SGD:The Sugarcane Saccharum Spontaneum Genome Database

Sugarcane?Saccharum spp.?is the most important sugar and biofuel crop in the world,and plays an important role for the daily life of people worldwide.Sugarcane is also very important in scientific research community due to special biological characteristic such as the C₄photosynthesis,high sugar accumulation,and high biomass.During the past several years,sequencing and genetic data have been rapidly accumulated for sugarcane.In this study,to store,mine,analyze,integrate and disseminate these large-scale datasets and to provide a central portal for the sugarcane research and breeding community,we have developed the Saccharum Genome Database?SGD:http://www.sugarcanetf.site/sgd/html/index.html?using Tripal toolkit.The main results of the study are as follows:?1?The development of the genomic resource in S.spontaneumWe annotated 99,708 genes with GO terms using BLAST2GO and65,277 genes with the KEGG biological pathway using EggNOG in AP85-441.Comparing with the gene families in rice,sorghum,maize,and Arabidopsis,about 1,278 of specific gene families were found in sugarcane.Then we annotated and enriched these genes,the results showed that they were mostly enriched in the response to wounding/external stimuli.In this study,MISA software was used to perform a genome-wide SSR locus search for the S.spontaneum AP85-441.A total of 577,299SSR loci were found,of which 98,271 were chromosome-specific,accounting for 17%of the total.Compared with the number of SSRs in other gramineous plants,we found that the abundance of SSR was positively correlated with genome size,while its relative abundance has no significant correlation with genome sizes.In this study,HMMER was used to predict the transcription factors in S.spontaneum AP85-441,and a total of 4,271 genes for 57 families transcription factors were predicted.?2?The development of the expressional profile for S.spontaneum based on RNA-seqThe transcriptome plays an important role in connecting genomes and proteomes in life science research.In this study,HISAT2 and Cufflinks were used to calculate the transcriptome expression of the SES-208 leaf segment development model,growth and development process,and circadian rhythm?2H?.These data can also help the research in the expression profiling of important biological gene families such as photosynthesis and sugar transport in sugarcane.?3?The development of genetic variation based on resequencing of64 S.spontaneum accessionsIn this study,GATK were used to identify variant,and a total of 4.48million high-confidence variants that included 3,961,408 SNPs were mined based on resequencing of 64 64 S.spontaneum accessions.These data provided the resources for the study of the natural group genetic backgrounds and the utilization of breeding parents for sugarcane.?4?Construction of the Saccharum Genome DatabaseBased on the genomic resources we developed herein before described,we established the first S.spontaneum whole genome database?SGD?in the world.SGD is a user-friendly,interactive database that provides datasets including genome,CDS,protein sequences,functional annotations,expression levels,transcription factors,molecular markers.Except for its high-quality datasets,SGD also provides users with detailed user manuals,data integration information and useful online tools including JBrowse and BLAST.The SGD website will be continuously updated to promote the development of molecular biology and genetics of sugarcane and its related species.