[DOI] 10.5524/102239

[Title] Supporting data for "First de novo whole genome sequencing and assembly of mutant Dendrobium hybrid cultivar Emma White"

[Release Date] 2022-08-04

[Citation] Sherpa, R; Devadas, R; Penna, S; Bolbhat, S, N; Nikam, T, D (2022): Supporting data for "First de novo whole genome sequencing and assembly of mutant Dendrobium hybrid cultivar Emma White" GigaScience Database. http://dx.doi.org/10.5524/102239

[Data Type] Genomic

[Dataset Summary]  <i>Dendrobium</i> hybrid cultivar Emma White is an ornamental orchid with high commercial demand. We have used gamma-ray induced &lsquo;early flowering mutant&rsquo; to generate draft genome sequences with total length of 678,650,699 bp (longest contig 447,500 bp) with N50 of 1,423 bp using the Illumina HiSeqX10 sequencing platform. Here, we report first <i>de novo</i> whole genome sequencing and assembly of an early flowering gamma mutant of Emma White hybrid for developing a genomics resource for further studies. The GC content of genome was 33.48%, and predicted 95,529 genes from contig assembly. The predicted genes from the MaSuRCA (version 4.0.3) assembled contigs, when compared with UniProt database using BLASTX program with e-value cutoff of 0.001 resulted in 60,741 potential genes governing different pathways in terms for molecular functions, biological process and cellular components. We also identified 216,232 SSRs and 138,856 microsatellite markers.<br />Chromosome level genome assembly of <i>Dendrobium huoshanense</i> species was used to RagTag scaffold the available contigs of mutant, where it contained total length of 687,254,899 bp with N50 value 2,096. The final contig lengths ranged from 30,571 bp to 18,000,059 bp. The genome completeness for Emma White RagTag scaffold assembly was assessed to be 93.6% using BUSCO v5.2.1 against the Viridiplantae odb10 orthologous dataset. <i>De novo</i> whole genome sequencing of gamma mutant <i>Dendrobium</i> hybrid cultivar Emma White (10Gy) isolate was deposited to National Centre for Biotechnology Information (NCBI) with SRA accession <a href="https://www.ncbi.nlm.nih.gov/sra/SRR16008784" target=blank>SRR16008784</a>, Genebank assembly accession <a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_021234465.1 target =_blank>GCA_021234465.1</a> under BioProject ID <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA763052" target=blank >PRJNA763052</a>. This study could provide valuable information for investigating the potential mechanisms of mutation, and guidance for developing <i>Dendrobium</i> hybrid cultivars using mutation breeding.

[File Location] https://ftp.cngb.org/pub/gigadb/pub/10.5524/102001_103000/102239/

[File name] - [File Description]
131021_Filtered_Dendrobium_mutatnt-assembly.fasta.gz  -  De novo MaSuRCA assembled contigs of Dendrobium Emma White genome
Dendrobium_mutant_10Gy41_DSC_0702.JPG  -  Photo of 10Gy/41 gamma mutant, not used in this study
Dendrobium_mutant_10Gy27_DSC_0042.JPG  -  Photo of 10Gy/27 gamma mutant, not used in this study
Dendrobium_mutant_10Gy8_DSC_0056.JPG  -  Photo of 10Gy/08 gamma mutant, not used in this study
Dendrobium_mutant_ragtag.scaffold.fasta  -  Final sequence assembly of Dendrobium Emma White using RagTag scaffolding tool
Dendrobium_mutant_busco_full_table.tsv  -  Full BUSCO values for final RagTag Scaffold assembly
Dendrobium_mutant_busco_missing_busco_list.tsv  -  Missing BUSCO values for final RagTag Scaffold assembly
Dendrobium_mutant_busco_short_summary.txt  -  Summary BUSCO results of final RagTag scaffold assembly
Dendrobium_mutant_quast_report.html  -  QUAST report file for the final RagTag scaffold assembly
Dendrobium_mutatnt-assembly.fasta.misa.gz  -  Simple sequence repeats from the final RagTag scaffold assembly
Dendrobium_mutatnt-assembly.fasta.misa.p3in.results.gz  -  138,856 microsatellite primers identified from the final RagTag scaffold assembly
NGS_P6657_Dendrobium_mutatnt_Predicted_proteins.fasta  -  Coding gene translated sequence in protein.fasta format based on the MaSuRCA contig assembly
readme_102239.txt  -  None
Dendrobium_mutant_different_lines_with_control_DSC_0071.JPG  -  Photo of gamma mutant lines with control, none of the plants pictured were used in this study
NGS_P6657_Dendrobium_mutatnt_Genes_Annotation.gff3  -  Coding genes annotation in GFF format based on the MaSuRCA contig assembly
NGS_P6657_Dendrobium_mutatnt_Predicted_genes.fasta  -  Coding nucleotide sequence in FASTA format based on the MaSuRCA contig assembly
NGS_P6657_Dendrobium_mutatnt_busco_short_summary.txt  -  Summary BUSCO result for the MaSuRCA contig assembly
Dendrobium_mutant_10Gy46_flower_DSC_4927.JPG  -  Photo of early flowering gamma mutant 10Gy/46 (used in this study) at flowering stage (12th June 2019)
Dendrobium_mutant_10Gy46_bud_DSC_4869.JPG  -  Photo of early flowering gamma mutant plant 10Gy/46 (used in this study) at bud stage (22nd May 2019)
Figure1_Early_flowering_mutant_lines.png  -  Early flowering mutant lines vs Control plants, none of the plants pictured were used in this study


[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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