Fragaria x ananassa Camarosa Genome Assembly v1.0 & Annotation v1.0.a1

Publication

Edger PP, Poorten TJ, VanBuren R, Hardigan MA, Colle M, McKain MR, Smith RD, Teresi SJ, Nelson ADL, Wai CM, Alger EI, Bird KA, Yocca AE, Pumplin N, Ou S, Ben-Zvi G, Brodt A, Baruch K, Swale T, Shiue L, Acharya CB, Cole GS, Mower JP, Childs KL, Jiang N, Lyons E, Freeling M, Puzey JR, Knapp SJ. Origin and evolution of the octoploid strawberry genome. Nature genetics. 2019 Feb 25.

About the Assembly

Overview

A near-complete chromosome-scale assembly for cultivated octoploid strawberry (Fragaria × ananassa).

Sequencing, Assembly, and Annotation

The genome of the cultivar 'Camarosa' was sequenced using a combination of short- and long-read approaches, including Illumina (San Diego, CA), 10X Genomics (Pleasanton, CA), and Pacific Biosciences (PacBio; Menlo Park, CA), totaling 615-fold coverage of the genome. Illumina (455-fold coverage) and 10X Genomics (117-fold coverage) data were assembled and scaffolded using the software package DenovoMAGIC3 (NRGene, Nes Ziona, Israel). The genome was further scaffolded to chromosome-scale using Hi-C data (401-fold coverage) in combination with the HiRise pipeline (Dovetail, Santa Cruz, CA), and gap-filled with 43-fold coverage error corrected PacBio reads using PBJelly. The total length of the final assembly is 805,488,706bp distributed across 28 chromosome-level pseudomolecules, representing ~99% of the estimated genome size based on flow cytometry measurements. A genetic map for F. x ananassa was used to correct any mis-assemblies and comparisons to F. vesca to identify homoeologous chromosomes.

108,087 protein-coding genes were annotated along with 30,703 long non-coding RNA (lncRNA) genes, which is divided up into 15,621 long intergenic ncRNAs (lincRNAs), 9,265 antisense overlapping transcripts (or AOT-lncRNAs), and 5,817 sense overlapping transcripts (or SOT123 lncRNAs). Gene annotation and genome assembly quality were evaluated using the Benchmarking Universal Single-Copy Orthologs V2 (BUSCO) method. Most (99.17%) of the 1,440 core genes in the embryophyta dataset were identified in the annotation, supporting a high-quality genome assembly. The repetitive components of the nuclear genome was annotated using a custom repeat library approach, including DNA transposons, long-terminal-repeat retrotransposons (LTR-RTs; e.g., Copia and Gypsy), and non-LTR retrotransposons. TE related sequences make up ~36% of the total genome assembly, with LTR-RT being the most abundant (~28%). The plastid and mitochondrial genomes were also assembled, annotated, and verified for completeness.