Malus asiatica MA Assembly & Annotation

Overview

Analysis Name Malus asiatica MA Assembly & Annotation
Sequencing technology PacBio
Assembly method FALCON v. 16.1
Release Date 2023-11-22
Reference Publication(s)

Wang T, Duan S, Xu C, Wang Y, Zhang X, Xu X, Chen L, Han Z, Wu T. Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits. Nat Commun. 2023 Nov 15;14(1):7377. doi: 10.1038/s41467-023-43270-7.

Abstract

Structural variations (SVs) and copy number variations (CNVs) contribute to trait variations in fleshy-fruited species. Here, we assemble 10 genomes of genetically diverse Malus accessions, including the ever-green cultivar 'Granny Smith' and the widely cultivated cultivar 'Red Fuji'. Combining with three previously reported genomes, we assemble the pan-genome of Malus species and identify 20,220 CNVs and 317,393 SVs. We also observe CNVs that are positively correlated with expression levels of the genes they are associated with. Furthermore, we show that the noncoding RNA generated from a 209 bp insertion in the intron of mitogen-activated protein kinase homology encoding gene, MMK2, regulates the gene expression and affects fruit coloration. Moreover, we identify overlapping SVs associated with fruit quality and biotic resistance. This pan-genome uncovers possible contributions of CNVs to gene expression and highlights the role of SVs in apple domestication and economically important traits.

Assembly statistics

Genome size662.4 Mb
Total ungapped length662.4 Mb
Number of chromosomes17
Number of scaffolds80
Scaffold N5037.5 Mb
Scaffold L508
Number of contigs91
Contig N5036.2 Mb
Contig L508
GC percent38
Genome coverage30.0x
Assembly levelChromosome

Assembly

The Malus asiatica MA Assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) GCA_033882615.1_MA_genomic.fna.gz

Gene Predictions

The Malus asiatica MA genome gene prediction files is available in GFF3 format.

Downloads

Genes (GFF3 file) MA.gff.gz

Functional Analysis

Functional annotation for the Malus asiatica MA is not available.

Downloads

Domain from InterProScan -

S genes

Summary

QueryChrSize(bp)CoordinatesBLASTn HitBLASTn %IDDomain
Loc1-SFBBCM066507.13820633930050256-30051443ON918627.1, PbrSFBB.XVI-S1797.98F-box; F_box_assoc
Loc2-SFBBCM066507.13820633930097956-30096772ON918628.1, PbrSFBB.XVIII-S1788.65F-box; F_box_assoc
Loc3-FBXCM066507.13820633930100297-30101481AB539854.1, FBX1199.24F-box; F_box_assoc
Loc4-SFBBCM066507.13820633930175616-30174414ON918620.1, PbrSFBB.IX-S1797.34F-box; F_box_assoc
Loc5-FBXCM066507.13820633930208677-30207499AB539848.1, MdFBX5-S398.22F-box; F_box_assoc
Loc6-FBXCM066507.13820633930284502-30285683AB539860.1, MdFBX1798.65F-box; F_box_assoc
Loc7-SFBBCM066507.13820633930332293-30331121ON918623.1, PbrSFBB.XII-S1795.74F-box; F_box_assoc
S-RNase-1CM066507.13820633930451867-30451616,30451468-30451034MG598501.1, S23-RNase99.7RNase_T2
Loc8-FBXCM066507.13820633930611096-30609915AB539849.1, MdFBX691.71F-box; F_box_assoc
Loc9-FBXCM066507.13820633930646018-30644816AB539852.1, MdFBX9-S391.81F-box; F_box_assoc
Loc10-FBXCM066507.13820633930682348-30681146XM_008355598.3, MdFBX997.84F-box; F_box_assoc
Loc11-FBXCM066507.13820633930752427-30751213XM_008388108.3, MdFBX2096.38F-box; F_box_assoc
Loc12-SLFBLCM066507.13820633930793733-30792549GU345813.1, SLFBL499.92F-box; F_box_assoc
Loc13-FBXCM066507.13820633930842510-30841332XM_029098579.1, FBX198.39F-box; F_box_assoc
Loc14-FBXCM066507.13820633930934667-30933486AB539845.1, MdFBX2-S397.45F-box; F_box_assoc
Loc15-FBXCM066507.13820633931049270-31048038AB539851.1, MdFBX8-S397.73F-box; F_box_assoc
Loc16-SFBBCM066507.13820633931069126-31067942ON918628.1, PbrSFBB.XVIII-S1798.31F-box; F_box_assoc
Loc17-FBXCM066507.13820633931157115-31155925AB539853.1, FBX1098.15F-box; F_box_assoc
Loc18-SLFBLCM066507.13820633936840455-36841645GU345807.1, SLFBL1197.9F-box; F_box_assoc
Loc19-SFBBCM066507.13820633936902621-36903805ON918628.1, PbrSFBB.XVIII-S1797.81F-box; F_box_assoc
Loc20-SLFBLCM066507.13820633937036708-37037886GU345810.1, SLFBL1499.75F-box; F_box_assoc
Loc21-SLFBLCM066507.13820633937101107-37102285GU345808.1, SLFBL1299.75F-box; F_box_assoc
S-RNase-2CM066507.13820633937188353-37188595,37188940-37189377MG598487.1, S1-RNase100RNase_T2
Loc22-FBXCM066507.13820633937255646-37254450XM_008355598.3, MdFBX988.88F-box; F_box_assoc
Loc23-SFBBCM066507.13820633937291490-37290315ON918623.1, PbrSFBB.XII-S1794.22F-box; F_box_assoc
Loc24-SFBBCM066507.13820633937467151-37468335ON918622.1, PbrSFBB.XI-S1795.87F-box; F_box_assoc
Loc25-FBXCM066507.13820633937536235-37537416AB539849.1, MdFBX696.62F-box; F_box_assoc
Loc26-SFBBCM066507.13820633937573528-37572326ON918613.1, PbrSFBB.I-S1797.65F-box; F_box_assoc
Loc27-SFBBCM066507.13820633937635826-37634612ON918626.1, PbrSFBB.XV-S1797.04F-box; F_box_assoc
Loc28-SLFCM066507.13820633937771562-37770381DQ422810.1, SLF199.92F-box; F_box_assoc
Loc29-FBXCM066507.13820633937801927-37800746AB539860.1, MdFBX1799.24F-box; F_box_assoc
Loc30-SFBBCM066507.13820633937896269-37897447HM013900.1, SFBBalpha98.98F-box; F_box_assoc
Loc31-SFBBCM066507.13820633937928045-37929247ON918620.1, PbrSFBB.IX-S1797.17F-box; F_box_assoc
Loc32-FBXCM066507.13820633938000723-37999539AB539854.1, FBX1199.24F-box; F_box_assoc
Loc33-SFBBCM066507.13820633938008685-38009869ON918628.1, PbrSFBB.XVIII-S1788.07F-box; F_box_assoc
Loc34-SFBBCM066507.13820633938040805-38039618ON918627.1, PbrSFBB.XVI-S1798.23F-box; F_box_assoc

Malus asiatica MA S genes Nucleotide

Malus asiatica MA S genes Protein

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