@article{ee331613ab324300a0d8060ec0217ce9,
title = "A reference genome sequence for giant sequoia",
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 = "Assembly, Conifer, Disease, Genes, Genome, Giant sequoia, Giganteum, Gymnosperm, Resistance, Sequoiadendron",
author = "Scott, {Alison D.} and Zimin, {Aleksey V.} and Daniela Puiu and Rachael Workman and Monica Britton and Sumaira Zaman and Madison Caballero and Read, {Andrew C.} and Bogdanove, {Adam J.} and Emily Burns and Jill Wegrzyn and Winston Timp and Salzberg, {Steven L.} and Neale, {David B.}",
note = "Funding Information: This project was supported by a grant from Save The Redwoods League for the Redwood Genome Project (to DN), and by grants from the National Institute of Food and Agriculture of the U.S. Department of Agriculture (http://nifa.usda.gov; 2018-67011-28025 to AR and 2018-67015-28199 to AZ). Illumina and PacBio sequencing were carried out by the DNA Technologies and Expression Analysis Cores at the UC Davis Genome Center, supported by NIH Shared Instrumentation Grant 1S10OD010786-01. Parts of this research project was conducted using computational resources at the UC Davis Genome Center Bioinformatics Core High Performance Compute Cluster, and at the Maryland Advanced Research Computing Center (MARCC) and at the Computational Biology Core, Institute for Systems Genomics, University of Connecticut. Professor Stephen C. Sillett and his group at Humboldt State University made this project possible by climbing SEGI 21 and obtaining cones and foliage for sequencing. Marc Crepeau's skill at megagametophyte dissection, DNA extraction, and library prep is well appreciated. Bill Libby provided valuable support for this project, in the form of scientific guidance and both enthusiasm and expertise in giant sequoia genetics. Thank you to Sequoia/Kings Canyon National Park for allowing us to conduct research inside the park. Funding Information: This project was supported by a grant from Save The Redwoods League for the Redwood Genome Project (to DN), and by grants from the National Institute of Food and Agriculture of the U.S. Department of Agriculture (http://nifa.usda.gov; 2018-67011-28025 to AR and 2018-67015-28199 to AZ). Illumina and PacBio sequencing were carried out by the DNA Technologies and Expression Analysis Cores at the UC Davis Genome Center, supported by NIH Shared Instrumentation Grant 1S10OD010786-01. Parts of this research project was conducted using computational resources at the UC Davis Genome Center Bioinformatics Core High Performance Compute Cluster, and at the Maryland Advanced Research Computing Center (MARCC) and at the Computational Biology Core, Institute for Systems Genomics, University of Connecticut. Professor Stephen C. Sillett and his group at Humboldt State University made this project possible by climbing SEGI 21 and obtaining cones and foliage for sequencing. Marc Crepeau{\textquoteright}s skill at megagametophyte dissection, DNA extraction, and library prep is well appreciated. Bill Libby provided valuable support for this project, in the form of scientific guidance and both enthusiasm and expertise in giant sequoia genetics. Thank you to Sequoia/Kings Canyon National Park for allowing us to conduct research inside the park. Publisher Copyright: Copyright {\textcopyright} 2020 Scott et al.",
year = "2020",
month = nov,
doi = "10.1534/g3.120.401612",
language = "English (US)",
volume = "10",
pages = "3907--3919",
journal = "G3: Genes, Genomes, Genetics",
issn = "2160-1836",
publisher = "Genetics Society of America",
number = "11",
}