DOI: 10.5061/dryad.573n5tbdr
title: Data supporting: Chromosome-level genome of the transformable northern wattle, Acacia crassicarpa

description: The genus Acacia is a large group of woody legumes containing an enormous
 amount of morphological diversity in leaf shape. This diversity is at
 least in part the result of an innovation in leaf development where many
 Acacia species are capable of developing leaves of both bifacial and
 unifacial morphology. While not unique in the plant kingdom, unifaciality
 is most commonly associated with monocots, and its developmental genetic
 mechanisms have yet to be explored beyond this group. Here we identify an
 accession of Acacia crassicarpa with high regeneration rates and isolate a
 clone for genome sequencing. We generate a chromosome-level assembly of
 this readily transformable clone and using comparative analyses confirm a
 whole genome duplication unique to Caesalpinoid legumes. This resource
 will be important for future work examining genome evolution in legumes
 and the unique developmental genetic mechanisms underlying unifacial
 morphogenesis in Acacia.
description: The genomes were assembled using hifiasm using Omni-C reads to
 generate haplotype-resolved assemblies. The larger of the two haplotype
 assemblies was then used for scaffolding using SALSA and the Omni-C
 reads. Masked assemblies were generated using
 RepeatMasker (v.4.0.7) using an <em>A. crassicarpa</em> de
 novo repeat library made with RepeatModeler (v.2.0.1).
 BRAKER3 was used to identify protein coding genes of the
 softmasked genome on scaffolds larger than 1 Mb. The
 dataset contains the following: Acra_USDA_v1.100k.fa   
                         Scaffolds larger than 100 kb from the SALSA
 scaffolding step.<br>Acra_USDA_v1.1M.hrd.msk                   
  Hardmasked scaffolds larger than 1 Mb.<br>Acra_USDA_v1.1M.sft.msk 
                     Softmasked scaffolds larger than 1
 Mb.<br>Acra_USDA_v1_cds.fa                             Coding
 sequences for Acra_USDA_v1.fsa assembly.<br>Acra_USDA_v1.fsa       
                            Scaffolds larger than 1 Mb. No
 masking.<br>Acra_USDA_v1.gtf                                   
 Annotations for protein coding genes from the Acra_USDA_v1.fsa
 assembly.<br>Acra_USDA_v1.hap1.fa                           
 Haplotype 1 before SALSA scaffolding (no size
 filtering).<br>Acra_USDA_v1.hap2.fa                           
 Haplotype 2 before SALSA scaffolding (no size
 filtering).<br>Acra_USDA_v1_proteins.fa                      Protein
 sequences for Acra_USDA_v1.fsa assembly.
 Assembly_pipeline_ACRA3RX.txt            Computational pipeline
 for assembling and annotating genome.
description: # Data supporting "Chromosome-level genome of the transformable
 northern wattle, Acacia crassicarpa" *** Assemblies and annotations
 for Acacia crassicarpa, clone Acra3RX. ## Description of the data and file
 structure Extended genome assemblies and annotation files for
 Acra\_USDA\_v1 (Bioproject PRJNA975180). ## Sharing/Access information The
 assembly, associated sample information and raw sequencing data is linked
 to the Bioproject PRJNA975180. This dataset contains the following:
 Acra\_USDA\_v1.100k.fa Scaffolds larger than 100 kb from the SALSA
 scaffolding step. Acra\_USDA\_v1.1M.hrd.msk Hardmasked scaffolds larger
 than 1 Mb. Acra\_USDA\_v1.1M.sft.msk Softmasked scaffolds larger than 1
 Mb. Acra\_USDA\_v1\_cds.fa Coding sequences for Acra\_USDA\_v1.fsa
 assembly. Acra\_USDA\_v1.fsa Scaffolds larger than 1 Mb. No masking.
 Acra\_USDA\_v1.gtf Annotations for protein coding genes from the
 Acra\_USDA\_v1.fsa assembly. Acra\_USDA\_v1.hap1.fa Haplotype 1 before
 SALSA scaffolding (no size filtering). Acra\_USDA\_v1.hap2.fa Haplotype 2
 before SALSA scaffolding (no size filtering). Acra\_USDA\_v1\_proteins.fa
 Protein sequences for Acra\_USDA\_v1.fsa assembly.
 Assembly\_pipeline\_ACRA3RX.txt            Computational pipeline for
 assembling and annotating genome.