The Chinese white pear(Pyrus bretschneideri)is an economically significant fruit crop worldwide.Previous versions of the P.bretschneideri genome assembly contain numerous gaps and unanchored genetic regions.Here,we ge...The Chinese white pear(Pyrus bretschneideri)is an economically significant fruit crop worldwide.Previous versions of the P.bretschneideri genome assembly contain numerous gaps and unanchored genetic regions.Here,we generated two high-quality,gap-free genome assemblies for‘Dangshansu’(DS;503.92 Mb)and‘Lianglizaosu’(ZS;509.01 Mb),each anchored to 17 chromosomes,achieving a benchmarking universal single-copy ortholog completeness score of nearly 99.0%.Our genome-wide association studies explored the associations between genetic variations and stone cell traits,revealing a significant association peak on DS chromosome 3 and identifying a novel non-tandem CCCH-type zinc finger gene,designated PbdsZF.Through genetic transformation,we verified the pivotal role of PbdsZF in regulation of both lignin biosynthesis and stone cell formation,as it transcriptionally activates multiple genes involved in these processes.By binding to the CT-rich motifs CT1(CTTTTTTCT)and CT2(CTCTTTTT),PbdsZF significantly influences the transcription of genes essential for lignin production,underscoring its regulatory importance in plant lignin metabolism.Our study illuminates the complex biology of fruit development and delineates the gene regulatory networks that influence stone cell and lignocellulose formation,thereby enriching genetic resources and laying the groundwork for the molecular breeding of perennial trees.展开更多
Lettuce(Lactuca sativa)is a globally important leafy vegetable.Understanding the genetic factors underlying its growth and regeneration is critical for advancing agricultural productivity and biotechnological applicat...Lettuce(Lactuca sativa)is a globally important leafy vegetable.Understanding the genetic factors underlying its growth and regeneration is critical for advancing agricultural productivity and biotechnological applications.To address this,the study aimed to comprehensively identify and characterize the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE(SPL)gene family in lettuce and investigate their potential roles in plant development and regeneration.As a result,22 SPL genes were identified within the lettuce genome.Fourteen of these genes contain recognition sites for microRNA156,suggesting post-transcriptional regulation.Each LsSPL protein has the highly conserved SBP domain and is predicted to localize in the nucleus.Analysis of public RNA-seq datasets revealed tissue-specific expression patterns of the 22 LsSPL genes,with five highly expressed in leaves,four in roots,and three in stems,indicating their distinct roles in plant development.Overexpression of lettuce miRNA156c(miR156-OX)led to reduced leaf size and delayed flowering time,whereas suppression of miR156(miR156-STTM)resulted in increased leaf size.Surprisingly,cotyledon explants from miR156-OX lettuce lines exhibited a 1.9-fold increase in shoot regeneration compared to wild-type,whereas miR156-STTM lines exhibited a 54.3%decrease.This enhanced in vitro shoot regeneration was also observed in ectopic miR156-overexpression tomato lines,suggesting a conserved mechanism.Quantitative RT-PCR analysis confirmed the downregulation of LsSPL13A.1,LsSPL13A.2,and LsSPL12.2 in miR156-OX lines and their upregulation in miR156-STTM lines after 5 days of callus induction,implicating their specific roles in in vitro organo genesis and plant re generation.This comprehensive analysis provides valuable insights into the SPL gene family and the miR156-SPLs regulatory network,specifically highlighting its role in regeneration.These findings hold the potential for improving plant growth,development,and biotechnological applications.展开更多
基金supported by the National Natural Science Foundation of China(Grant Nos.32201602,32101486,32102364)the Natural Science Fund of Hubei Province(Grant No.2023AFB1036)+2 种基金the Funding of China Tobacco Genome Project(Grant No.110202201012[JY-12])the Beijing Life Science Academy Project(Grant No.2023200CC0270)the Shanxi Provincial Higher Education Youth Academic Leader Project(Grant No.2024Q031)。
文摘The Chinese white pear(Pyrus bretschneideri)is an economically significant fruit crop worldwide.Previous versions of the P.bretschneideri genome assembly contain numerous gaps and unanchored genetic regions.Here,we generated two high-quality,gap-free genome assemblies for‘Dangshansu’(DS;503.92 Mb)and‘Lianglizaosu’(ZS;509.01 Mb),each anchored to 17 chromosomes,achieving a benchmarking universal single-copy ortholog completeness score of nearly 99.0%.Our genome-wide association studies explored the associations between genetic variations and stone cell traits,revealing a significant association peak on DS chromosome 3 and identifying a novel non-tandem CCCH-type zinc finger gene,designated PbdsZF.Through genetic transformation,we verified the pivotal role of PbdsZF in regulation of both lignin biosynthesis and stone cell formation,as it transcriptionally activates multiple genes involved in these processes.By binding to the CT-rich motifs CT1(CTTTTTTCT)and CT2(CTCTTTTT),PbdsZF significantly influences the transcription of genes essential for lignin production,underscoring its regulatory importance in plant lignin metabolism.Our study illuminates the complex biology of fruit development and delineates the gene regulatory networks that influence stone cell and lignocellulose formation,thereby enriching genetic resources and laying the groundwork for the molecular breeding of perennial trees.
基金funded by the USDA-NIFA grant 2019-67013-29236the USDA HATCH program FLA-MFC-006387。
文摘Lettuce(Lactuca sativa)is a globally important leafy vegetable.Understanding the genetic factors underlying its growth and regeneration is critical for advancing agricultural productivity and biotechnological applications.To address this,the study aimed to comprehensively identify and characterize the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE(SPL)gene family in lettuce and investigate their potential roles in plant development and regeneration.As a result,22 SPL genes were identified within the lettuce genome.Fourteen of these genes contain recognition sites for microRNA156,suggesting post-transcriptional regulation.Each LsSPL protein has the highly conserved SBP domain and is predicted to localize in the nucleus.Analysis of public RNA-seq datasets revealed tissue-specific expression patterns of the 22 LsSPL genes,with five highly expressed in leaves,four in roots,and three in stems,indicating their distinct roles in plant development.Overexpression of lettuce miRNA156c(miR156-OX)led to reduced leaf size and delayed flowering time,whereas suppression of miR156(miR156-STTM)resulted in increased leaf size.Surprisingly,cotyledon explants from miR156-OX lettuce lines exhibited a 1.9-fold increase in shoot regeneration compared to wild-type,whereas miR156-STTM lines exhibited a 54.3%decrease.This enhanced in vitro shoot regeneration was also observed in ectopic miR156-overexpression tomato lines,suggesting a conserved mechanism.Quantitative RT-PCR analysis confirmed the downregulation of LsSPL13A.1,LsSPL13A.2,and LsSPL12.2 in miR156-OX lines and their upregulation in miR156-STTM lines after 5 days of callus induction,implicating their specific roles in in vitro organo genesis and plant re generation.This comprehensive analysis provides valuable insights into the SPL gene family and the miR156-SPLs regulatory network,specifically highlighting its role in regeneration.These findings hold the potential for improving plant growth,development,and biotechnological applications.
