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The genus Rhododendron (Ericaceae), which includes horticulturally important plants such as azaleas, is a highly diverse and widely distributed genus of more than 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 paralogous 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.
This article was published in the following journal.
Name: Genome biology and evolution
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The objective of this work was to analyze four essential oils (EOs) from Rhododendron species in China and evaluate their repellent activity against Tribolium castaneum, Lasioderma serricorne, and Lip...
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A research technique to measure solvent exposed regions of molecules that is used to provide insight about PROTEIN CONFORMATION.
Beliefs and values shared by all members of the organization. These shared values are reflected in the day to day operations of the organization.
A plant genus of the family ERICACEAE.
An organization of insurers or reinsurers through which particular types of risk are shared or pooled. The risk of high loss by a particular insurance company is transferred to the group as a whole (the insurance pool) with premiums, losses, and expenses shared in agreed amounts.
Component of the NATIONAL INSTITUTES OF HEALTH. It conducts and supports research into the mapping of the human genome and other organism genomes. The National Center for Human Genome Research was established in 1989 and re-named the National Human Genome Research Institute in 1997.
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. During DNA sequencing, the bases of a small fragment of DNA are sequentially identified from signals emitted as each fragment is re-synthesized from a ...