Comparative Analysis Of Transcriptomes Of Sugarcane Cultivar Hybrids And Two Saccharum Founding Species Obtained By Single-molecule Sequencing And Pineapple Genomics Database

The article consists of two parts.The first part is comparative analysis of transcriptomes of sugarcane cultivar hybrids and two Saccharum founding species obtained by single-molecule sequencing.The second part is pineapple genomics database(PGD).The two parts are summarized as follows.Part ?,comparative analysis of transcriptomes of sugarcane cultivar hybrids and two Saccharum founding species obtained by single-molecule sequencing Sugarcane belongs to the genus Saccharum L,a perennial tropical and subtropical crop.Sucrose is an important sugar and bio-biofuel crop.It's genome is the most complex genome among all domesticated crops.The sugarcane genome has not been deciphered for a long time,which has greatly restricted the basic research of the genetic background of important transcriptomes.Recently,our project team deciphered firstly the genome of S.spontaneum AP85-441.On this basis,our study carried out full-length transcriptome sequencing of S.spontaneum SES 208,S.officinarum LA Purple and cultivars hybrids to reveal the characteristics of their transcriptomes.The main results are as follows,1)Identification of splicing events,gain and loss of conserved domains among isoforms of each AS gene 18082,34662,25882 AS events was identified in S.spontaneum SES 208 and S.officinarum LA purple,as well as modern cultivars respectively,with intron retention was the predominant splicing pattern in all events.Types and quantitative of AS also undergoes changes under drought stress;it can also lead to the gain and loss of transcript protein domains,which may leads to change in function.2)The allelic dominance for the AS in SES 208 and LA purple Remarkably,270(93.4%)and 1,105(91.7%)of these genes which had at least two alleles respectively in had significantly higher PSI value for AS in one of alleles than the rest gene alleles in S.spontaneum SES 208 and S.officinarum LA purple,as reflected by its high Z-score,suggesting the allelic dominance for the AS in both species.3)AS events coupled with nonsense-mediated m RNA decay(NMD)We identified 29.0%,30.0% and 28.3% of alternative splicing events respectively in SES 208,LA purple and ROC 22 can lead to NMD,and non-NMD isoforms were more highly expressed than NMD isoforms in both species,indicating that this mechanism is an important m RNA monitoring mechanism in sugarcane to ensure that the translated protein is normal.4)Identification of alternative polyadenylation(APA),long no-coding RNA(LncRNA)and transcript factors(TFs) 25,915(73.8%),51,098(80.4%)and 53,379(78.7%)expressed genes were predicted to supported least one poly A site in S.spontaneum SES 208,S.officinarum LA purple and cultivar hybrids ROC 22,respectively,most of which is located in the 3' UTR region.7,268,3,064 and 15,414 LncRNAs were predicted and classified in three species.It has also been found that the occurrence of AS also leads to the production of LncRNA,which may play an important biological role;4,425,8,300 and 8,012 TFs are predicted in three species,respectively.Moreover,the ratio of AS patterns of the TFs are similar to the overall AS pattern.5)Conserved transcripts among three species A total of 21,075 conserved transcripts and 4,352 conserved AS events between two funding species,and the highest proportion of intron retention splicing types were identified.There were 14,68 and 1,599 conserved NMD in each species.There are 22,228 conserved transcripts between cultivar hybrids ROC 22 and SES 208,35,535 conserved transcripts between the cultivar hybrids ROC 22 and LA purple and 11,548 transcripts conserved with both.Part ?,pineapple genomics database(PGD)Pineapple is a monocotyledonous plant that is closely related to Poaceae(including maize,sorghum,rice,and wheat)in phylogenetic trees.It is the best reference genome for comparative genomic analysis of Poaceae crops,and is a model for studying the evolution the Bromeliaceae family and the crassulacean acid metabolism(CAM)photosynthesis.Here,we developed a pineapple genomics database(PGD,http://pineapple.zhangjisenlab.cn/pineapple/html/index.html)as a central online platform for storing and integrating bio-data for pineapple.The main information of the database is,1)Gene function annotation: In this study,47.2%,15.6%,and 25.0% of the genes were annotated into the protein domain and function,KEGG bio-path pathway,and GO function,respectively,and a total of 50.2% of the gene models were functionally annotated.In PGD,these data can be accessed and queried based on Gene ID,GO ID,KEGG ID,and Inter Pro ID.2)Genetic marker annotation: 4,629 gene coding sequence SSR markers and 46,860 genome SSR markers were identified.A total of 89 genome resequencing pineapple germplasms were collected,and 7,252,423 SNPs and 923,469 indels were identified,and 17,500 IP markers were identified.These results were displayed in the PGD.3)Comparative genomics: The critical phylogenetic position on the Poales level result in the revision of the date of the cereal genome duplication event ?,which was initially thought to have occurred between 9.5 and 11.5 millions years ago(MYA).Pineapples that have not had a ?WGD can be used as representative plants of the sequenced lineage closest to the species,making it an excellent outer group for comparative genomic studies of grass species and presenting the results to pineapples.This study carried out comparative genomic studies between pineapple and the eight species(Oryza,sativa,Vitis vinifera,Spirodela polyrhiza,Asparagus aofficinalis,Elaeis guineensis,Phoenix dactylifera,S.bicolor,and Musa acuminata).A genome-wide comparative analysis and detailed information for orthologous pairs can be queried in PGD.4)Search tools for gene expression and gene co-expression: In this study,the gene expression level and pairwise gene expression correlation co-efficiency of multiple tissues of pineapple multiple varieties are presented in PGD,and users can easily access and query in the PGD.5)BLAST alignment and genome visualization tools: BLAST was implemented by using Viro Blast for sequence homology searches.Gene annotation and structure,functionally annotated genes,SNPs,and various tissue transcriptome(including leaf,root,flower,and fruit)data were visualized using JBrowse.