Tracing the Diploid Ancestry of the Cultivated Octoploid Strawberry

Feng, Chao; Wang, Jing; Harris, AJ; Folta, Kevin M.; Zhao, Mizhen; Kang, Ming

doi:10.1093/molbev/msaa238

Cited by 60 publications

(60 citation statements)

References 50 publications

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“…Edger et al (2019) [13] suggested that the possible progenitors of strawberry were F. vesca, F. iinumae, F. nipponica, and F virdis based on sequence similarity with the wild Fragaria species. However, later reports suggested that F. vesca and F. iinumae were possible progenitors, whereas F. nipponica and F. virdis were not [17,34,35]. The result of our clustering analysis also denied the possibility of F. nipponica and F. virdis as progenitors of the strawberry genome.…”

Section: Assignment Of Chromosome Numbers and Subgenome Names To The Pseudomolecule Sequencescontrasting

confidence: 59%

A chromosome-scale strawberry genome assembly of a Japanese variety, Reikou

Shirasawa

Hirakawa

Nakayama

et al. 2021

Preprint

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Cultivated strawberry (Fragaria × ananassa) is an octoploid species (2n = 8x= 56) that is widely consumed around the world as both fresh and processed fruit. In this study, we report a chromosome-scale strawberry genome assembly of a Japanese variety, Reikou. The Illumina short reads derived from paired-end, mate-pair, and 10X Genomics libraries were assembled using Denovo MAGIC 3.0. The generated phased scaffolds consisted of 32,715 sequences with a total length of 1.4 Gb and an N50 length of 3.9 Mb. A total of 63 pseudomolecules including chr0 were created by aligning the scaffolds onto the Reikou S1 linkage maps with the IStraw90 Axiom SNP array and ddRAD-Seq. Meanwhile, genomes of diploid Fragaria species were resequenced and compared with the most similar chromosome-scale scaffolds to investigate the possible progenitor of each subgenome. Clustering analysis suggested that the most likely progenitors were F. vesca and F. iinumae. The phased pseudomolecules were assigned the scaffolds names with Av, Bi, and X, representing sequence similarity with F. vesca (Av), F. iinumae (Bi), and others (X), respectively. The result of a comparison with the Camerosa genome suggested the possibility of subgenome structure differences between the two varieties.

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Section: Assignment Of Chromosome Numbers and Subgenome Names To The Pseudomolecule Sequencescontrasting

confidence: 59%

A chromosome-scale strawberry genome assembly of a Japanese variety, Reikou

Shirasawa

Hirakawa

Nakayama

et al. 2021

Preprint

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“… Liston et al. (2020) and Feng et al. (2021) challenged the validity of two of the closest available surrogates applied in our study ( F. nipponica and F. viridis ).…”

Section: Resultsmentioning

confidence: 71%

“…iinumae -like, which cast serious doubt on the Liston et al. (2020) or Feng et al. (2021) hypotheses.…”

Section: Resultsmentioning

confidence: 99%

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Unraveling the Complex Hybrid Ancestry and Domestication History of Cultivated Strawberry

Hardigan

Lorant

Pincot

et al. 2021

Molecular Biology and Evolution

160

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Cultivated strawberry (Fragaria × ananassa) is one of our youngest domesticates, originating in early eighteenth-century Europe from spontaneous hybrids between wild allo-octoploid species (F. chiloensis and F. virginiana). The improvement of horticultural traits by 300 years of breeding has enabled the global expansion of strawberry production. Here, we describe the genomic history of strawberry domestication from the earliest hybrids to modern cultivars. We observed a significant increase in heterozygosity among interspecific hybrids and a decrease in heterozygosity among domesticated descendants of those hybrids. Selective sweeps were found across the genome in early and modern phases of domestication— 59-76% of the selectively swept genes originated in the three less dominant ancestral subgenomes. Contrary to the tenet that genetic diversity is limited in cultivated strawberry, we found that the octoploid species harbor massive allelic diversity and that Fragaria × ananassa harbors as much allelic diversity as either wild founder. We identified 41.8M subgenome-specific DNA variants among resequenced wild and domesticated individuals. Strikingly, 98% of common alleles and 73% of total alleles were shared between wild and domesticated populations. Moreover, genome-wide estimates of nucleotide diversity were virtually identical in F. chiloensis, F. virginiana, and Fragaria × ananassa (π = 0.0059-0.0060). We found, however, that nucleotide diversity and heterozygosity were significantly lower in modern Fragaria × ananassa populations that have experienced significant genetic gains and have produced numerous agriculturally important cultivars.

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“…Asterisks indicate significant differences at 0.05 level (*) and 0.01 level (**). Feng et al, 2020). Therefore, BR downstream gene expansion may have resulted from gene duplication and WGD.…”

Section: Genome-wide Identification and Characteristics Analysis Of Bmentioning

confidence: 99%

Genome-Wide Identification of Brassinosteroid Signaling Downstream Genes in Nine Rosaceae Species and Analyses of Their Roles in Stem Growth and Stress Response in Apple

Zheng

Yang

et al. 2021

Front. Genet.

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Brassinosteroid signaling downstream genes regulate many important agronomic traits in rice. However, information on such genes is limited in Arabidopsis and Rosaceae species. We identified these genes in Arabidopsis and nine Rosaceae species. They were, respectively, named based on chromosomal locations. Segmental duplication and whole-genome duplication under purifying selection, as determined by Ka/Ks analysis, likely contributed to Rosaceae gene expansion. Apple (Malus domestica), Arabidopsis, and rice genes were generally similar, while several Rosaceae genes differed from their rice homologs in various characteristics, such as gene length, subcellular localization, transmembrane topology, conserved domains, secondary structures, and responses to external signals. The brassinosteroid downstream genes in apple were, respectively, induced or repressed by five phytohormones. Furthermore, these apple downstream genes were differentially expressed in different apple grafting combinations (“Nagafu No. 2”/“Malling 9” and “Nagafu No. 2”/“Nagafu No. 2”) and long–short shoot varieties (“Yanfu No. 6” and “Nagafu No. 2”). Responses of the MdBZR genes to diverse stress signals were examined and candidate hub genes were identified. These findings indicated that several brassinosteroid signaling downstream genes in Rosaceae functionally differed from their rice homologs, and certain apple genes may play roles in plant height and stress responses. This study provided valuable information and presented enriched biological theories on brassinosteroid signaling downstream genes in apple. Identification of such genes serve to help expand apple breeding and growth. This study provides useful information for brassinosteroid signaling downstream genes.

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Tracing the Diploid Ancestry of the Cultivated Octoploid Strawberry

Cited by 60 publications

References 50 publications

A chromosome-scale strawberry genome assembly of a Japanese variety, Reikou

A chromosome-scale strawberry genome assembly of a Japanese variety, Reikou

Unraveling the Complex Hybrid Ancestry and Domestication History of Cultivated Strawberry

Genome-Wide Identification of Brassinosteroid Signaling Downstream Genes in Nine Rosaceae Species and Analyses of Their Roles in Stem Growth and Stress Response in Apple

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