,a homozygous self-pollinating variant of common buckwheat.Comparative genomics revealed that two cultivated buckwheat species,common buckwheat(F.esculentum)and Tartary buckwheat(F.tataricum),underwent metabolomic divergence and ecotype differentiation.The expansion of several gene families in common buckwheat,including FhFAR genes,is associated with its wider distribution than Tartary buckwheat.Copy number variation of genes involved in the metabolism of flavonoids is associated with the difference of rutin content between common and Tartary buckwheat.Furthermore,we present a comprehensive atlas of genomic variation based on whole-genome resequencing of 572 accessions of common buckwheat.Population and evolutionary genomics reveal genetic variation associated with environmental adaptability and floral development between Chinese and non-Chinese cultivated groups.Genome-wide association analyses of multi-year agronomic traits with the content of flavonoids revealed that Fh05G014970 is a potential major regulator of flowering period,a key agronomic trait controlling the yield of outcrossing crops,and that Fh06G015130 is a crucial gene underlying flavor-associated flavonoids.Intriguingly,we found that the gene translocation and sequence variation of FhS-ELF3 contribute to the homomorphic self-compatibility of common buckwheat.Collectively,our results elucidate the genetic basis of speciation,ecological adaptation,fertility,and unique flavor of common buckwheat,and provide new resources for future genomics-assisted breeding of this economically important crop.

The First High-quality Reference Genome of Sika Deer Provides Insights into High-tannin Adaptation

Sika deer are known to prefer oak leaves,which are rich in tannins and toxic to most mammals;however,the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear.In identifying the mechanism responsible for the tolerance of a highly toxic diet,we have made a major advancement by explaining the genome of sika deer.We generated the first high-quality,chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments.Comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food,especially the expansion of the UGT family 2 subfamily B of UGT genes.The first chromosome-level assembly and genetic characterization of the tolerance to a highly toxic diet suggest that the sika deer genome may serve as an essential resource for understanding evolutionary events and tannin adaptation.Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals.

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.