Soybean(Glycine max)stands as a globally significant agricultural crop,and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary history.Nev...Soybean(Glycine max)stands as a globally significant agricultural crop,and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary history.Nevertheless,previous soybean genome assemblies have harbored gaps and incompleteness,which have constrained in-depth investigations into soybean.Here,we present Telomere-to-Telomere(T2T)assembly of the Chinese soybean cultivar Zhonghuang 13(ZH13)genome,termed ZH13-T2T,utilizing PacBio Hifi and ONT ultralong reads.We employed a multi-assembler approach,integrating Hifiasm,NextDenovo,and Canu,to minimize biases and enhance assembly accuracy.The assembly spans 1,015,024,879 bp,effectively resolving all 393 gaps that previously plagued the reference genome.Our annotation efforts identified 50,564 high-confidence protein-coding genes,707 of which are novel.ZH13-T2T revealed longer chromosomes,421 not-aligned regions(NARs),112 structure variations(SVs),and a substantial expansion of repetitive element compared to earlier assemblies.Specifically,we identified 25.67 Mb of tandem repeats,an enrichment of 5S and 48S rDNAs,and characterized their genotypic diversity.In summary,we deliver the first complete Chinese soybean cultivar T2T genome.The comprehensive annotation,along with precise centromere and telomere characterization,as well as insights into structural variations,further enhance our understanding of soybean genetics and evolution.展开更多
Soybean was domesticated in China and has become one of the most important oilseed crops. Due to bottlenecks in their introduction and dissemination, soybeans from different geographic areas exhibit extensive genetic ...Soybean was domesticated in China and has become one of the most important oilseed crops. Due to bottlenecks in their introduction and dissemination, soybeans from different geographic areas exhibit extensive genetic diversity. Asia is the largest soybean market; therefore, a high-quality soybean reference genome from this area is critical for soybean research and breeding.Here, we report the de novo assembly and sequence analysis of a Chinese soybean genome for "Zhonghuang 13" by a combination of SMRT, Hi-C and optical mapping data. The assembled genome size is 1.025 Gb with a contig N50 of 3.46 Mb and a scaffold N50 of 51.87 Mb. Comparisons between this genome and the previously reported reference genome(cv. Williams82) uncovered more than 250,000 structure variations. A total of 52,051 protein coding genes and 36,429 transposable elements were annotated for this genome, and a gene co-expression network including 39,967 genes was also established. This high quality Chinese soybean genome and its sequence analysis will provide valuable information for soybean improvement in the future.展开更多
The soybean E1 gene is a major regulator that plays an important role in flowering time and maturity.However,it remains unclear how cultivars carrying the dominant E1 allele adapt to the higher latitudinal areas of no...The soybean E1 gene is a major regulator that plays an important role in flowering time and maturity.However,it remains unclear how cultivars carrying the dominant E1 allele adapt to the higher latitudinal areas of northern China.We mapped the novel quantitative trait locus QNE1(QTL near E1) for flowering time to the region proximal to E1 on chromosome 6 in two mapping populations.Positional cloning revealed Glyma.06G204300,encoding a TCP-type transcription factor,as a strong candidate gene for QNE1.Association analysis further confirmed that functional single nucleotide polymorphisms(SNPs) at nucleotides 686 and 1,063 in the coding region of Glyma.06G204300 were significantly associated with flowering time.The protein encoded by the candidate gene is localized primarily to the nucleus.Furthermore,soybean and Brassica napus plants overexpressing Glyma.06G204300 exhibited early flowering.We conclude that despite their similar effects on flowering time,QNE1 and E4 may control flowering time through different regulatory mechanisms,based on expression studies and weighted gene co-expression network analysis of flowering time-related genes.Deciphering the molecular basis of QNE1 control of flowering time enriches our knowledge of flowering gene networks in soybean and will facilitate breeding soybean cultivars with broader latitudinal adaptation.展开更多
基金This work has been supported by the National Key Research and Development Program of China(2021YFF1200105)National Natural Science Foundation of China(62172125,62371161).
文摘Soybean(Glycine max)stands as a globally significant agricultural crop,and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary history.Nevertheless,previous soybean genome assemblies have harbored gaps and incompleteness,which have constrained in-depth investigations into soybean.Here,we present Telomere-to-Telomere(T2T)assembly of the Chinese soybean cultivar Zhonghuang 13(ZH13)genome,termed ZH13-T2T,utilizing PacBio Hifi and ONT ultralong reads.We employed a multi-assembler approach,integrating Hifiasm,NextDenovo,and Canu,to minimize biases and enhance assembly accuracy.The assembly spans 1,015,024,879 bp,effectively resolving all 393 gaps that previously plagued the reference genome.Our annotation efforts identified 50,564 high-confidence protein-coding genes,707 of which are novel.ZH13-T2T revealed longer chromosomes,421 not-aligned regions(NARs),112 structure variations(SVs),and a substantial expansion of repetitive element compared to earlier assemblies.Specifically,we identified 25.67 Mb of tandem repeats,an enrichment of 5S and 48S rDNAs,and characterized their genotypic diversity.In summary,we deliver the first complete Chinese soybean cultivar T2T genome.The comprehensive annotation,along with precise centromere and telomere characterization,as well as insights into structural variations,further enhance our understanding of soybean genetics and evolution.
基金supported by the National Natural Science Foundation of China (91531304, 31525018, 31370266, and 31788103)the “Strategic Priority Research Program” of the Chinese Academy of Sciences (XDA08000000)the State Key Laboratory of Plant Cell and Chromosome Engineering (PCCE-KF-2017-03)
文摘Soybean was domesticated in China and has become one of the most important oilseed crops. Due to bottlenecks in their introduction and dissemination, soybeans from different geographic areas exhibit extensive genetic diversity. Asia is the largest soybean market; therefore, a high-quality soybean reference genome from this area is critical for soybean research and breeding.Here, we report the de novo assembly and sequence analysis of a Chinese soybean genome for "Zhonghuang 13" by a combination of SMRT, Hi-C and optical mapping data. The assembled genome size is 1.025 Gb with a contig N50 of 3.46 Mb and a scaffold N50 of 51.87 Mb. Comparisons between this genome and the previously reported reference genome(cv. Williams82) uncovered more than 250,000 structure variations. A total of 52,051 protein coding genes and 36,429 transposable elements were annotated for this genome, and a gene co-expression network including 39,967 genes was also established. This high quality Chinese soybean genome and its sequence analysis will provide valuable information for soybean improvement in the future.
基金supported by the Strategic Priority Research Program(XDA24010105-4,XDA28070000)the Key Deployment Projects(ZDRW-ZS-2019-2)of the Chinese Academy of Sciences+1 种基金the National Natural Science Foundation of China(U21A20215,31771818,31771869)the Young Scientists Group Project(2022QNXZ05)of Northeast Institute of Geography and Agroecology,Chinese Academy of Sciences。
文摘The soybean E1 gene is a major regulator that plays an important role in flowering time and maturity.However,it remains unclear how cultivars carrying the dominant E1 allele adapt to the higher latitudinal areas of northern China.We mapped the novel quantitative trait locus QNE1(QTL near E1) for flowering time to the region proximal to E1 on chromosome 6 in two mapping populations.Positional cloning revealed Glyma.06G204300,encoding a TCP-type transcription factor,as a strong candidate gene for QNE1.Association analysis further confirmed that functional single nucleotide polymorphisms(SNPs) at nucleotides 686 and 1,063 in the coding region of Glyma.06G204300 were significantly associated with flowering time.The protein encoded by the candidate gene is localized primarily to the nucleus.Furthermore,soybean and Brassica napus plants overexpressing Glyma.06G204300 exhibited early flowering.We conclude that despite their similar effects on flowering time,QNE1 and E4 may control flowering time through different regulatory mechanisms,based on expression studies and weighted gene co-expression network analysis of flowering time-related genes.Deciphering the molecular basis of QNE1 control of flowering time enriches our knowledge of flowering gene networks in soybean and will facilitate breeding soybean cultivars with broader latitudinal adaptation.
