‘Vanilla’(XQC,brassica variety chinensis)is an important vegetable crop in the Brassica family,named for its strong volatile fragrance.In this study,we report the high-quality chromosome-level genome sequence of XQC...‘Vanilla’(XQC,brassica variety chinensis)is an important vegetable crop in the Brassica family,named for its strong volatile fragrance.In this study,we report the high-quality chromosome-level genome sequence of XQC.The assembled genome length was determined as 466.11 Mb,with an N50 scaffold of 46.20 Mb.A total of 59.50%repetitive sequences were detected in the XQC genome,including 47570 genes.Among all examined Brassicaceae species,XQC had the closest relationship with B.rapa QGC(‘QingGengCai’)and B.rapa Pakchoi.Two whole-genome duplication(WGD)events and one recent whole-genome triplication(WGT)event occurred in the XQC genome in addition to an ancient WGT event.The recent WGT was observed to occur during 21.59-24.40 Mya(after evolution rate corrections).Our findings indicate that XQC experienced gene losses and chromosome rearrangements during the genome evolution of XQC.The results of the integrated genomic and transcriptomic analyses revealed critical genes involved in the terpenoid biosynthesis pathway and terpene synthase(TPS)family genes.In summary,we determined a chromosome-level genome of B.rapa XQC and identified the key candidate genes involved in volatile fragrance synthesis.This work can act as a basis for the comparative and functional genomic analysis and molecular breeding of B.rapa in the future.展开更多
Cucurbitaceae is one of the most important plant families distributed worldwide.Transcription factors(TFs)regulate plant growth at the transcription level.Here,we performed a systematic analysis of 42641 TFs from 63 f...Cucurbitaceae is one of the most important plant families distributed worldwide.Transcription factors(TFs)regulate plant growth at the transcription level.Here,we performed a systematic analysis of 42641 TFs from 63 families in 14 Cucurbitaceae and 10 non-cucurbit species.Whole-genome duplication(WGD)was the dominant event type in almost all Cucurbitaceae plants.The TF families were divided into 1210 orthogroups(OGs),of which,112 were unique to Cucurbitaceae.Although the loss of several gene families was detected in Cucurbitaceae,the gene families expanded in five species that experienced a WGD event comparing with grape.Our findings revealed that the recent WGD events that had occurred in Cucurbitaceae played important roles in the expansion of most TF families.The functional enrichment analysis of the genes that significantly expanded or contracted uncovered five gene families,AUX/IAA,NAC,NBS,HB,and NF-YB.Finally,we conducted a comprehensive analysis of the TCP gene family and identified 16 tendril-related(TEN)genes in 11 Cucurbitaceae species.Interestingly,the characteristic sequence changed from CNNFYFP to CNNFYLP in the TEN gene(Bhi06M000087)of Benincasa hispida.Furthermore,we identified a new characteristic sequence,YNN,which could be used for TEN gene exploitation in Cucurbitaceae.In conclusion,this study will serve as a reference for studying the relationship between gene family evolution and genome duplication.Moreover,it will provide rich genetic resources for functional Cucurbitaceae studies in the future.展开更多
基金This work was supported by the Suzhou Agricultural Science and Technology Innovation project(SNG2020065SNG2020045)+1 种基金Suzhou Municipal Bureau of Agriculture and Rural Affairs,the National Natural Science Foundation of China(32172583)the Natural Science Foundation of Hebei(C2021209005).The genome sequencing was performed in the Novogene Corporation.
文摘‘Vanilla’(XQC,brassica variety chinensis)is an important vegetable crop in the Brassica family,named for its strong volatile fragrance.In this study,we report the high-quality chromosome-level genome sequence of XQC.The assembled genome length was determined as 466.11 Mb,with an N50 scaffold of 46.20 Mb.A total of 59.50%repetitive sequences were detected in the XQC genome,including 47570 genes.Among all examined Brassicaceae species,XQC had the closest relationship with B.rapa QGC(‘QingGengCai’)and B.rapa Pakchoi.Two whole-genome duplication(WGD)events and one recent whole-genome triplication(WGT)event occurred in the XQC genome in addition to an ancient WGT event.The recent WGT was observed to occur during 21.59-24.40 Mya(after evolution rate corrections).Our findings indicate that XQC experienced gene losses and chromosome rearrangements during the genome evolution of XQC.The results of the integrated genomic and transcriptomic analyses revealed critical genes involved in the terpenoid biosynthesis pathway and terpene synthase(TPS)family genes.In summary,we determined a chromosome-level genome of B.rapa XQC and identified the key candidate genes involved in volatile fragrance synthesis.This work can act as a basis for the comparative and functional genomic analysis and molecular breeding of B.rapa in the future.
基金supported by the Natural Science Foundation of Hebei(Grant No.C2021209005)National Natural Science Foundation of China(Grant No.32172583)+1 种基金the Natural Science Foundation for Distinguished Young Scholar of Hebei Province(Grant No.C2022209010)the China Postdoctoral Science Foundation(Grant Nos.2020M673188,2021T140097).
文摘Cucurbitaceae is one of the most important plant families distributed worldwide.Transcription factors(TFs)regulate plant growth at the transcription level.Here,we performed a systematic analysis of 42641 TFs from 63 families in 14 Cucurbitaceae and 10 non-cucurbit species.Whole-genome duplication(WGD)was the dominant event type in almost all Cucurbitaceae plants.The TF families were divided into 1210 orthogroups(OGs),of which,112 were unique to Cucurbitaceae.Although the loss of several gene families was detected in Cucurbitaceae,the gene families expanded in five species that experienced a WGD event comparing with grape.Our findings revealed that the recent WGD events that had occurred in Cucurbitaceae played important roles in the expansion of most TF families.The functional enrichment analysis of the genes that significantly expanded or contracted uncovered five gene families,AUX/IAA,NAC,NBS,HB,and NF-YB.Finally,we conducted a comprehensive analysis of the TCP gene family and identified 16 tendril-related(TEN)genes in 11 Cucurbitaceae species.Interestingly,the characteristic sequence changed from CNNFYFP to CNNFYLP in the TEN gene(Bhi06M000087)of Benincasa hispida.Furthermore,we identified a new characteristic sequence,YNN,which could be used for TEN gene exploitation in Cucurbitaceae.In conclusion,this study will serve as a reference for studying the relationship between gene family evolution and genome duplication.Moreover,it will provide rich genetic resources for functional Cucurbitaceae studies in the future.