Abstract

Sequencing, assembly, and annotation of the 26.5 Gbp hexaploid genome of coast redwood (Sequoia sempervirens) was completed leading toward discovery of genes related to climate adaptation and investigation of the origin of the hexaploid genome. Deep-coverage short-read Illumina sequencing data from haploid tissue from a single seed were combined with long-read Oxford Nanopore Technologies sequencing data from diploid needle tissue to create an initial assembly, which was then scaffolded using proximity ligation data to produce a highly contiguous final assembly, SESE 2.1, with a scaffold N50 size of 44.9 Mbp. The assembly included several scaffolds that span entire chromosome arms, confirmed by the presence of telomere and centromere sequences on the ends of the scaffolds. The structural annotation produced 118,906 genes with 113 containing introns that exceed 500 Kbp in length and one reaching 2 Mb. Nearly 19 Gbp of the genome represented repetitive content with the vast majority characterized as long terminal repeats, with a 2.9:1 ratio of Copia to Gypsy elements that may aid in gene expression control. Comparison of coast redwood to other conifers revealed species-specific expansions for a plethora of abiotic and biotic stress response genes, including those involved in fungal disease resistance, detoxification, and physical injury/structural remodeling and others supporting flavonoid biosynthesis. Analysis of multiple genes that exist in triplicate in coast redwood but only once in its diploid relative, giant sequoia, supports a previous hypothesis that the hexaploidy is the result of autopolyploidy rather than any hybridizations with separate but closely related conifer species.

Details

Title
Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin
Author
Neale, David B 1 ; Zimin, Aleksey V 2 ; Zaman, Sumaira 3 ; Scott, Alison D 1 ; Shrestha, Bikash 4 ; Workman, Rachael E 5 ; Puiu, Daniela 2 ; Allen, Brian J 1 ; Moore, Zane J 1 ; Sekhwal, Manoj K 6 ; Amanda R De La Torre 6 ; McGuire, Patrick E 1 ; Burns, Emily 7 ; Timp, Winston 8 ; Wegrzyn, Jill L 9 ; Salzberg, Steven L 10 

 Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA 
 Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA 
 Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA; Department of Computer Science & Engineering, University of Connecticut, Storrs, CT 06269, USA 
 Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA 
 Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD 21205, USA 
 School of Forestry, Northern Arizona University, Flagstaff, AZ 86011, USA 
 Save the Redwoods League, San Francisco, CA 94104, USA 
 Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA; Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD 21205, USA 
 Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA 
10  Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA 
Publication year
2022
Publication date
Jan 2022
Publisher
Oxford University Press
e-ISSN
21601836
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
3169742112
Copyright
© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America. This work is published under https://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.