Additional file 5 of Phylogenetic analysis and stress response of the plant U2 small nuclear ribonucleoprotein B″ gene family

Additional file 5: Table S4. Expression of U2B″ in rice under different stresses

Additional file 2 of Phylogenetic analysis and stress response of the plant U2 small nuclear ribonucleoprotein B″ gene family

Additional file 2: Table S1. Sequence summary of plant U2B″ gene phylogenetic analysis

Additional file 6 of Phylogenetic analysis and stress response of the plant U2 small nuclear ribonucleoprotein B″ gene family

Additional file 6: Table S5. Sequence summary of plant U2B″ protein-protein interaction network

Additional file 1 of Phylogenetic analysis and stress response of the plant U2 small nuclear ribonucleoprotein B″ gene family

Additional file 1: Fig. S1. Formation of mature 17S U2 snRNP. The upper one is12S core particle, the middle one is 15S pre-mature particle, and the lower oneis 17S functional maturity particle. Continuous thin black lines represent U2 snRNA. Fig. S2. The design process of the whole article. Fig. S3. Circle phylogenetic tree representation of the available plant U2B″ gene family. Phylogenetic analysisof plant U2B″ gene family was carried out by using software MrBayes v3.2.2. The posterior probability values are labeled at each major branch. Blue for dicotyledons, pink for monocotyledons,white for ferns, green for bryophytes, and yellow for algae. Fig. S4. Motifs of genomic structure and protein structure analysis. (A)  Consensus sequence of top ten identified DNA motifs are listed in ascending order. (B)  Consensus sequence of top ten identified amino-acid motifs are listed in ascending order. Fig. S5. The multiple sequence alignment of RRM domains for the conservative analysis. The sequences are arranged from top to bottom in phylogenetic tree. Fig. S6. Promoter classification and enrichment analysis. (A) Statistics of motifs function and number. The x-axis represents the number of elements. (B)Overall enrichment statistics of motifs in response to stress, hormones and light.Fig. S7. AS profile analysis. Summary of annotated alternatively spliced transcript isoforms for identified U2B″ genes. Pink represents monocotyledons, blue represents dicotyledons, green represents bryophytes, and yellow represents algae

Additional file 4 of Phylogenetic analysis and stress response of the plant U2 small nuclear ribonucleoprotein B″ gene family

Additional file 4: Table S3. Statistical analysis of promoter distribution

Additional file 3 of Phylogenetic analysis and stress response of the plant U2 small nuclear ribonucleoprotein B″ gene family

Additional file 3: Table S2. Specific data of enrichment analysis

File 1 SVs in the 453 high sequencing-depth rice accessions

Presence/Absence (1/0) matrix of SVs (deletion, duplication, inversion and translocation) in 453 rice accessions. In the matrix, '1' represents that SV is present in the accession, while '0' means absent. Before creating the matrix, SV were detected in 3,010 rice accession using NovoBreak. SVs passed the filter cretia were remained to make the presence/absence (1/0) matrix for 453 high depth sequenced rice accessions

File 4 Gene presence/absence variations of 453 rice accessions

This file includes gene presence/absence variations of 453 rice accessions as a key output of 3k RG. The first column represents the gene ids and the next 453 columns represent the 453 rice accessions. The file contains a binary (0/1) matrix, where 1 means presence of a gene while 0 means absence of a gene. <br

File 2 The an-genome sequences of O.sativa

This file includes the pan-genome sequences of rice as a key output of 3k RG. The pan-genome is built by combining IRGSP-1.0 genome and non-redundant novel sequences from de novo assemblies of 3,010 rice genomes. The novel sequences were combined to artifitial chromosomes by connecting sequences with 100 consecutive Ns. This file is also available in the rice pan-genome database (RPAN, http://cgm.sjtu.edu.cn/3kricedb/).<br