Rosa rugosa,commonly known as rugged rose,is a perennial ornamental shrub.It produces beautiful flowers with a mild fragrance and colorful seed pods.Unlike many other cultivated roses,R.rugosa adapts to a wide range o...Rosa rugosa,commonly known as rugged rose,is a perennial ornamental shrub.It produces beautiful flowers with a mild fragrance and colorful seed pods.Unlike many other cultivated roses,R.rugosa adapts to a wide range of habitat types and harsh environmental conditions such as salinity,alkaline,shade,drought,high humidity,and frigid temperatures.Here,we produced and analyzed a high-quality genome sequence for R.rugosa to understand its ecology,floral characteristics and evolution.PacBio HiFi reads were initially used to construct the draft genome of R.rugosa,and then Hi-C sequencing was applied to assemble the contigs into 7 chromosomes.We obtained a 382.6Mb genome encoding 39,704 protein-coding genes.The genome of R.rugosa appears to be conserved with no additional whole-genome duplication after the gamma whole-genome triplication(WGT),which occurred~100 million years ago in the ancestor of core eudicots.Based on a comparative analysis of the high-quality genome assembly of R.rugosa and other high-quality Rosaceae genomes,we found a unique large inverted segment in the Chinese rose R.chinensis and a retroposition in strawberry caused by post-WGT events.We also found that floral development-and stress response signaling-related gene modules were retained after the WGT.Two MADS-box genes involved in floral development and the stress-related transcription factors DREB2A-INTERACTING PROTEIN 2(DRIP2)and PEPTIDE TRANSPORTER 3(PTR3)were found to be positively selected in evolution,which may have contributed to the unique ability of this plant to adapt to harsh environments.In summary,the high-quality genome sequence of R.rugosa provides a map for genetic studies and molecular breeding of this plant and enables comparative genomic studies of Rosa in the near future.展开更多
Averrhoa carambola is commonly known as star fruit because of its peculiar shape,and its fruit is a rich source of minerals and vitamins.It is also used in traditional medicines in countries such as India,China,the Ph...Averrhoa carambola is commonly known as star fruit because of its peculiar shape,and its fruit is a rich source of minerals and vitamins.It is also used in traditional medicines in countries such as India,China,the Philippines,and Brazil for treating various ailments,including fever,diarrhea,vomiting,and skin disease.Here,we present the first draft genome of the Oxalidaceae family,with an assembled genome size of 470.51 Mb.In total,24,726 protein-coding genes were identified,and 16,490 genes were annotated using various well-known databases.The phylogenomic analysis confirmed the evolutionary position of the Oxalidaceae family.Based on the gene functional annotations,we also identified enzymes that may be involved in important nutritional pathways in the star fruit genome.Overall,the data from this first sequenced genome in the Oxalidaceae family provide an essential resource for nutritional,medicinal,and cultivational studies of the economically important star-fruit plant.展开更多
基金F.C.acknowledges funding from the National Natural Science Foundation of China(31801898)This work is supported by the high-performance computing platform of the Bioinformatics Center,Nanjing Agricultural UniversityThis work is supported by the Fundamental Funds for the Central Universities,NJAU(KYXJ202004)。
文摘Rosa rugosa,commonly known as rugged rose,is a perennial ornamental shrub.It produces beautiful flowers with a mild fragrance and colorful seed pods.Unlike many other cultivated roses,R.rugosa adapts to a wide range of habitat types and harsh environmental conditions such as salinity,alkaline,shade,drought,high humidity,and frigid temperatures.Here,we produced and analyzed a high-quality genome sequence for R.rugosa to understand its ecology,floral characteristics and evolution.PacBio HiFi reads were initially used to construct the draft genome of R.rugosa,and then Hi-C sequencing was applied to assemble the contigs into 7 chromosomes.We obtained a 382.6Mb genome encoding 39,704 protein-coding genes.The genome of R.rugosa appears to be conserved with no additional whole-genome duplication after the gamma whole-genome triplication(WGT),which occurred~100 million years ago in the ancestor of core eudicots.Based on a comparative analysis of the high-quality genome assembly of R.rugosa and other high-quality Rosaceae genomes,we found a unique large inverted segment in the Chinese rose R.chinensis and a retroposition in strawberry caused by post-WGT events.We also found that floral development-and stress response signaling-related gene modules were retained after the WGT.Two MADS-box genes involved in floral development and the stress-related transcription factors DREB2A-INTERACTING PROTEIN 2(DRIP2)and PEPTIDE TRANSPORTER 3(PTR3)were found to be positively selected in evolution,which may have contributed to the unique ability of this plant to adapt to harsh environments.In summary,the high-quality genome sequence of R.rugosa provides a map for genetic studies and molecular breeding of this plant and enables comparative genomic studies of Rosa in the near future.
基金supported by funding from the National Key R&D Program of China(No.2019YFC1711000)the Shenzhen Municipal Government of China(grants JCYJ20170817145512476 and JCYJ20160510141910129)+1 种基金the Guangdong Provincial Key Laboratory of Genome Read and Write(grant 2017B030301011)the NMPA Key Laboratory for the Rapid Testing Technology of Drugs.
文摘Averrhoa carambola is commonly known as star fruit because of its peculiar shape,and its fruit is a rich source of minerals and vitamins.It is also used in traditional medicines in countries such as India,China,the Philippines,and Brazil for treating various ailments,including fever,diarrhea,vomiting,and skin disease.Here,we present the first draft genome of the Oxalidaceae family,with an assembled genome size of 470.51 Mb.In total,24,726 protein-coding genes were identified,and 16,490 genes were annotated using various well-known databases.The phylogenomic analysis confirmed the evolutionary position of the Oxalidaceae family.Based on the gene functional annotations,we also identified enzymes that may be involved in important nutritional pathways in the star fruit genome.Overall,the data from this first sequenced genome in the Oxalidaceae family provide an essential resource for nutritional,medicinal,and cultivational studies of the economically important star-fruit plant.
