Supporting data for "Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis)" ============================================================================================================================ Zhao H; Chen C; Fei B; Wang S; Shi C; Liu X; Zhang H; Lou Y; Chen L; Sun H; Zhou X; Wang S; Zhang C; Xu H; Li L; Yang Y; Wei Y; Yang W; Gao Q; Yang H; Gao Z; Zhao S; Jiang Z (2018): Supporting data for "Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis)" GigaScience Database. http://dx.doi.org/10.5524/100498 Summary: -------- Bamboo is one of the most important non-timber forest products worldwide. However, a chromosome-level reference genome is lacking, and the evolutionary landscape of alternative splicing (AS) in bamboo remains unclear despite emerging data and improved technologies. Here, we provide a chromosome-level de novo genome assembly of the moso bamboo (Phyllostachys edulis) using additional abundance data and different assembly strategies. The significantly improved genome is a Scaffold N50 of 79.90 Mb, approximately 243 times longer than the previous version, and 51,074 high-quality protein-coding loci with intact structures were identified using single-molecule real-time sequencing and manual verification. Moreover, we provide a comprehensive AS profile based on the identification of 266,771 uniform AS events in 25,225 AS genes by large-scale transcriptomic sequencing of 26 representative bamboo tissues using both the Illumina and PacBio sequencing platforms. Via comparison with orthologous genes in related plants, we observed dramatic evolutionary characteristics, suggesting that the AS genes are concentrated in more conserved genes that tend to accumulate higher expressed transcripts and share less specificity. Furthermore, gene family expansion, abundant AS and positive selection were identified in crucial genes involved in lignin biosynthesis, indicating that moso bamboo's specificity in being a woody plant in the grass family. These fundamental studies provide useful information for future studies performing in-depth analyses of comparative genome and AS features. Additionally, our results highlight a global perspective of AS during evolution and diversification in bamboo. Files: ------ assembly_fasta/Bamboo.WGS.genome.fasta.gz WSG assembly of Bamboo genome assembly_fasta/Bamboo.HIC.agp.txt.gz Relationship list between WGS scaffolds and Hic Chromomsome for Bamboo genome assembly_fasta/Bamboo.HIC.genome.fasta.gz Hic assembly of Bamboo genome BUSCO/full_table_bamboo.txt Full table of the BUSCO assessment file for Bamboo genome BUSCO/short_summary_bamboo.txt Summary of the BUSCO assessment file for Bamboo genome Gene_CDS/Bamboo.Hic.cds.gz coding gene file (CDS) for Bamboo genome Gene_GFF/Bamboo.Hic.gff.gz coding gene file(gff) for Bamboo genome Gene_PEP/Bamboo.Hic.pep.gz coding gene file (PEP) for Bamboo genome Repeat/Repeat/denovo_tmp.zip Results of Denovo-method prediction based on the LTR-finding for Bamboo genome Repeat/Repeat/proteinmask.zip Results of Proteinmask-methods based on Proteinmask database for Bamboo genome Repeat/Repeat/repeatmasker.zip Results of Proteinmask-methods based on repeatmasker database for Bamboo genome Repeat/ncRNA/Bamboo.miRNA.gff Result file of miRNA for Bamboo genome Repeat/ncRNA/Bamboo.rRNA.gff Result file of rRNA for Bamboo genome Repeat/ncRNA/Bamboo.snRNA.gff Result file of snRNA for Bamboo genome Repeat/ncRNA/Bamboo.tRNA.gff Result file of tRNA for Bamboo genome perl_python_scripts_pipelines/annotation/1.repeat.bin.tar.gz Pipeline script for annotation of genome sequences of Bamboo genome perl_python_scripts_pipelines/annotation/1.repeat.sh Shell script for annotation of genome sequences of Bamboo genome perl_python_scripts_pipelines/annotation/2.gene.prediction.bin.tar.gz Pipeline script for annotation of genome sequences of Bamboo genome perl_python_scripts_pipelines/annotation/ncRNA.bin.tar.gz Pipeline script for annotation of genome sequences of Bamboo genome perl_python_scripts_pipelines/assembly/DBG2OLC.sh Shell script for assembly of genome sequences for Bamboo genome perl_python_scripts_pipelines/assembly/gapclose.sh Shell script for assembly of genome sequences for Bamboo genome perl_python_scripts_pipelines/assembly/platanus_contig.sh Shell script for assembly of genome sequences for Bamboo genome perl_python_scripts_pipelines/assembly/SSPACE.sh Shell script for assembly of genome sequences for Bamboo genome perl_python_scripts_pipelines/BUSCO/Busco.bin.tar.gz Pipeline script for BUSCO assessment of Bamboo genome perl_python_scripts_pipelines/BUSCO/Busco.sh Shell script for BUSCO assessment of Bamboo genome perl_python_scripts_pipelines/evolution/1.OrthoMCL.bin.tar.gz Pipeline script for OrthoMCL analysis of Bamboo genome perl_python_scripts_pipelines/evolution/1.OrthoMCL.sh Shell script for OrthoMCL analysis of Bamboo genome perl_python_scripts_pipelines/evolution/2.Phylogeny.bin.tar.gz Pipeline script for phylogenetic analysis of Bamboo genome perl_python_scripts_pipelines/evolution/2.Phylogeny.sh Shell script for phylogenetic analysis of Bamboo genome perl_python_scripts_pipelines/evolution/3.divertime.bin.tar.gz Pipeline script for Divertime analysis of Bamboo genome perl_python_scripts_pipelines/evolution/3.divertime.sh Shell script for Divertime analysis of Bamboo genome Alternative_Splicing/Pacbio.A3SS.tab Alternative splicing results for bamboo sample tissues. Type A3SS: Alternative acceptor site Alternative_Splicing/S10.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S10.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S10.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S10.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S11.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S11.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S11.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S11.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S12.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S12.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S12.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S12.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S13.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S13.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S13.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S13.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S14.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S14.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S14.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S14.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S15.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S15.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S15.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S15.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S16.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S16.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S16.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S16.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S17.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S17.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S17.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S17.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S18.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S18.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S18.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S18.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S19.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S19.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S19.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S19.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S1.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S1.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S1.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S1.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S20.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S20.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S20.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S20.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S21.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S21.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S21.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S21.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S22.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S22.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S22.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S22.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S23.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S23.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S23.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S23.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S24.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S24.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S24.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S24.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S25.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S25.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S25.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S25.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S26.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S26.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S26.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S26.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S2.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S2.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S2.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S2.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S3.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S3.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S3.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S3.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S4.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S4.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S4.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S4.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S5.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S5.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S5.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S5.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S6.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S6.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S6.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S6.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S7.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S7.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S7.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S7.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S8.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S8.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S8.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S8.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention Alternative_Splicing/S9.A3SS.tab Alternative splicing results for bamboo sample tissue. Type A3SS: Alternative acceptor site Alternative_Splicing/S9.A5SS.tab Alternative splicing results for bamboo sample tissue. Type A5SS: Alternative donor site Alternative_Splicing/S9.ES.tab Alternative splicing results for bamboo sample tissue. Type ES: Exon skipping or cassette exon Alternative_Splicing/S9.IR.tab Alternative splicing results for bamboo sample tissue. Type IR: Intron retention