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.

Chromosome-level genome of Himalayan yew provides insights into the origin and evolution of the paclitaxel biosynthetic pathway

“…Long terminal repeat retrotransposons (LTR-RTs) were identified by LTR_retriever (Ou and Jiang, 2018), and all LTR-RTs were further classified by TEsorter (https://github.com/ zhangrengang/TEsorter). Second, the annotation of protein-coding genes mainly followed the gene annotation of the Giant Sequoia genome (Scott et al, 2020). The main steps included soft-masking of repetitive regions, de novo annotating the genome using Braker (Hoff et al, 2019), assembling and annotating RNA-seq data, annotating the genome based on the homologous protein evidence, and combining different annotation methods using EVM (Haas et al, 2008).…”

Breeding for Climate Change Resilience: A Case Study of Loblolly Pine (Pinus taeda L.) in North America

“…In recent years, reduced sequencing cost and high throughput systems have increased the available transcriptome datasets and the number of scientists who attempt to sequence and assemble complex tree genomes. Reference genome sequence assemblies have been published for ten species of gymnosperms: Picea abies (Norway spruce) (Nystedt et al, 2013), Picea glauca (white spruce) (Birol et al, 2013;Warren et al, 2015), Pinus taeda (loblolly pine) (Neale et al, 2014;Wegrzyn et al, 2014;Zimin et al, 2014), Pinus lambertiana (sugar pine) (Stevens et al, 2016), Ginkgo biloba (ginkgo) (Guan et al, 2016), Pseudotsuga menziesii (Douglas fir) (Neale et al, 2017), Gnetum montanum (Wan et al, 2018), Larix sibirica (Siberian larch) (Kuzmin et al, 2019), Abies alba (European silver fir) (Mosca et al, 2019), and Sequoiadendron giganteum (giant sequoia) (Scott et al, 2020). The long term goal of plant genomic studies is to accelerate our understanding of the networks involved in both the normal-and the stress-functioning of the organisms, thus accelerating the breeding process.…”

Current applications and future promise of genetic/genomic data for conservation in an Aotearoa New Zealand context

“…With improving technologies and decreasing costs, long-read sequencing technologies are becoming more accessible. Long-read sequencing can produce reads tens of thousands of base pairs long, and is considered essential for assembly of large or complex genomes, such as those species with polyploid or highly repetitive genomes (Scott et al, 2020). Long reads act as a foundation for genome assembly to dramatically improve our ability to assemble high-quality genomes and ensure that a greater proportion of the genome can be assembled more accurately than with short-read sequencing alone (Figure 5; Morin et al, 2020).…”