Citrus australasica ASM2961858v1 Assembly & Annotation

Overview

Analysis Name Citrus australasica ASM2961858v1 Assembly & Annotation
Sequencing technology PacBio Sequel
Assembly method FALCON v. 1
Release Date 2023-04-07
Reference Publication(s)

Singh K, Huff M, Liu J, Park J-W, Rickman T, Keremane M, Krueger RR, Kunta M, Roose ML, Dardick C, et al. Chromosome-Scale, De Novo, Phased Genome Assemblies of Three Australian Limes: Citrus australasica, C. inodora, and C. glauca. Plants. 2024; 13(11):1460. https://doi.org/10.3390/plants13111460

Abstract

Huanglongbing (HLB) is a severe citrus disease worldwide. Wild Australian limes like Citrus australasica, C. inodora, and C. glauca possess beneficial HLB resistance traits. Individual trees of the three taxa were extensively used in a breeding program for over a decade to introgress resistance traits into commercial-quality citrus germplasm. We generated high-quality, phased, de novo genome assemblies of the three Australian limes using PacBio long-read sequencing. The genome assembly sizes of the primary and alternate haplotypes were determined for C. australasica (337 Mb/335 Mb), C. inodora (304 Mb/299 Mb), and C. glauca (376 Mb/379 Mb). The nine chromosome-scale scaffolds included 86–91% of the genome sequences generated. The integrity and completeness of the assembled genomes were estimated to be at 97.2–98.8%. Gene annotation studies identified 25,461 genes in C. australasica, 27,665 in C. inodora, and 30,067 in C. glauca. Genes belonging to 118 orthogroups were specific to Australian lime genomes compared to other citrus genomes analyzed. Significantly fewer canonical resistance (R) genes were found in C. inodora and C. glauca (319 and 449, respectively) compared to C. australasica (576), C. clementina (579), and C. sinensis (651). Similar patterns were observed for other gene families associated with potential HLB resistance, including Phloem protein 2 (PP2) and Callose synthase (CalS) genes predicted in the Australian lime genomes. The genomic information on Australian limes developed in the present study will help understand the genetic basis of HLB resistance.

Assembly statistics

Genome size336.7 Mb
Total ungapped length336.7 Mb
Number of scaffolds270
Scaffold N5029.9 Mb
Scaffold L505
Number of contigs291
Contig N5017.4 Mb
Contig L507
GC percent36.5
Genome coverage100.0x
Assembly levelScaffold

Assembly

The Citrus australasica ASM2961858v1 Assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) Caustralasica_v1.0.genome_v1.0.fasta.gz

Gene Predictions

The Citrus australasica ASM2961858v1 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (GFF3 file) Caustralasica_v1.0.gene.gff3.gz
CDS sequences (FASTA file) Caustralasica_v1.0.transcript.fasta.gz
Protein sequences (FASTA file) Caustralasica_v1.0.protein.fasta.gz

Functional Analysis

Functional annotation for the Citrus australasica ASM2961858v1 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).

Downloads

Domain from InterProScan Citrus_australasica_ASM2961858v1.Pfam.tsv.gz

S genes

Summary

QueryScaffoldSize(bp)CoordinatesBLASTn HitBLASTn %IDDomain
SLF2Alt_Scaffold_7281778091411-2505PP719841.1, S30-SLF290.884F-box; F_box_assoc
SLF3Alt_Scaffold_72817780933085-34197PP719842.1, S30-SLF390.999F-box; F_box_assoc
SLF4Alt_Scaffold_72817780949580-50701ASM2964120v1, SLF490.761F-box; F_box_assoc
SLF5Alt_Scaffold_72817780996570-97694ASM2964120v1, SLF590.4F-box; F_box_assoc
SLF6Alt_Scaffold_728177809117428-116292ASM2964120v1, SLF691.733F-box; F_box_assoc
SLF7Alt_Scaffold_728177809126214-125084PP719832.1, S2-SLF793.015F-box; F_box_assoc
SLF9Alt_Scaffold_728177809129740-130882ASM2964120v1, SLF993.438F-box; F_box_assoc
SLF9-2Alt_Scaffold_728177809139305-140447ASM2964120v1, SLF993.438F-box; F_box_assoc
SLF9-3Alt_Scaffold_7281778091022861-1024003ASM2964120v1, SLF993.613F-box; F_box_assoc
SLF8Alt_Scaffold_7281778091026548-1027687ASM2964120v1, SLF8-298.333F-box; F_box_assoc
SLF10Alt_Scaffold_7281778091046585-1047730ASM2964120v1, SLF1099.302F-box; F_box_assoc
SLF11Alt_Scaffold_7281778091050194-1049019ASM2964120v1, SLF1198.639F-box; F_box_assoc
SLF12Alt_Scaffold_7281778091054345-1053224ASM2964120v1, SLF1299.109F-box; F_box_assoc
SLF7-2Alt_Scaffold_7281778091136162-1137292PP719832.1, S2-SLF792.573F-box; F_box_assoc
SLF7-3Alt_Scaffold_7281778091140052-1141182ASM2964120v1, SLF7-298.851F-box; F_box_assoc
SLF5-2Alt_Scaffold_7281778091153631-1154755ASM2964120v1, SLF5-299.289F-box; F_box_assoc
SLF6-2Alt_Scaffold_7281778091179333-1178194ASM2964120v1, SLF6-299.123F-box; F_box_assoc
SLF4-2Alt_Scaffold_7281778091208654-1209760ASM2964120v1, SLF4-299.368F-box; F_box_assoc
SLF3-2Alt_Scaffold_7281778091235647-1234532ASM2964120v1, SLF3-299.283F-box; F_box_assoc
SLF2-2Alt_Scaffold_7281778091260321-1259209ASM2964120v1, SLF2-398.473F-box; F_box_assoc
SLF1Alt_Scaffold_7281778091263406-1262306PB533_SCSK_HAP2, SLF198.547F-box; F_box_assoc
SLF12-2Pri_Scaffold_728448369907109-908230PP719852.1, S30-SLF1299.109F-box; F_box_assoc
SLF11-2ψPri_Scaffold_728448369911245-912418ASM2964120v1, SLF1198.895-
SLF10-2Pri_Scaffold_728448369914827-913682ASM2964120v1, SLF1099.302F-box; F_box_assoc
SLF8-2Pri_Scaffold_728448369933596-932457ASM2964120v1, SLF8-297.544F-box; F_box_assoc
SLF9-4Pri_Scaffold_728448369937254-936112ASM2964120v1, SLF9-292.826F-box; F_box_assoc
SLF7-4Pri_Scaffold_728448369939691-940821PP719832.1, S2-SLF792.573F-box; F_box_assoc
SLF7-5Pri_Scaffold_728448369943581-944711PP719832.1, S2-SLF790.805F-box; F_box_assoc
SLF5-3Pri_Scaffold_728448369957160-958284ASM2964120v1, SLF5-299.289F-box; F_box_assoc
SLF6-3Pri_Scaffold_728448369982858-981719ASM2964120v1, SLF6-299.123F-box; F_box_assoc
SLF4-3Pri_Scaffold_7284483691012179-1013285ASM2964120v1, SLF4-299.368F-box; F_box_assoc
SLF3-3Pri_Scaffold_7284483691039172-1038057ASM2964120v1, SLF3-299.283F-box; F_box_assoc
SLF2-3Pri_Scaffold_7284483691063846-1062734ASM2964120v1, SLF2-398.473F-box; F_box_assoc
S-RNase-1Alt_Scaffold_72817780987340-87576,
87699-88127		MN652912.1, SmR-RNase99.1Ribonuclease T2
S-RNase-2Alt_Scaffold_7281778091211181-1210939,
1210814-1210380		OR359662.1, S37-RNase98.8Ribonuclease T2
S-RNase-3Pri_Scaffold_7284483691014706-1014464,
1014339-1013905		OR359662.1, S37-RNase98.8Ribonuclease T2

Citrus S genes Nucleotide

Citrus S genes Protein

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