Watermelon,Citrullus lanatus,is the world's third largest fruit crop.Reference genomes with gaps and a narrow genetic base hinder functional genomics and genetic improvement of watermelon.Here,we report the assemb...Watermelon,Citrullus lanatus,is the world's third largest fruit crop.Reference genomes with gaps and a narrow genetic base hinder functional genomics and genetic improvement of watermelon.Here,we report the assembly of a telomere-to-telomere gap-free genome of the elite watermelon inbred line G42 by incorporating high-coverage and accurate long-read sequencing data with multiple assembly strategies.All 11 chromosomes have been assembled into single-contig pseudomolecules without gaps,representing the highest completeness and assembly quality to date.The G42 reference genome is 369321829 bp in length and contains 24205 predicted protein-coding genes,with all 22 telomeres and 11 centromeres characterized.Furthermore,we established a pollen-EMS mutagenesis protocol and obtained over 200000M1 seeds from G42.In a sampling pool,48 monogenic phenotypic mutations,selected from 223M1and 78 M2 mutants with morphological changes,were confirmed.The average mutation density was 1 SNP/1.69Mband1 indel/4.55 Mb per M1 plant and 1SNP/1.08Mb and 1 indel/6.25 Mb per M2 plant.Taking advantage of the gap-free G42 genome,8039 mutations from 32 plants sampled from M1 and M2 families were identified with 100%accuracy,whereas only 25% of the randomly selected mutations identified using the 97103v2 reference genome could be confirmed.Using this library and the gap-free genome,two genes responsible for elongated fruit shape and male sterility(CiMs1)were identified,both caused by a single basechange from G to A.The validated gap-free genome and its EMS mutation library provide invaluable resources for functional genomics and genetic improvement of watermelon.展开更多
Rosa banksiae,known as Lady Banks'rose,is a perennial ornamental crop and a versatile herb in traditional Chinese medicine.Given the lack of genomic resources,we assembled a Hi Fi and Nanopore sequencing-derived 4...Rosa banksiae,known as Lady Banks'rose,is a perennial ornamental crop and a versatile herb in traditional Chinese medicine.Given the lack of genomic resources,we assembled a Hi Fi and Nanopore sequencing-derived 458.58 Mb gap-free telomere-to-telomere high-quality R.banksiae genome with a scaffold N50=63.90 Mb.The genome of R.banksiae exhibited no lineage-specific whole-genome duplication compared with other Rosaceae.The phylogenomic analysis of 13 Rosaceae and Arabidopsis through a comparative genomics study showed that numerous gene families were lineage-specific both before and after the diversification of Rosaceae.Some of these genes are candidates for new genes that have evolved from parental genes through fusion events.Fusion genes are divided into three types:Type-I and Type-II genes contain two parental genes that are generated by duplication,distributed in the same and different regions of the genome,respectively;and Type-III can only be detected in one parental gene.Here,Type-I genes are found to have more relaxed selection pressure and lower Ks values than Type-II,indicating that these newly evolved Type-I genes may play important roles in driving phenotypic evolution.Functional analysis exhibited that newly formed fusion genes can regulate the phenotype traits of plant growth and development,suggesting the functional significance of these genes.This study identifies new fusion genes that could be responsible for phenotype evolution and provides information on the evolutionary history of recently diverged species in the Rosa genus.Our data represents the major progress in understanding the new fusion genes evolution pattern of Rosaceae and provides an invaluable resource for phylogenomic studies in plants.展开更多
基金This work was supported by the Provincial Technology Innovation Program of Shandong,Ningxia Hui Autonomous Region agricultural breeding special project(NXNYYZ202001)Jiangsu Seed Industry Revitalization Competitive Project JBGS(2021)072,Ningbo Science and Technology Innovation Project 2021Z132,and Weifang Seed InnovationGroup.
文摘Watermelon,Citrullus lanatus,is the world's third largest fruit crop.Reference genomes with gaps and a narrow genetic base hinder functional genomics and genetic improvement of watermelon.Here,we report the assembly of a telomere-to-telomere gap-free genome of the elite watermelon inbred line G42 by incorporating high-coverage and accurate long-read sequencing data with multiple assembly strategies.All 11 chromosomes have been assembled into single-contig pseudomolecules without gaps,representing the highest completeness and assembly quality to date.The G42 reference genome is 369321829 bp in length and contains 24205 predicted protein-coding genes,with all 22 telomeres and 11 centromeres characterized.Furthermore,we established a pollen-EMS mutagenesis protocol and obtained over 200000M1 seeds from G42.In a sampling pool,48 monogenic phenotypic mutations,selected from 223M1and 78 M2 mutants with morphological changes,were confirmed.The average mutation density was 1 SNP/1.69Mband1 indel/4.55 Mb per M1 plant and 1SNP/1.08Mb and 1 indel/6.25 Mb per M2 plant.Taking advantage of the gap-free G42 genome,8039 mutations from 32 plants sampled from M1 and M2 families were identified with 100%accuracy,whereas only 25% of the randomly selected mutations identified using the 97103v2 reference genome could be confirmed.Using this library and the gap-free genome,two genes responsible for elongated fruit shape and male sterility(CiMs1)were identified,both caused by a single basechange from G to A.The validated gap-free genome and its EMS mutation library provide invaluable resources for functional genomics and genetic improvement of watermelon.
基金supported by the National Natural Science Foundation of China(Grant Nos.32201602,82304680)the Natural Science Fund of Hubei Province(Grant No.2023AFB1036)+5 种基金the Program for Excellent Sci-tech Innovation Teams of Universities in Anhui Province(Grant No.2022AH010074)Anhui Provincial Natural Science Foundation(Grant No.2308085QH295)Natural Science Research Project of Anhui Educational Committee(Grant No.2023AH040259)the Talent Scientific Research Startup Foundation,Wannan Medical College(Grant No.YR20230110)the Anhui Provincial Department of Education Young Backbone Teachers Overseas Visiting and Training Funding Program(Grant No.JWFX2023033)Beijing Life Science Academy Project(Grant No.2023200CC0270)。
文摘Rosa banksiae,known as Lady Banks'rose,is a perennial ornamental crop and a versatile herb in traditional Chinese medicine.Given the lack of genomic resources,we assembled a Hi Fi and Nanopore sequencing-derived 458.58 Mb gap-free telomere-to-telomere high-quality R.banksiae genome with a scaffold N50=63.90 Mb.The genome of R.banksiae exhibited no lineage-specific whole-genome duplication compared with other Rosaceae.The phylogenomic analysis of 13 Rosaceae and Arabidopsis through a comparative genomics study showed that numerous gene families were lineage-specific both before and after the diversification of Rosaceae.Some of these genes are candidates for new genes that have evolved from parental genes through fusion events.Fusion genes are divided into three types:Type-I and Type-II genes contain two parental genes that are generated by duplication,distributed in the same and different regions of the genome,respectively;and Type-III can only be detected in one parental gene.Here,Type-I genes are found to have more relaxed selection pressure and lower Ks values than Type-II,indicating that these newly evolved Type-I genes may play important roles in driving phenotypic evolution.Functional analysis exhibited that newly formed fusion genes can regulate the phenotype traits of plant growth and development,suggesting the functional significance of these genes.This study identifies new fusion genes that could be responsible for phenotype evolution and provides information on the evolutionary history of recently diverged species in the Rosa genus.Our data represents the major progress in understanding the new fusion genes evolution pattern of Rosaceae and provides an invaluable resource for phylogenomic studies in plants.
