DOI: 10.5061/dryad.3xsj3txqv
title: Sequencing and assembly of the Mexican lime genome

description: Many citrus species show high levels of heterozygosity due to their hybrid
 origin and clonal propagation. This heterozygosity can both hinder and aid
 efforts to study and improve these cultivars, making it increasingly clear
 that diploid assemblies have significant advantages over the previous
 generation of haploid assemblies. In this work, we assemble both
 subgenomes of Mexican lime (Citrus x aurantifolia), an interspecific
 hybrid between C. hystrix var. micrantha and C. medica. The resulting
 diploid assembly is nearly telomere-to-telomere, spanning 680 Mb. Using
 subgenome-specific repeats, we were able to phase the 18 chromosomes based
 on their parent of origin. The resulting hystrix and medica haplotypes
 show a number of large structural variations, consistent with their
 distant hybrid ancestry. Despite divergence between haplotypes, syntenic
 gene pairs were identified for over 90% of the annotated protein-coding
 genes. Within these genes, we find extensive divergence between
 haplotypes, with at least 89% harboring polymorphisms at an average rate
 of 13 per kilobase of coding sequence. Knowledge of this variation will be
 important for future efforts to improve this cultivar using genetic
 engineering technologies.
description: ## Sequencing and assembly of the Mexican lime genome
 https://doi.org/10.5061/dryad.3xsj3txqv The genomes were assembled using
 hifiasm using HiC reads to generate haplotype assemblies. Both haplotype
 assemblies were then used for scaffolding using SALSA and the HiC reads.
 Masked assemblies were generated using RepeatMasker (v.4.0.7) using a de
 novo repeat library for Mexican lime made with RepeatModeler (v.2.0.1).
 BRAKER3 was used to identify protein-coding genes of the softmasked genome
 on the 9 chromosomes for each haplotype. The dataset contains the
 following: Mxlime_hifiasm_hap1.fa HiFi assembly before scaffolding and
 subgenome assignment (haplotype 1). Mxlime_hifiasm_hap2.fa HiFi assembly
 before scaffolding and subgenome assignment (haplotype 2).
 Mxlime_USDA_v1.fa Diploid assembly, no masking (diploid assembly, 18
 chromosomes). Mxlime_USDA_v1.hrd.msk Hardmasked chromosomes (diploid
 assembly, 18 chromosomes). Mxlime_USDA_v1.sft.msk Softmasked chromosomes
 (diploid assembly, 18 chromosomes). Mxlime_USDA_v1_unplaced_scaffolds.fa
 Unplaced scaffolds following pseudomolecule construction.
 Mxlime_USDA_v1_cds.fa Coding sequences for Mxlime_USDA_v1.fa assembly.
 Mxlime_USDA_v1_proteins.fa Protein sequences for Mxlime_USDA_v1.fa
 assembly. Mxlime_USDA_v1.gtf Annotations for protein-coding genes from the
 Mxlime_USDA_v1.fa assembly. Assembly_pipeline_MXLIME.txt Computational
 pipeline for assembling and annotating the genome. Assemblies and
 annotations for Mexican lime. Description of the data and file structure
 Extended genome assemblies and annotation files for Mxlime_USDA_v1
 (Bioproject PRJNA1137419). Sharing/Access information The assembly,
 associated sample information, and raw sequencing data are linked to the
 Bioproject PRJNA1137419. The dataset contains the following:
 Mxlime_hifiasm_hap1.fa HiFi assembly before scaffolding and subgenome
 assignment (haplotype 1). Mxlime_hifiasm_hap2.fa HiFi assembly before
 scaffolding and subgenome assignment (haplotype 2). Mxlime_USDA_v1.fa
 Diploid assembly, no masking (diploid assembly, 18 chromosomes).
 Mxlime_USDA_v1.hrd.msk Hardmasked chromosomes (diploid assembly, 18
 chromosomes). Mxlime_USDA_v1.sft.msk Softmasked chromosomes (diploid
 assembly, 18 chromosomes). Mxlime_USDA_v1_unplaced_scaffolds.fa Unplaced
 scaffolds following pseudomolecule construction. Mxlime_USDA_v1_cds.fa
 Coding sequences for Mxlime_USDA_v1.fa assembly.
 Mxlime_USDA_v1_proteins.fa Protein sequences for Mxlime_USDA_v1.fa
 assembly. Mxlime_USDA_v1.gtf Annotations for protein-coding genes from the
 Mxlime_USDA_v1.fa assembly. Assembly_pipeline_MXLIME.txt Computational
 pipeline for assembling and annotating the genome.