Gillenia trifoliata Whole Genome v1.0 Assembly & Annotation
Data provided by Chen Wu, The New Zealand Institute for Plant and Food Research Limited
Mature plants of G. trifoliata were obtained from Wake Robin Nursery, Balclutha, New Zealand. High molecular weight (HMW) nuclear genomic DNA (ngDNA) was extracted from isolated nuclei. HMW ngDNA was submitted for short-read Illumina 10X Chromium sequencing conducted by Novogene (Hong Kong) and long-read Oxford Nanopore Technologies (ONT) sequencing conducted by Australian Genome Research Facility (AGRF; Melbourne, Australia). The initial de novo haplotype assemblies were generated from 10X Chromium short reads with effective coverage of 45X using Supernova (v1.2.2). The later obtained ONT long reads were used to post-scaffold the cleaned contigs followed by gap-filling with the long reads. For long-range Hi-C sequencing that was used to construct chromosomal-level assembly, chromatin was extracted from isolated nuclei purified using polyvinylpolypyrrolidone and Percoll gradients and paired-end Illumina reads were generated at AGRF.
Homology of the Gillenia trifoliata Genome v1.0 proteins was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e-9 was used for the NCBI nr (Release 2018-05) and 1e-6 for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2019-01), and UniProtKB/TrEMBL (Release 2019-01) databases. The best hit reports are available for download in Excel format.
Functional annotation for the Gillenia trifoliata Genome v1.0 are available for download below. The Gillenia trifoliata Genome v1.0 proteins were analyzed using InterProScan in order to assign InterPro domains and Gene Ontology (GO) terms. Pathways analysis was performed using the KEGG Automatic Annotation Server (KAAS).
Transcript alignments were performed by the GDR Team of Main Bioinformatics Lab at WSU. The alignment tool 'BLAT' was used to map transcripts to the Gillenia trifoliata genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3 format.