Genome assembly is a fundamental step in decoding the genetic information of life.Its significance lies in constructing a complete DNA sequence map of organisms,providing the foundation for elucidating the mechanisms ...Genome assembly is a fundamental step in decoding the genetic information of life.Its significance lies in constructing a complete DNA sequence map of organisms,providing the foundation for elucidating the mechanisms of species evolution,exploring gene functions,and identifying disease-related variations.However,some of the repetitive DNA sequences remain“dark materials”in the genome as they are difficult to reveal by the second-generation sequencing approaches.In recent years,breakthroughs in third-generation sequencing technologies have significantly improved the accuracy and continuity of genome assemblies,therefore,being able to resolve the“last piece of the puzzle”in the genome.展开更多
The bread wheat genome harbors a high content of repetitive DNA,which is amenable to detection and characterization using fluorescence in situ hybridization(FISH)karyotyping.An integrated genetic map was derived from ...The bread wheat genome harbors a high content of repetitive DNA,which is amenable to detection and characterization using fluorescence in situ hybridization(FISH)karyotyping.An integrated genetic map was derived from a recombinant inbred population bred from a cross between a synthetic hexaploid wheat and a commercial Chinese bread wheat cultivar,based on 28 variable FISH sites and>150000 single nucleotide polymorphism(SNP)loci.The majority(20/28)of the variable FISH sites were physically located within a chromosomal region consistent with the genetic location inferred from that of their co-segregating SNP loci.The eight exceptions reflected the presence of either a translocation(1 R/1 B,1 A/7 A)or a presumptive intra-chromosomal inversion(4 A).For eight out of the nine FISH sites detected on the Chinese Spring(CS)karyotype,there was a good match with the reference genome sequence,indicating that the most recent assembly has dealt well with the problem of placing tandem repeats.The integrated genetic map produced for wheat is informative as to the location of blocks of tandemly repeated DNA and can aid in improving the quality of the genome sequence assembly in regions surrounding these blocks.展开更多
Knob-associated tandem repeats,180-bp repeats and TR-1 elements,together with 45S rDNA were located on mitotic chromosomes of Zea diploperennis(DP),maize inbred line F102 and their hybrid.In DP,knobs on the short arm ...Knob-associated tandem repeats,180-bp repeats and TR-1 elements,together with 45S rDNA were located on mitotic chromosomes of Zea diploperennis(DP),maize inbred line F102 and their hybrid.In DP,knobs on the short arm of chromosomes 1 and 4 and on the long arm ofthe chromosomes 4 and 5 are composed predominantly of the 180-bp repeats.In addition,180-bp repeats existed together with TR-1 elements were also detected on the short arm ofchromosomes 2 and 5 and on the long arm of the chromosomes 2,6,7,8 and 9.In maize inbred line F102,180-bp repeats were present in chromosomes 7S and one homologue of chromosomes 8L.TR-1 elements appeared on satellite of chromosome 6 and no detectable hybridization site co-located with 180-bp repeats was observed in maize F102.Polymorphism of size,number,and distribution of 180-bp and TR-1 signals were revealed among different chromosomes in these two species and heteromorphism existed between some homologous chromosomes in the same species.Using these excellent landmarks,the interspecific hybrid of maize and DP were identified.The results suggest that comparative analysis of 180-bp repeats and TR-1 elements may help understand the genome organization and the evolution in Zea.展开更多
Knobs are blocks of heterochromatin present on chromosomes of maize （Zea mays L.） and its relatives that have effects on the frequency of genetic recombination, as well as on chromosome behavior. Knob heterozygosity...Knobs are blocks of heterochromatin present on chromosomes of maize （Zea mays L.） and its relatives that have effects on the frequency of genetic recombination, as well as on chromosome behavior. Knob heterozygosity and instability in six maize inbred lines and one Z. diploperennis Iltis Doebley line were investigated using the fluorescence in situ hybridization （FISH） technique with knob-associated tandem repeats （180 bp and 350 bp （TR- 1）） as probes. Signals of seven heterozygous knobs containing 180- bp repeats and of one heterozygous knob containing TR- 1 were captured in chromosomes of all materials tested according to the results of FISH, which demonstrates that the 180-bp repeat is the main contributor to knob heterozygosity compared with the TR- 1 element. In addition, one target cell with two TR- 1 signals on one homolog of chromosome 2L, which was different from the normal cells in the maize inbred line GB57, was observed, suggesting knob duplication and an instability phenomenon in the maize genome.展开更多
基金supported by the National Natural Science Foundation of China(32090034)Zhejiang Provincial Natural Science Foundation of China(2022XHSJJ001)+3 种基金Hangzhou City Leading Innovation and Entrepreneurship Team(TD2020004)“Pioneer”and“Leading Goose”Research and Development Program of Zhejiang(2024SSYS0033)Westlake Education FoundationWestlake Laboratory of Life Sciences and Biomedicine.
文摘Genome assembly is a fundamental step in decoding the genetic information of life.Its significance lies in constructing a complete DNA sequence map of organisms,providing the foundation for elucidating the mechanisms of species evolution,exploring gene functions,and identifying disease-related variations.However,some of the repetitive DNA sequences remain“dark materials”in the genome as they are difficult to reveal by the second-generation sequencing approaches.In recent years,breakthroughs in third-generation sequencing technologies have significantly improved the accuracy and continuity of genome assemblies,therefore,being able to resolve the“last piece of the puzzle”in the genome.
基金financially supported by the National Key Research and Development Program of China(2016YFD0102000)。
文摘The bread wheat genome harbors a high content of repetitive DNA,which is amenable to detection and characterization using fluorescence in situ hybridization(FISH)karyotyping.An integrated genetic map was derived from a recombinant inbred population bred from a cross between a synthetic hexaploid wheat and a commercial Chinese bread wheat cultivar,based on 28 variable FISH sites and>150000 single nucleotide polymorphism(SNP)loci.The majority(20/28)of the variable FISH sites were physically located within a chromosomal region consistent with the genetic location inferred from that of their co-segregating SNP loci.The eight exceptions reflected the presence of either a translocation(1 R/1 B,1 A/7 A)or a presumptive intra-chromosomal inversion(4 A).For eight out of the nine FISH sites detected on the Chinese Spring(CS)karyotype,there was a good match with the reference genome sequence,indicating that the most recent assembly has dealt well with the problem of placing tandem repeats.The integrated genetic map produced for wheat is informative as to the location of blocks of tandemly repeated DNA and can aid in improving the quality of the genome sequence assembly in regions surrounding these blocks.
基金was supported by the National Natural Science Foundation of China(Grant No.39870423).
文摘Knob-associated tandem repeats,180-bp repeats and TR-1 elements,together with 45S rDNA were located on mitotic chromosomes of Zea diploperennis(DP),maize inbred line F102 and their hybrid.In DP,knobs on the short arm of chromosomes 1 and 4 and on the long arm ofthe chromosomes 4 and 5 are composed predominantly of the 180-bp repeats.In addition,180-bp repeats existed together with TR-1 elements were also detected on the short arm ofchromosomes 2 and 5 and on the long arm of the chromosomes 2,6,7,8 and 9.In maize inbred line F102,180-bp repeats were present in chromosomes 7S and one homologue of chromosomes 8L.TR-1 elements appeared on satellite of chromosome 6 and no detectable hybridization site co-located with 180-bp repeats was observed in maize F102.Polymorphism of size,number,and distribution of 180-bp and TR-1 signals were revealed among different chromosomes in these two species and heteromorphism existed between some homologous chromosomes in the same species.Using these excellent landmarks,the interspecific hybrid of maize and DP were identified.The results suggest that comparative analysis of 180-bp repeats and TR-1 elements may help understand the genome organization and the evolution in Zea.
文摘Knobs are blocks of heterochromatin present on chromosomes of maize （Zea mays L.） and its relatives that have effects on the frequency of genetic recombination, as well as on chromosome behavior. Knob heterozygosity and instability in six maize inbred lines and one Z. diploperennis Iltis Doebley line were investigated using the fluorescence in situ hybridization （FISH） technique with knob-associated tandem repeats （180 bp and 350 bp （TR- 1）） as probes. Signals of seven heterozygous knobs containing 180- bp repeats and of one heterozygous knob containing TR- 1 were captured in chromosomes of all materials tested according to the results of FISH, which demonstrates that the 180-bp repeat is the main contributor to knob heterozygosity compared with the TR- 1 element. In addition, one target cell with two TR- 1 signals on one homolog of chromosome 2L, which was different from the normal cells in the maize inbred line GB57, was observed, suggesting knob duplication and an instability phenomenon in the maize genome.
