Citrus inodora UN-2024b Assembly & Annotation

Overview

Analysis Name Citrus inodora UN-2024b Assembly & Annotation
Sequencing technology PacBio Sequel
Assembly method hifiasm v. v.0.19.8
Release Date 2024-12-17
Reference Publication(s)

Nakandala U, Furtado A, Masouleh AK, Smith MW, Mason P, Williams DC, Henry RJ. The genomes of Australian wild limes. Plant Mol Biol. 2024 Sep 24;114(5):102. doi: 10.1007/s11103-024-01502-4.

Abstract

Australian wild limes occur in highly diverse range of environments and are a unique genetic resource within the genus Citrus. Here we compare the haplotype-resolved genome assemblies of six Australian native limes, including four new assemblies generated using PacBio HiFi and Hi-C sequencing data. The size of the genomes was between 315 and 391 Mb with contig N50s from 29.5 to 35 Mb. Gene completeness of the assemblies was estimated to be from 98.4 to 99.3% and the annotations from 97.7 to 98.9% based upon BUSCO, confirming the high contiguity and completeness of the assembled genomes. High collinearity was observed among the genomes and the two haplotype assemblies for each species. Gene duplication and evolutionary analysis demonstrated that the Australian citrus have undergone only one ancient whole-genome triplication event during evolution. The highest number of species-specific and expanded gene families were found in C. glauca and they were primarily enriched in purine, thiamine metabolism, amino acids and aromatic amino acids metabolism which might help C. glauca to mitigate drought, salinity, and pathogen attacks in the drier environments in which this species is found. Unique genes related to terpene biosynthesis, glutathione metabolism, and toll-like receptors in C. australasica, and starch and sucrose metabolism genes in both C. australis and C. australasica might be important candidate genes for HLB tolerance in these species. Expanded gene families were not lineage specific, however, a greater number of genes related to plant-pathogen interactions, predominantly disease resistant protein, was found in C. australasica and C. australis.

Assembly statistics

Assembly

The Citrus inodora UN-2024b Assembly files are available in FASTA format.

Downloads

Chromosomes (FASTA file) GCA_046118865.1_ASM4611886v1_genomic.fna.gz
Chromosomes (FASTA file) GCA_046118875.1_ASM4611887v1_genomic.fna.gz

Gene Predictions

The Citrus inodora UN-2024b genome gene prediction files are not available.

Downloads

Genes (GFF3 file) -
CDS sequences (FASTA file) -
Protein sequences (FASTA file) -

Functional Analysis

Functional annotation for the Citrus inodora UN-2024b is not available.

Downloads

Domain from InterProScan -

S genes

Summary

QueryChrSize(bp)CoordinatesBLASTn HitBLASTn %IDDomain
SLF1CM100387.12873346927556835-27557935PP719840.1, S30-SLF197F-box; F_box_assoc
SLF2aCM100387.12873346927559914-27561038PP719841.1, S30-SLF297F-box; F_box_assoc
SLF3CM100387.12873346927565889-27567010PP719842.1, S30-SLF395F-box; F_box_assoc
SLF4CM100387.12873346927570708-27571823PP719843.1, S30-SLF491F-box; F_box_assoc
SLF5CM100387.12873346927589031-27587904PP719830.1, S2-SLF586F-box; F_box_assoc
SLF2bCM100387.12873346927601981-27600869PP719841.1, S30-SLF288F-box; F_box_assoc
SLF9aψCM100387.12873346927626562-27627700PP719834.1, S2-SLF974-
SLF7CM100387.12873346927629874-27628744PP719832.1, S2-SLF792F-box; F_box_assoc
SLF8CM100387.12873346927632488-27633630PP719847.1, S30-SLF8a75F-box; F_box_assoc
SLF9bCM100387.12873346927636328-27637467PP719834.1, S2-SLF974F-box; F_box_assoc
SLF10CM100387.12873346927657970-27659115PP719835.1, S2-SLF1099F-box; F_box_assoc
SLF11ψCM100387.12873346927661554-27660384PP719851.1, S30-SLF1198-
SLF12CM100387.12873346927667242-27666121PP719837.1, S2-SLF1299F-box; F_box_assoc
S-RNaseCM100387.12873346927574785-27574543,27574449-27573997MN652903.1, S7-RNase98RNase T2
SLF1CM100396.12827736126580397-26581497PP719840.1, S30-SLF197F-box; F_box_assoc
SLF7CM100396.12827736126684648-26683518PP719832.1, S2-SLF792F-box; F_box_assoc
SLF8CM100396.12827736126687262-26688404PP719847.1, S30-SLF8a75F-box; F_box_assoc
SLF9CM100396.12827736126691219-26692358PP719834.1, S2-SLF974F-box; F_box_assoc
SLF10CM100396.12827736126712855-26714000PP719835.1, S2-SLF1099F-box; F_box_assoc
SLF11ψCM100396.12827736126716443-26715269PP719851.1, S30-SLF1198-
SLF12CM100396.12827736126720594-26719473PP719837.1, S2-SLF1299F-box; F_box_assoc
SLF2CM100396.12827736126583485-26584609PP719841.1, S30-SLF294F-box; F_box_assoc
SLF3CM100396.12827736126592374-26593495PP719842.1, S30-SLF391F-box; F_box_assoc
SLF4CM100396.12827736126619294-26620409PP719843.1, S30-SLF490F-box; F_box_assoc
SLF5CM100396.12827736126661252-26660128PP719830.1, S2-SLF588F-box; F_box_assoc
SLF6CM100396.12827736126673712-26672588PP719845.1, S30-SLF691F-box; F_box_assoc

Citrus inodora UN-2024b S genes Nucleotide

Citrus inodora UN-2024b S genes Protein

© 2023 National Genomics Data Center, China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences