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bioRxiv · 10.1101/2022.06.25.497579

First De novo whole genome sequencing and assembly of mutant Dendrobium hybrid cultivar 'Emma White'

Sherpa, R.·Devadas, R.·Penna, S.·Bolbhat, S. N.·Nikam, T.
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Abstract

Dendrobium hybrid cultivar Emma White is an ornamental orchid with high commercial demand. We have used gamma-ray induced early flowering mutant to generate draft genome sequences with total length (bp) with 678,650,699 and contigs at 447,500 with N50 at 1,423 using the Illumina HiSeqX10 sequencing platform. Here, we report first de novo 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-valuecutoff of 10-3 resulted 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. Chromosome level genome assembly of Dendrobium huoshanense 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. Largest contiguous length was found with 18,000,059 bp from 30,571 bp. The genome completeness for Emma White RagTag scaffold assembly was assessed to be 93.6% complete using BUSCO v5.2.1 against the Viridiplantae odb10 orthologous dataset. De novo whole genome sequencing of gamma mutant Dendrobium hybrid cultivar Emma White (10Gy) isolate was deposited to National Centre for Biotechnology Information (NCBI) with SRA accession SRR16008784, Genebank assembly accession GCA_021234465.1(https://www.ncbi.nlm.nih.gov/assembly/GCA_021234465.1#/st) and Transcriptional Shot Gun assembly accession GJVE00000000 under BioProject ID PRJNA763052. This study could provide valuable information for investigating the potential mechanisms of mutation, and guidance for developing Dendrobium hybrid cultivars using mutation breeding.

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Sherpa, R., Devadas, R., Penna, S., Bolbhat, S. N., Nikam, T.. 2022-06-29. First De novo whole genome sequencing and assembly of mutant Dendrobium hybrid cultivar 'Emma White'. https://doi.org/10.1101/2022.06.25.497579

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