DOI: 10.5061/dryad.ns1rn8pqw
title: The Rhododendron genome and chromosomal organization provide insight into shared whole-genome duplications across the heath family (Ericaceae)

description: The genus Rhododendron (Ericaceae), which includes
 horticulturally important plants such as azaleas, is a highly diverse and
 widely distributed genus of &gt;1,000 species. Here, we report the
 chromosome-scale de novo assembly and genome annotation
 of Rhododendron williamsianum as a basis for continued
 study of this large genus. We created multiple short fragment genomic
 libraries, which were assembled using ALLPATHS-LG. This was followed by
 contiguity preserving transposase sequencing (CPT-seq) and fragScaff
 scaffolding of a large fragment library, which improved the assembly by
 decreasing the number of scaffolds and increasing scaffold length.
 Chromosome-scale scaffolding was performed by proximity-guided assembly
 (LACHESIS) using chromatin conformation capture (Hi-C) data.
 Chromosome-scale scaffolding was further refined and linkage groups
 defined by restriction-site associated DNA (RAD) sequencing of the parents
 and progeny of a genetic cross. The resulting linkage map confirmed the
 LACHESIS clustering and ordering of scaffolds onto chromosomes and
 rectified large-scale inversions. Assessments of
 the R. williamsianum genome assembly and gene
 annotation estimate them to be 89% and 79% complete, respectively.
 Predicted coding sequences from genome annotation were used in syntenic
 analyses and for generating age distributions of synonymous
 substitutions/site between paralgous gene pairs, which identified
 whole-genome duplications (WGDs) in R. williamsianum. We
 then analyzed other publicly available Ericaceae genomes for shared WGDs.
 Based on our spatial and temporal analyses of paralogous gene pairs, we
 find evidence for two shared, ancient WGDs
 in Rhododendron and Vaccinium (cranberry/blueberry) members that predate the Ericaceae family and, in one case, the Ericales order.
description: For the genome assembly of R. williamsianum, we created multiple
 short fragment genomic libraries, which were assembled using ALLPATHS-LG.
 This was followed by contiguity preserving transposase sequencing
 (CPT-seq) and fragScaff scaffolding of a large fragment library, which
 improved the assembly by decreasing the number of scaffolds and increasing
 scaffold length. Chromosome-scale scaffolding was performed by
 proximity-guided assembly (LACHESIS) using chromatin conformation capture
 (Hi-C) data. Chromosome-scale scaffolding was further refined and linkage
 groups defined by restriction-site associated DNA (RAD) sequencing of the
 parents and progeny of a genetic cross. The resulting linkage map
 confirmed the LACHESIS clustering and ordering of scaffolds onto
 chromosomes and rectified large-scale inversions. We then performed repeat
 annotation and masking with MAKER v2.31.9 (Cantarel et al. 2008; Holt
 & Yandell 2011) using a <i>de novo</i>
 species-specific repeat database and homology-based methods within MAKER,
 followed by gene annotation done within Maker
 v2.31.9 (Cantarel et al. 2008; Holt & Yandell 2011).
description: README Files deposited in Dryad are below with
 file descriptions.<br> Files include whole genome assembly and
 annotations for Rhododendron williamsianum and pseudochromosomal files
 used in syntenic analyses in the study below:<br> Soza VL et al.
 2019. The Rhododendron genome and chromosomal organization provide insight
 into shared whole genome duplications across the heath family (Ericaceae).
 Genome Biol. Evol. 11:3353–3371. doi: 10.1093/gbe/evz245.
 Rwill.assembly.renamed.fixed042418.fasta.gz - entire genome
 assembly in fasta format for Rhododendron williamsianum.<br>
 Rwill10.masked.pseudochromos.fasta.gz - fasta sequences for
 pseudochromosomes of R. williamsianum. These were generated by stitching
 ordered scaffolds assigned to linkage groups (LGs) together with 100-N
 spacers.<br>
 Rwill10.pseudochromos.maker.sorted.renamed.blast.function.iprdomains.gff -
 gff file for gene annotations on R. williamsianum
 pseudochromosomes.<br> Rwill10.repeatmasker.runner.match.sorted.gff
 - repeatmasker and repeatrunner annotations from Maker for the entire
 genome assembly of R. williamsianum.<br>
 Rwill10standard2.maker.proteins.renamed.fasta - predicted protein
 sequences from Maker for the entire genome assembly of R. williamsianum;
 gene IDs not sorted.<br> Rwill10standard2.maker.sorted.renamed.gff -
 gff file for gene annotations for the entire genome assembly of R.
 williamsianum.<br> Rwill10standard2.maker.transcripts.renamed.fasta
 - predicted transcript sequences from Maker for the entire genome assembly
 of R. williamsianum; gene IDs not sorted.<br>
 V.macrocarpon.allLGs.sorted.offset.gff3.2 - gff file for gene annotations
 on Vaccinium macrocarpon pseudochromosomes. These annotations were
 extracted from Cranberry_Gene_Models.gff at
 http://cyanophora.rutgers.edu/cranberry/ based on LGs identified
 below.<br> V.macrocarpon.masked.pseudochromos.fasta.gz - fasta
 sequences for pseudochromosomes of V. macrocarpon. These were generated
 from anchored scaffolds within LGs from FileS2.csv in Schlautman et al
 2017 and the Cranberry_masked_assembly.fa available at
 http://cyanophora.rutgers.edu/cranberry/ from Polashock et al. (2014),
 stitching scaffolds within each LG together with 100-N spacers.
 References:<br> Polashock J, et al. 2014. The American
 cranberry: first insights into the whole genome of a species adapted to
 bog habitat. BMC Plant Biol. 14(1):165.<br> Schlautman B, et al.
 2017. Construction of a high-density American cranberry (Vaccinium
 macrocarpon Ait.) composite map using genotyping-by-sequencing for
 multi-pedigree linkage mapping. G3 (Bethesda) 7:1177–1189. <br>