[DOI] 10.5524/102329

[Title] Supporting data for "The whole-genome assembly of an endangered Salicaceae species: Chosenia arbutifolia (Pall.) A. Skv."

[Release Date] 

[Citation] He, X; Wang, Y; Lian, J; Zheng, J; Zhou, J; Li, J; Jiao, Z; Niu, Y; Wang, W; Zhang, J; Wang, B; Zhuge, Q (): Supporting data for "The whole-genome assembly of an endangered Salicaceae species: Chosenia arbutifolia (Pall.) A. Skv." GigaScience Database. http://dx.doi.org/10.5524/102329

[Data Type] Genomic

[Dataset Summary]  As a fast-growing tree species, <i>Chosenia arbutifolia</i> has a unique, but controversial taxonomic status in the family Salicaceae. Despite its importance as an industrial material, in ecological protection, and in landscaping, <i>C. arbutifolia</i> is seriously endangered in Northeast China because of artificial destruction and its low reproductive capability.<br />To clarify its phylogenetic relationships with other Salicaceae species, we assembled a high-quality chromosome-level genome of <i>C. arbutifolia</i> using PacBio HiFi reads and Hi-C sequencing data, with a total size of 338.93 Mb and contig N50 of 1.68 Mb. Repetitive sequences, which accounted for 42.34% of the assembly length, were identified. In total, 33,229 protein-coding genes and 11,474 small ncRNAs were predicted. Phylogenetic analysis suggested that <i>C. arbutifolia</i> and poplars diverged approximately 15.3 million years ago, and a large interchromosomal recombination between <i>C. arbutifolia</i> and other Salicaceae species was observed.<

[File Location] https://ftp.cngb.org/pub/gigadb/pub/10.5524/102001_103000/102329/

[File name] - [File Description]
readme_102329.txt  -  None
C.arbutifolia.genome.fasta.gz  -  Salix arbutifolia genome assembly file
C.arbutifolia.gene.gff3.gz  -  Salix arbutifolia coding gene annotations made on the genome assembly
C.arbutifolia.cds_primary.fasta.gz  -  Salix arbutifolia coding gene nucleotide sequences
C.arbutifolia.repeat.gff.gz  -  Salix arbutifolia repeat sequences
C.arbutifolia.miRNA.gff.gz  -  Salix arbutifolia miRNA annotations
C.arbutifolia.rRNA.gff.gz  -  Salix arbutifolia rRNA annotations
C.arbutifolia.snRNA.gff.gz  -  Salix arbutifolia snRNA annotations
C.arbutifolia.tRNA.gff.gz  -  Salix arbutifolia tRNA annotations
C.arbutifolia_fpkm.txt  -  Gene Expression levels (fpkm table) calculated from RNA-seq data
C.arbutifolia.full_length_transcripts.polished.hq.fasta.gz  -  full length transcriptome fasta
tree_root.newick  -  Phylogenetic tree file (newick) generated from the soingle copy gene family alignment
C.arbutifolia.short_summary.txt  -  BUSCO v5 short summary results file
C.arbutifolia.BUSCO.full_table.txt  -  BUSCO v5  full results file
C.arbutifolia.missing_busco_list.tsv  -  BUSCO v5 missing gene results file
willow.chr.karyotype.txt  -  karyotype map
circos_links.txt  -  Circos plot links file
willow.chr.1Mb_window.TE_coverage.txt  -  None
willow.chr.1Mb_window.gene_density.txt  -  None
willow.circos.conf.txt  -  Circos plot configuration file
calculate_4DTV.pl  -  perl script to calculate 4DTv transversion rates
C.arbutifolia_vs_C.arbutifolia.KaKs.txt  -  Whole Genome Duplication analysis results file for comparison between 2 C.arbutifolia assemblies
C.arbutifolia_vs_S.purpurea.KaKs.txt  -  Whole Genome Duplication analysis results file for comparison between C.arbutifolia and S.purpurea
C.arbutifolia_vs_P.trichocarpa.KaKs.txt  -  Whole Genome Duplication analysis results file for comparison between C.arbutifolia and P.trichocarpa
C.arbutifolia_vs_A.thaliana.KaKs.txt  -  Whole Genome Duplication analysis results file for comparison between C.arbutifolia and A.thaliana
Matrix.hic  -  HiC analysis matrix file of C arbutifolia genome sequence, can be visualized using Juicebox
bioinformatics_analysis.sh  -  shell script to reproduce the bioinformatics analysis in the manuscript
single-copy.pep.fasta.gz  -  Single copy gene family alignments (multi-fasta) between Salix species
C.arbutifolia.protein_primary.fasta.gz  -  Salix arbutifolia coding gene protein sequences


[License]
All files and data are distributed under the Creative Commons Attribution-CC0 License unless specifically stated otherwise, see http://gigadb.org/site/term for more details.

[Comments]
[End]