Chromosome-scale genome for a red-fruited, perpetual flowering and runnerless woodland strawberry (Fragaria vesca)

Authors: ALGER, ELIZABETH - Michigan State University; PLATTS, ADRIAN - Michigan State University; DEB, SONTOSH - University Of Alabama; LUO, XI - University Of Maryland; OU, SHUJUN - Iowa State University; Hummer, Kim; XIONG, ZHIYONG - Inner Mongolia University; KNAPP, STEVE - University Of California; LIU, ZHONGCHI - University Of Maryland; MCKAIN, MICHAEL - University Of Alabama; EDGER, PATRICK - Michigan State University

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/31/2021
Publication Date: 7/16/2021
Citation: Alger, E.I., Platts, A.E., Deb, S.K., Luo, X., Ou, S., Hummer, K.E., Xiong, Z., Knapp, S.J., Liu, Z., Mckain, M.R., Edger, P.P. 2021. Chromosome-scale genome for a red-fruited, perpetual flowering and runnerless woodland strawberry (Fragaria vesca). Frontiers in Genetics. 12. Article 671371. https://doi.org/10.3389/fgene.2021.671371.
DOI: https://doi.org/10.3389/fgene.2021.671371

Interpretive Summary: Strawberry is emerging as an important model system for the Rose family, Research on strawberry has largely utilized the woodland strawberry species, the alpine strawberry, due to it’s small chromosome size, short generation time, and ease of transformation. In addition to its ease of use, this strawberry is also the closest extant relative of the diploid progenitor for the dominant subgenome in the cultivated garden strawberry, which has 8 sets of chromosomes, making it an useful organism for studying high numbers of chromosome sets. The strawberry“Hawaii-4” has been widely used in previous genetic studies. The diverse accessions of this species exhibit a wide range of traits, including several such as flowering time, fruit color, and runner production that are relevant to breeding programs. In strawberry, the growing tip can develop into either daughter-plant producing runners or into fruit-bearing shoots. Strawberry cultivars are maintained and grown from these runners rather than from seeds, because runners allow for easy clonal propagation. However, runnering is also associated with a decrease in fruit yield as increased runner production reduces the number of fruit-bearing shoots. Therefore, while the fruit is the consumer product, runners are also essential for strawberry propagation. Beyond influencing fruit yields, runners can also grow quickly and abundantly, resulting in the need for frequent trimming for plant maintenance. With these considerations, better understanding genetic factors influencing the switch between inflorescence and runner growth would be valuable. The objective of this paper was to expand the model species by providing a second high quality complete gene sequence from an accession with different phenotypic traits compared to the current high quality F. vesca Hawaii-4 genome. To accomplish this, we combined longread Oxford Nanopore sequencing and high coverage short read Illumina sequencing. We generated 2.3million Nanopore reads collectively, totalling over 30 Gb, providing >120x coverage for the CFRA 2339 genome, and exhibiting an N50 length of 34.1kb and a maximum length of 311kb. The raw Nanopore reads were then corrected and assembled using the Canu assembler (Koren et al., 2017). Strawberrry species has seven base chromosomes. Chromosomes 1, 5, and 7 were captured by a single group, 2, 4, and 6 were split between two groups, and chromosome 3 was split among three groups, thus requiring minimal further sequencing determinations. RagTag was used to correct misassemblies and merge scaffolds into pseudomolecules using Hawaii-4 as a reference and then polished with two rounds of Pilon with over 35.5 Gb Illumina data. The final assembly spanned 229.5Mb across 311 contigs with an N50 length of 29.6Mb. Seven pseudomolecules were obtained for the CFRA 2339 genome. The gene sequence described here for the runnerless strawberry PI 698244 will be a valuable new resource for the strawberry community. Furthermore, being runnerless, PI 698244 (CFRA 2339) does not require the frequent trimming that is necessary for most other accessions, but can be propagated easily by splitting and replanting the crown. The strawberry clone shares the perpetual flowering trait with Hawaii-4, leading to high flower and fruit production.

Technical Abstract: Strawberry (Fragaria L.) is emerging as an important model system for the family Rosaceae, Fragaria research has largely utilized the woodland strawberry species, Fragaria vesca, due to it’s small size, short generation time, and ease of transformation. In addition to its ease of use, F. vesca is also the closest extant relative of the diploid progenitor for the dominant subgenome in the allo-octoploid cultivated garden strawberry (F. × ananassa) making it an useful organism for studying polyploidy in cultivated strawberry The F. vesca accession “Hawaii-4” has been widely used in previous genetic studies. The diverse accessions of F. vesca exhibit a wide range of phenotypes, including several traits relevant to breeding programs such as flowering time, fruit color, and runner production. In strawberry, the axillary meristem can develop into either daughter-plant producing runners or into fruit-bearing shoots. Strawberry cultivars are maintained and grown from these runners rather than from seeds, as runners allow for easy clonal propagation. However, runnering is also associated with a decrease in fruit yield as increased runner production reduces the number of fruit-bearing shoots. Therefore, while the fruit is the consumer product, runners are also essential for strawberry propagation. Beyond influencing fruit yields, runners can also grow quickly and abundantly, resulting in the need for frequent trimming for plant maintenance. With these considerations, better understanding genetic factors influencing the switch between inflorescence and runner growth would be a valuable. The aim of this paper was to expand the resources of the model species F. vesca by providing a second high quality genome from an accession with different phenotypic traits compared to the current high quality F. vesca Hawaii-4 genome. To accomplish this, we combined longread Oxford Nanopore sequencing and high coverage short read Illumina sequencing. We generated 2.3million Nanopore reads collectively, totalling over 30 Gb, providing >120x coverage for the CFRA 2339 genome, and exhibiting an N50 length of 34.1kb and a maximum length of 311kb. The raw Nanopore reads were then corrected and assembled using the Canu assembler (Koren et al., 2017). Fragaria vesca has seven chromosomes. Chromosomes 1, 5, and 7 were captured by a single contig, 2, 4, and 6 were split between two contigs, and chromosome 3 was split among three contigs, thus requiring minimal further scaffolding. RagTag was then used to correct misassemblies and merge scaffolds into pseudomolecules using Hawaii-4 as a reference and then polished with two rounds of Pilon with over 35.5 Gb Illumina data. The final assembly spanned 229.5Mb across 311 contigs with an N50 length of 29.6Mb. Seven pseudomolecules were obtained for the CFRA 2339 genome. The genome described here for F. vesca CFRA 2339 will be a valuable new resource for the strawberry community. Furthermore, being runnerless, CFRA 2339 does not require the frequent trimming that is necessary for most other accessions, but can still be propagated easily by splitting and replanting the crown. The accession shares the perpetual flowering trait with Hawaii-4, leading to high flower and fruit production.