README

Citation:  Jaggi et al. (2024) A Pangenome Reveals LTR Repeat Dynamics as a Major Driver of Genome Evolution in Chenopodium.  The Plant Genome.  In submission

Genome Assembly: A primary contig assembly for species was generated using hifiasm v0.16.1 with default parameters for inbred species (-l0) using PacBio HiFi long reads. Hi-C (high-throughput chromosome conformation capture) was used to scaffold the primary contig assembly into pseudo-molecules. Gaps between contigs within the scaffolded assembly were filled with 100 Ns.  Subgenomes were identified and chromosomes named and oriented relative to B. vulgaris (vEL10) chromosomes.

Annotation:  Prior to annotation, repetitive elements were identified and masked using RepeatModeler2 v2.0.1 and RepeatMasker v.4.1.2. To standardize the annotation across the genomes, we de novo annotated each soft-masked genome with Braker3 v.3.0.7 (Gabriel et al., 2024) using a genus-level IsoSeq dataset consisting of the combined raw IsoSeq data derived from root, leaf, stem, and whole flower tissues from C. acuminatum, C. strictum, C. ficifolium, C. berlandieri ssp. nuttaliae, and C. formosanum as primary evidence. The Viridiplantae OrthoDB v.11, Caryophyllales UniProtKB and the NCBI Caryophyllales RefSeq (www.ncbi.nlm.nih.gov/protein) databases served as training evidence for AUGUSTUS. Functional annotation and gene ontology terms (PANTHER-15.0, Pfam-33.1, PIRSF-3.10, PIRSR-2021_02, PRINTS-42.0, and SUPERFAMILY-1.75) were added to the gene models using BLASTp (e-value < 1.0e-6) by querying predicted protein models against the Swiss-Prot and InterProScan databases. 

Files:
epazote_final_nuclear_cp_mt_assembly_l60.fasta.gz - genome assembly
epazote_braker3_LongestTranscript_functional.cds.gz - gene models, CDS sequences, longest isoform only
epazote_braker3_LongestTranscript_functional.gff3.gz - annotations, longest isoform only 
epazote_braker3_LongestTranscript_functional.pep.gz - gene models, protein sequences, longest isoform only
epazote_braker3_functional.cds.gz - gene models, coding sequences
epazote_braker3_functional.gff3.gz - annotations
epazote_braker3_functional.pep.gz - gene models, protein sequences

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QuinoaDB was made possible by funding from the U.S. Department of Agriculture, National Institute of Food and Agriculture, accession number 1022158. The database is maintained through generous support from personnel in the College of Life Sciences at Brigham Young University. The Quinoa Germinate Database is maintained by King Abdullah University of Science and Technology.