Gillenia trifoliata Whole Genome v1.0 Assembly & Annotation

Overview
Analysis NameGillenia trifoliata Whole Genome v1.0 Assembly & Annotation
MethodSupernova
Source10X Chromium reads
Date performed2021-05-03

Publication: 
Hilary S. Ireland, Chen Wu, Cecilia Deng, Elena Hilario, Ali Saei, Sylvia Erasmuson, Ross Crowhurst, Karine M. David, Robert J. Schaffer, David Chagné.The Gillenia trifoliata genome reveals dynamics correlated with growth and reproduction in Rosaceae. Submitted to Horticultural Research

Data provided by Chen Wu, The New Zealand Institute for Plant and Food Research Limited

 

Overview

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

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. 

 

Protein Homologs

Gillenia trifoliata Gillenia trifoliata v1.0 proteins with NCBI nr homologs (EXCEL file) Gtrifoliata_genome_v1.0_vs_nr.xlsx.gz
Gillenia trifoliata Gillenia trifoliata v1.0 proteins with NCBI nr (FASTA file) Gtrifoliata_genome_v1.0_vs_nr_hit.fasta.gz
Gillenia trifoliata Gillenia trifoliata v1.0 proteins without NCBI nr (FASTA file) Gtrifoliata_genome_v1.0_vs_nr_noHit.fasta.gz
Gillenia trifoliata Gillenia trifoliata v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Gtrifoliata_genome_v1.0_vs_arabidopsis.xlsx.gz
Gillenia trifoliata Gillenia trifoliata v1.0 proteins with arabidopsis (Araport11) (FASTA file) Gtrifoliata_genome_v1.0_vs_arabidopsis_hit.fasta.gz
Gillenia trifoliata Gillenia trifoliata v1.0 proteins without arabidopsis (Araport11) (FASTA file) Gtrifoliata_genome_v1.0_vs_arabidopsis_noHit.fasta.gz
Gillenia trifoliata Gillenia trifoliata v1.0 proteins with SwissProt homologs (EXCEL file) Gtrifoliata_genome_v1.0_vs_swissprot.xlsx.gz
Gillenia trifoliata Gillenia trifoliata v1.0 proteins with SwissProt (FASTA file) Gtrifoliata_genome_v1.0_vs_swissprot_hit.fasta.gz
Gillenia trifoliata Gillenia trifoliata v1.0 proteins without SwissProt (FASTA file) Gtrifoliata_genome_v1.0_vs_swissprot_noHit.fasta.gz
Gillenia trifoliata Gillenia trifoliata v1.0 proteins with TrEMBL homologs (EXCEL file) Gtrifoliata_genome_v1.0_vs_trembl.xlsx.gz
Gillenia trifoliata Gillenia trifoliata v1.0 proteins with TrEMBL (FASTA file) Gtrifoliata_genome_v1.0_vs_trembl_hit.fasta.gz
Gillenia trifoliata Gillenia trifoliata v1.0 proteins without TrEMBL (FASTA file) Gtrifoliata_genome_v1.0_vs_trembl_noHit.fasta.gz

 

Assembly

The Gillenia trifoliata Genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) Gtrifoliata_genome_v1.0.fasta.gz

 

Gene Predictions

The Gillenia trifoliata v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) Gtrifoliata_genome_v1.0.proteins.fasta.gz
CDS  (FASTA file) Gtrifoliata_genome_v1.0.cds.fasta.gz
Genes (GFF3 file) Gtrifoliata_genome_v1.0.genes.gff3.gz

 

Functional Analysis

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).

Downloads

GO assignments from InterProScan Gtrifoliata_genome_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Gtrifoliata_genome_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways Gtrifoliata_genome_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs Gtrifoliata_genome_v1.0_KEGG-pathways.xlsx.gz

 

Transcript Alignments
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.

 

Fragaria x ananassa GDR RefTrans v1 Gtrifoliata_genome_v1.0_f.x.ananassa_GDR_reftransV1
Malus_x_domestica GDR RefTrans v1 Gtrifoliata_genome_v1.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 Gtrifoliata_genome_v1.0_pyrus_GDR_reftransV1
fragaria avium GDR RefTrans v1 Gtrifoliata_genome_v1.0_p.avium_GDR_reftransV1
fragaria persica GDR RefTrans v1 Gtrifoliata_genome_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Gtrifoliata_genome_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Gtrifoliata_genome_v1.0_rubus_GDR_reftransV2