Recent advances in genome sequencing and assembly techniques have made it possible to achieve chromosome level reference genomes for citrus.Relatively few genomes have been anchored at the chromosome level and/or are ...Recent advances in genome sequencing and assembly techniques have made it possible to achieve chromosome level reference genomes for citrus.Relatively few genomes have been anchored at the chromosome level and/or are haplotype phased,with the available genomes of varying accuracy and completeness.We now report a phased high-quality chromosome level genome assembly for an Australian native citrus species;Citrus australis(round lime)using highly accurate PacBio HiFi long reads,complemented with Hi-C scaffolding.Hifiasm with Hi-C integrated assembly resulted in a 331 Mb genome of C.australis with two haplotypes of nine pseudochromosomes with an N50 of 36.3 Mb and 98.8% genome assembly completeness(BUSCO).Repeat analysis showed that more than 50% of the genome contained interspersed repeats.Among them,LTR elements were the predominant type(21.0%),of which LTR Gypsy(9.8%)and LTR copia(7.7%)elements were the most abundant repeats.A total of 29464 genes and 32009 transcripts were identified in the genome.Of these,28222 CDS(25753 genes)had BLAST hits and 21401 CDS(75.8%)were annotated with at least one GO term.Citrus specific genes for antimicrobial peptides,defense,volatile compounds and acidity regulation were identified.The synteny analysis showed conserved regions between the two haplotypes with some structural variations in Chromosomes 2,4,7 and 8.This chromosome scale,and haplotype resolved C.australis genome will facilitate the study of important genes for citrus breeding and will also allow the enhanced definition of the evolutionary relationships between wild and domesticated citrus species.展开更多
Wild relatives of crop are key genetic resources serving as diversity reservoirs for crop improvement under changing environments.Rice(Oryza sativa)is one of the most important crops in the world,providing staple food...Wild relatives of crop are key genetic resources serving as diversity reservoirs for crop improvement under changing environments.Rice(Oryza sativa)is one of the most important crops in the world,providing staple food for half of the world's population.Wild rice is thus a critical germplasm resource for sustained global food security,ensuring high production yields,improved quality,and stress resistance in the face of climate change.Wild rice is closely related to domesticated rice and has a rich genetic diversity and exceptional adaptability to extreme environments.It has played a pivotal role in the history of rice hybridization and has become a key resource for rice breeding programs.The identification of wild-type cytoplasmic male sterility resources paved the way for the achievement of the“three lines”goal in hybrid rice,leading to a significant increase in rice yields.In addition,the use of resistance alleles found in wild rice is making rice production more resilient to losses caused by environmental stresses.However,wild rice germplasm resources are threatened due to habitat destruction and other anthropogenic factors.At the same time,the lack of centralized distribution of wild rice has hampered the sharing of basic information on wild rice resources and the utilization and conservation of wild rice in each country,as well as collaboration among scientists.展开更多
Rice was domesticated in Asia(Oryza sativa)and Africa(Oryza glaberrima)from Oryza rufipogon and Oryza bathii,respectively.The Oryza genus has a pantropical distribution.The genetic diversity in Oryza provides an exten...Rice was domesticated in Asia(Oryza sativa)and Africa(Oryza glaberrima)from Oryza rufipogon and Oryza bathii,respectively.The Oryza genus has a pantropical distribution.The genetic diversity in Oryza provides an extensive gene pool to adapt rice to climate change and address future food security.The primary gene pool of domesticated rice includes species that are readily accessible for rice breeding due to ease of crossing,while more distant species are also sources of useful genes that can be recovered with greater difficulty(Figure 1).Advances in genomics and gene editing provide a path for use of this wider diversity.Studies of Oryza species also offer potential insights into rice biology that may be critical for ongoing rice food security.展开更多
CHALLENGES TO EXiSTING LEGAL SCHEMES Over the last 40 years or so,a complex web of international legal agreements was developed that regulate the access,transfer,and use of plant genetic resources.These include the Co...CHALLENGES TO EXiSTING LEGAL SCHEMES Over the last 40 years or so,a complex web of international legal agreements was developed that regulate the access,transfer,and use of plant genetic resources.These include the Convention on Biological Diversity(CBD),the Nagoya Protocol,and the International Treaty on Plant Genetic Resources(Figure 1).展开更多
文摘Recent advances in genome sequencing and assembly techniques have made it possible to achieve chromosome level reference genomes for citrus.Relatively few genomes have been anchored at the chromosome level and/or are haplotype phased,with the available genomes of varying accuracy and completeness.We now report a phased high-quality chromosome level genome assembly for an Australian native citrus species;Citrus australis(round lime)using highly accurate PacBio HiFi long reads,complemented with Hi-C scaffolding.Hifiasm with Hi-C integrated assembly resulted in a 331 Mb genome of C.australis with two haplotypes of nine pseudochromosomes with an N50 of 36.3 Mb and 98.8% genome assembly completeness(BUSCO).Repeat analysis showed that more than 50% of the genome contained interspersed repeats.Among them,LTR elements were the predominant type(21.0%),of which LTR Gypsy(9.8%)and LTR copia(7.7%)elements were the most abundant repeats.A total of 29464 genes and 32009 transcripts were identified in the genome.Of these,28222 CDS(25753 genes)had BLAST hits and 21401 CDS(75.8%)were annotated with at least one GO term.Citrus specific genes for antimicrobial peptides,defense,volatile compounds and acidity regulation were identified.The synteny analysis showed conserved regions between the two haplotypes with some structural variations in Chromosomes 2,4,7 and 8.This chromosome scale,and haplotype resolved C.australis genome will facilitate the study of important genes for citrus breeding and will also allow the enhanced definition of the evolutionary relationships between wild and domesticated citrus species.
文摘Wild relatives of crop are key genetic resources serving as diversity reservoirs for crop improvement under changing environments.Rice(Oryza sativa)is one of the most important crops in the world,providing staple food for half of the world's population.Wild rice is thus a critical germplasm resource for sustained global food security,ensuring high production yields,improved quality,and stress resistance in the face of climate change.Wild rice is closely related to domesticated rice and has a rich genetic diversity and exceptional adaptability to extreme environments.It has played a pivotal role in the history of rice hybridization and has become a key resource for rice breeding programs.The identification of wild-type cytoplasmic male sterility resources paved the way for the achievement of the“three lines”goal in hybrid rice,leading to a significant increase in rice yields.In addition,the use of resistance alleles found in wild rice is making rice production more resilient to losses caused by environmental stresses.However,wild rice germplasm resources are threatened due to habitat destruction and other anthropogenic factors.At the same time,the lack of centralized distribution of wild rice has hampered the sharing of basic information on wild rice resources and the utilization and conservation of wild rice in each country,as well as collaboration among scientists.
文摘Rice was domesticated in Asia(Oryza sativa)and Africa(Oryza glaberrima)from Oryza rufipogon and Oryza bathii,respectively.The Oryza genus has a pantropical distribution.The genetic diversity in Oryza provides an extensive gene pool to adapt rice to climate change and address future food security.The primary gene pool of domesticated rice includes species that are readily accessible for rice breeding due to ease of crossing,while more distant species are also sources of useful genes that can be recovered with greater difficulty(Figure 1).Advances in genomics and gene editing provide a path for use of this wider diversity.Studies of Oryza species also offer potential insights into rice biology that may be critical for ongoing rice food security.
文摘CHALLENGES TO EXiSTING LEGAL SCHEMES Over the last 40 years or so,a complex web of international legal agreements was developed that regulate the access,transfer,and use of plant genetic resources.These include the Convention on Biological Diversity(CBD),the Nagoya Protocol,and the International Treaty on Plant Genetic Resources(Figure 1).
