Abstract Detail



Ericaceae: Systematics, Ecology and Evolution

Lindsley, Dale [1], Waalkes, Adam [1], Soza , Valerie Lynn [1], Ramage, Elizabeth W [1], Patwardhan, Rupali [2], Burton, Josh [2], Adey, Andrew [2], Qiu, Ruolan [2], Shendure, Jay [2], Hall, Benjamin [1].

Assembly, chromosomal mapping, and evolution of the Rhododendron genome.

The genus Rhododendron is a highly diverse and widely distributed genus of more than 1,000 species. An important question raised by the recent availability of Rhododendron genomic sequence is: how strictly conserved is the gross organization of the genome within and outside Rhododendron? We sought to examine this first within the subgenus Hymenanthes, a large subgenus that contains over 200 evergreen, elepidote representatives on all Northern hemisphere continents. Since rhododendrons in India and China first came to the attention of European plant explorers (ca. AD 1800), elepidote species have been widely planted and extensively hybridized with one another to produce new varieties. Therefore, knowledge of genome architecture and conservation in these rhododendrons will facilitate future plant breeding efforts. The rhododendrons of subgenus Hymenanthes studied to date have a haploid chromosome number of 13 and a mean haploid genome size of approximately 735 Mb. Within subgenus Hymenanthes, interspecies crosses are fertile; thus, we would expect species within this group to share synteny. We selected R. williamsianum from subgenus Hymenanthes to compile a de novo genome assembly, from which we mapped DNA sequence scaffolds to the 13 chromosomes. Our next-generation sequencing libraries were assembled using two different methods that improved the assembly by decreasing the number of scaffolds and increasing scaffold length. We obtained chromosome-scale scaffolding by proximity-guided assembly using chromatin conformation capture (Hi-C). We then produced a linkage map from restriction-site associated DNA sequencing (RADseq) of the progeny from a genetic cross between R. 'Moonstone' (R. williamsianum x R. campylocarpum) and R. campylocarpum to further refine the chromosomal map. Our final assembly of the R. williamsianum genome, totaling ~532 Mb, is estimated to be 89% complete based on Benchmarking Universal Single-Copy Orthologs (BUSCO) analyses. We were able to assign 74% of the assembled genome to chromosomes, with 69% of the assembled genome ordered along these chromosomes. We then performed structural genome annotation within the MAKER pipeline to predict coding sequences in the R. williamsianum genome to compare genomic content and organization of R. williamsianum to another member of subgenus Hymemanthes (R. delavayi). Finally, we compare chromosome structure of R. williamsianum to other members of the Ericales with available chromosomal maps using synteny analyses to understand genome evolution across Rhododendron and the Ericales.


1 - University of Washington, Department of Biology, Box 351800, Seattle, WA, 98195-1800, USA
2 - University of Washington, Department of Genome Sciences, Seattle, WA, 98195, USA

Keywords:
Ericales
chromatin conformation capture (Hi-C)
RADseq
linkage map
Synteny.

Presentation Type: Colloquium Presentations
Session: C07b, Ericaceae: Systematics, Ecology, and Evolution Part 2
Location: 114/Mayo Civic Center
Date: Tuesday, July 24th, 2018
Time: 3:15 PM
Number: C07b007
Abstract ID:291
Candidate for Awards:None


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