TY - JOUR
T1 - The Rhododendron Genome and Chromosomal Organization Provide Insight into Shared Whole-Genome Duplications across the Heath Family (Ericaceae)
AU - Soza, Valerie L.
AU - Lindsley, Dale
AU - Waalkes, Adam
AU - Ramage, Elizabeth
AU - Patwardhan, Rupali P.
AU - Burton, Joshua N.
AU - Adey, Andrew
AU - Kumar, Akash
AU - Qiu, Ruolan
AU - Shendure, Jay
AU - Hall, Benjamin
AU - Van De Peer, Yves
N1 - Funding Information:
We thank Rollo Adams, Dennis Bottemiller, Atsuko Gibson, and Steve Hootman at Rhododendron Species Botanical Garden, Federal Way, WA, for the genetic crossing and growth of seedlings; Christopher Liu for assistance with adjustments to the final assembly from the linkage map results; Kyle McKinney and Ursula Schick for technical assistance; Jeanine Smith for R. “Moonstone” material; Martin Kircher and University of Washington Department of Genome Sciences Information Technology (IT) Services for IT assistance; and three anonymous reviewers for valuable comments and suggestions. This work was supported by the National Institute of Health/National Human Genome Research Institute (NHGRI) [HG006283 to J.S.]; the NHGRI [T32HG000035 to J.N.B.]; and the National Science Foundation [DGE-0718124 to A.A.]. J.S. is an Investigator of the Howard Hughes Medical Institute.
Publisher Copyright:
© 2019 The Author(s). Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
PY - 2019/11/19
Y1 - 2019/11/19
N2 - The genus Rhododendron (Ericaceae), which includes horticulturally important plants such as azaleas, is a highly diverse and widely distributed genus of >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.
AB - The genus Rhododendron (Ericaceae), which includes horticulturally important plants such as azaleas, is a highly diverse and widely distributed genus of >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.
KW - chromatin conformation capture (Hi-C)
KW - chromosome-scale scaffolding
KW - de novo genome assembly
KW - linkage map
KW - restriction-site associated DNA (RAD) sequencing
KW - synteny
UR - http://www.scopus.com/inward/record.url?scp=85076063198&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85076063198&partnerID=8YFLogxK
U2 - 10.1093/gbe/evz245
DO - 10.1093/gbe/evz245
M3 - Article
C2 - 31702783
AN - SCOPUS:85076063198
SN - 1759-6653
VL - 11
SP - 3353
EP - 3371
JO - Genome Biology and Evolution
JF - Genome Biology and Evolution
IS - 12
ER -