A Reference Genome Sequence for Giant Sequoia

Alison D Scott; Aleksey V Zimin; Daniela Puiu; Rachael Workman; Monica Britton; Sumaira Zaman; Madison Caballero; Andrew C Read; Adam J Bogdanove; Emily Burns; Jill Wegrzyn; Winston Timp; Steven L Salzberg; David B Neale

doi:10.1534/g3.120.401612

A Reference Genome Sequence for Giant Sequoia

G3 (Bethesda). 2020 Nov 5;10(11):3907-3919. doi: 10.1534/g3.120.401612.

Authors

Alison D Scott¹, Aleksey V Zimin^{2

3

4}, Daniela Puiu^{2

4}, Rachael Workman⁴, Monica Britton⁵, Sumaira Zaman⁶, Madison Caballero⁷, Andrew C Read⁸, Adam J Bogdanove⁸, Emily Burns⁹, Jill Wegrzyn¹⁰, Winston Timp⁴, Steven L Salzberg^{2

4

11}, David B Neale¹²

Affiliations

¹ Department of Plant Sciences, University of California, Davis, CA 95616 aliscott@ucdavis.edu.
² Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21211.
³ Institute for Physical Sciences and Technology, University of Maryland, College Park, MD 20742.
⁴ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218.
⁵ Bioinformatics Core, University of California, Davis, CA 95616.
⁶ Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269.
⁷ Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850.
⁸ Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853.
⁹ Save the Redwoods League, San Francisco, CA 94104.
¹⁰ Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269.
¹¹ Departments of Computer Science and Biostatistics, Johns Hopkins University, Baltimore, MD 21218.
¹² Department of Plant Sciences, University of California, Davis, CA 95616.

Abstract

The giant sequoia (Sequoiadendron giganteum) of California are massive, long-lived trees that grow along the U.S. Sierra Nevada mountains. Genomic data are limited in giant sequoia and producing a reference genome sequence has been an important goal to allow marker development for restoration and management. Using deep-coverage Illumina and Oxford Nanopore sequencing, combined with Dovetail chromosome conformation capture libraries, the genome was assembled into eleven chromosome-scale scaffolds containing 8.125 Gbp of sequence. Iso-Seq transcripts, assembled from three distinct tissues, was used as evidence to annotate a total of 41,632 protein-coding genes. The genome was found to contain, distributed unevenly across all 11 chromosomes and in 63 orthogroups, over 900 complete or partial predicted NLR genes, of which 375 are supported by annotation derived from protein evidence and gene modeling. This giant sequoia reference genome sequence represents the first genome sequenced in the Cupressaceae family, and lays a foundation for using genomic tools to aid in giant sequoia conservation and management.

Keywords: Sequoiadendron giganteum; conifer; disease resistance genes; genome assembly; giant sequoia; gymnosperm.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Chromosomes
Genome
High-Throughput Nucleotide Sequencing
Molecular Sequence Annotation
Sequoiadendron*
Trees

Abstract

Publication types

MeSH terms

Grants and funding