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Comparative Genomics/Transcriptomics

Scott, Alison Dawn [1], Zaman, Sumaira [2], Shrestha, Bikash [3], Vuruputoor, Vidya [4], Wegrzyn, Jill [5].

Genome evolution in California redwoods .

Though polyploidy is rampant across most plant lineages, whole genome duplications (WGDs) are conspicuously rare in gymnosperms, and even more infrequent in conifers. Coast redwood (Sequoia sempervirens; Cupressaceae) is a polyploid, and provides a unique system to understand the patterns and mechanisms of WGDs in gymnosperms. Fossil data suggest polyploidization of S. sempervirens was complete by the end of the Eocene, chromosome pairing reveals both multivalent and bivalent formation, and molecular data demonstrate limited divergence among subgenomes, suggesting an extended period of multisomic inheritance following genome duplication.
The forthcoming coast redwood genome assembly, in combination with the recently published chromosome-level assembly of its closest relative, diploid giant sequoia (Sequoiadendron giganteum) together provide a foundation for comparative genomics between the diploid-hexaploid taxon pair. Using these new genomic resources, we investigate the dynamics of duplicated genes and their fates, estimate the timing of polyploidization, and provide evidence that coast redwood is indeed an autopolyploid. This includes examination of repeat family dynamics, including mechanisms for transcriptional control in this complex hexaploid. Additionally, we observe almost 10,000 genes that are located 3 Kbp up/down-stream from Copia retro-elements. We evaluate these genes for function, selection pressure, and their role in gene regulation.

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1 - Max Planck Institute for Plant Breeding Research, Carl-von-Linne-weg, 10, Köln, Nordrhein-Westfalen, 50829, Germany
2 - University of Connecticut, Department of Computer Science & Engineering, Storrs, CT
3 - University of Connecticut, Department of Ecology and Evolutionary Biology, Storrs, CT
4 - University Of Connecticut, Ecology And Evolutionary Biology, 75 N. Eagleville Road, Unit 3043, Storrs, CT, 06269-3043, United States
5 - University of Connecticut, Ecology & Evolutionary Biology, 75 N. Eagleville Road, Unit 3043, Storrs, CT, 06269-3043, United States


Presentation Type: Oral Paper
Session: CGT3, Comparative Genomics/Transcriptomics III
Location: /
Date: Tuesday, July 20th, 2021
Time: 4:30 PM(EDT)
Number: CGT3007
Abstract ID:733
Candidate for Awards:None

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