Argentina lineata Genome v1.0 Assembly & Annotation

Overview
Analysis NameArgentina lineata Genome v1.0 Assembly & Annotation
MethodHifiasm-temp (0.16.1)
SourceArgentina lineata reads
Date performed2025-04-12

Publication

Wu, X., Qiao, Q., Cao, Q., Tian, Z., Qiong, L., & Zhang, T. (2025). Two gap-free genomes of Argentina provide insights into their genetic relationships. Molecular Horticulture, 5, Article 50.

 

Supplementary Table 2. Results of BUSCO assessment of genome integrity statistics

 

Argentina anserina

Percent (%)

Argentina lineata

Percent (%)

Complete BUSCOs (C)

1378

95.7

1363

94.6

Complete and single-copy BUSCOs (S)

572

39.7

1324

91.9

Complete and duplicated BUSCOs (D)

806

56

39

2.7

Fragmented BUSCOs (F)

11

0.8

26

1.8

Missing BUSCOs (M)

51

3.5

51

3.6

Total BUSCO groups searched

1440

100

1440

100

 

Homology

Homology of the Argentina lineata 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-6  for the Arabidoposis proteins (Araport11, 2022-09), UniProtKB/SwissProt (Release 2025-02), and UniProtKB/TrEMBL (Release 2025-02) databases. The best hit reports are available for download in Excel format. 

Protein Homologs

A. lineata v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Argentina_lineata_v1.0_vs_arabidopsis.xlsx
A. lineata v1.0 proteins with arabidopsis (Araport11) (FASTA file) Argentina_lineata_v1.0_vs_arabidopsis_hit.fasta.gz
A. lineata v1.0 proteins without arabidopsis (Araport11) (FASTA file) Argentina_lineata_v1.0_vs_arabidopsis_noHit.fasta.gz
A. lineata v1.0 proteins with SwissProt homologs (EXCEL file) Argentina_lineata_v1.0_vs_swissprot.xlsx.gz
A. lineata v1.0 proteins with SwissProt (FASTA file) Argentina_lineata_v1.0_vs_swissprot_hit.fasta.gz
A. lineata v1.0 proteins without SwissProt (FASTA file) Argentina_lineata_v1.0_vs_swissprot_noHit.fasta.gz
A. lineata v1.0 proteins with TrEMBL homologs (EXCEL file) Argentina_lineata_v1.0_vs_trembl.xlsx.gz
A. lineata v1.0 proteins with TrEMBL (FASTA file) Argentina_lineata_v1.0_vs_trembl_hit.fasta.gz
A. lineata v1.0 proteins without TrEMBL (FASTA file) Argentina_lineata_v1.0_vs_trembl_noHit.fasta.gz
Assembly

The Argentina lineata YNAU v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) Argentina_lineata_ynau_v1.0.fasta.gz
Gene Predictions

The Argentina lineata YNAU v1.0 genome gene prediction files are available in GFF3 and FASTA formats.

Downloads

Genes (GFF3 file) Argentina_lineata_ynau_v1.0.genes.gff3.gz
CDS (FASTA file) Argentina_lineata_ynau_v1.0.cds.fasta.gz
Protein sequences (FASTA file) Argentina_lineata_ynau_v1.0.protein.fasta.gz
TE (GFF3 file) Argentina_lineata_ynau_v1.0.TE.gff3.gz
Functional Analysis

Functional annotation for the Argentina lineata genome v1.0 are available for download below. The Argentina lineata 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 Argentina_lineata_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Argentina_lineata_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Argentina_lineata_v1.0_KEGG-orthologis.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 Argentina lineata genome v1.0 assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3.
Fragaria x ananassa GDR RefTrans v1 Argentina_lineata_v1.0_f.x.ananassa_GDR_reftransV1
Prunus avium GDR RefTrans v1 Argentina_lineata_v1.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Argentina_lineata_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Argentina_lineata_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Argentina_lineata_v1.0_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 Argentina_lineata_v1.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 Argentina_lineata_v1.0_pyrus_GDR_reftransV1