[DOI] 10.5524/100689

[Title] Supporting data for "De novo genome assembly and Hi-C analysis reveal the association between chromatin architecture alterations and sex differentiation in the woody plant Jatropha curcas"

[Release Date] 2020-01-24

[Citation] Chen, M; Niu, L; Zhao, M; Xu, C; Pan, B; Fu, Q; Tao, Y; He, H; Hou, C; Xu, Z (2020): Supporting data for "De novo genome assembly and Hi-C analysis reveal the association between chromatin architecture alterations and sex differentiation in the woody plant Jatropha curcas" GigaScience Database. http://dx.doi.org/10.5524/100689

[Data Type] Genomic,Transcriptomic

[Dataset Summary]  Chromatin architecture is an essential factor in regulating gene transcription in different cell types and developmental phases. However, studies of chromatin architecture in perennial woody plants and the function of chromatin organization in sex determination have not been reported. <br />Here, we report a chromosome-scale de novo genome assembly of the woody plant Jatropha curcas with a total length of 379.5 Mb and scaffold N50 of 30.7 Mb using PacBio long-reads combined with genome-wide chromosome conformation capture (Hi-C) technology. Based on this high-quality reference genome, we detected chromatin architecture differences between the monoecious and gynoecious inflorescence buds of Jatropha. Differentially expressed genes (DEGs) were significantly enriched in the changed A/B compartments and topologically associated domain (TAD) regions and occurred preferentially in differential contact regions between monoecious and gynoecious inflorescence buds. Twelve DEGs related to flower development or hormone synthesis displayed significantly different genomic interaction patterns in monoecious and gynoecious inflorescence buds. 

[File Location] ftp://parrot.genomics.cn/gigadb/pub/10.5524/100001_101000/100689/

[File name] - [File Description]
Busco_Wu_2015.tar.gz  -  File contains the BUSCO output of four Wu et al. 2015 genome
newgenomejc.ncRNA.gff  -  File contains annotation of non-coding RNA of new Jatropha assembly
newgenomejc.genes.gff  -  File contains annotation of coding genes
newgenomejc.transcripts.fasta  -  File contains nucleotide sequences of coding genes
newgenomejc.fasta  -  File contains genome sequences of new Jatropha assembly
newgenomejc.proteins.fasta  -  File contains protein sequences of coding genes
newgenomejc.repeat.gff  -  File contains annotation of repeat sequences of new Jatropha assembly
Busco_Ha_2019.tar.gz  -  File contains the BUSCO output of Kancharla et al. 2019 genome
Busco_Hirakawa_2012.tar.gz  -  File contains the BUSCO output of Hirakawa et al. 2012 genome
readme_100689.txt  -  None
Jc-mbud-1_R1.fq.gz  -  File contains Hi-C sequencing data of the monoecious  inflorescence buds (m-bud), replicate one
Jc-mbud-1_R2.fq.gz  -  File contains Hi-C sequencing data of the monoecious  inflorescence buds (m-bud), replicate one
Jc-mbud-2_R1.fq.gz  -  File contains Hi-C sequencing data of the monoecious  inflorescence buds (m-bud), replicate two
Jc-mbud-2_R2.fq.gz  -  File contains Hi-C sequencing data of the monoecious  inflorescence buds (m-bud), replicate two
Jc-mleaf-1_R1.fq.gz  -  File contains Hi-C sequencing data of the monoecious  inflorescence leaves (m-leaf), replicate one
Jc-mleaf-1_R2.fq.gz  -  File contains Hi-C sequencing data of the monoecious  inflorescence leaves (m-leaf), replicate one
Jc-mleaf-2_R1.fq.gz  -  File contains Hi-C sequencing data of the monoecious  inflorescence leaves (m-leaf), replicate two
Jc-mleaf-2_R2.fq.gz  -  File contains Hi-C sequencing data of the monoecious  inflorescence leaves (m-leaf), replicate two
Jc-gbud-1_R1.fq.gz  -  File contains Hi-C sequencing data of the gynoecious  inflorescence buds (g-bud), replicate one
Jc-gbud-1_R2.fq.gz  -  File contains Hi-C sequencing data of the gynoecious  inflorescence buds (g-bud), replicate one
Jc-gbud-2_R1.fq.gz  -  File contains Hi-C sequencing data of the gynoecious  inflorescence buds (g-bud), replicate two
Jc-gbud-2_R2.fq.gz  -  File contains Hi-C sequencing data of the gynoecious  inflorescence buds (g-bud), replicate two
m54139_171121_091135.subreads.bam  -  File contains PacBio sequencing data for de novo assembly of Jatropha genome
m54136_171120_084641.subreads.bam  -  File contains PacBio sequencing data for de novo assembly of Jatropha genome
m54061_171122_190040.subreads.bam  -  File contains PacBio sequencing data for de novo assembly of Jatropha genome
Busco_new_Jatropha_assembly.tar.gz  -  File contains the BUSCO output of four new Jatropha assembly genome
m54171_180429_073957.subreads.bam  -  File contains PacBio sequencing data for de novo assembly of Jatropha genome
m54171_180426_015945.subreads.bam  -  File contains PacBio sequencing data for de novo assembly of Jatropha genome


[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.

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