Note:

• Follow examples of the gene ID format: AT2G14210 (Arabidopsis), FvH4_2g11353 (strawberry), Rid.02g074810 (raspberry), Prupe.1G489400 (peach), and MD02G1025500 (apple)

Note:

• The comparable stages among species are provided in the 'More - Tissue & Stage Comparison' page.


• Please notice the scale bars that are different for each gene.

Note:

• TissueEnrich (Jain et al., 2019) was used to identify the genes that are specifically expressed in a tissue at certain stage (Tissue&Stage-Enriched) or the genes that are expressed in a specific tissue at multiple stages (Tissue-Enriched). Tissue- and stage-enriched genes are the genes with TPM >= 1 whose expression level in a particular tissue at a certain stage is at least two/five-fold higher than those in all other conditions (condition: combination of tissue and stage). Tissue-enriched genes are the genes that are not counted as tissue- and stage-enriched genes and are the genes with TPM >= 1 whose expression levels in a particular tissue at multiple stages are at least two/five-fold higher than those in all other conditions.


• Strawberry fruit development: Stage 1(0 DPA), Stage 2(2-4 DPA), Stage 3(6-7 DPA), Stage 4(8-10 DPA), and Stage 5(10-13 DPA)


• The downloaded table includes the information about the gene's best Arabidopsis BLAST hit (Arabidopsis gene ID, BLAST e-value, gene symbol, and gene description). The table also includes the expression of the gene in different samples. The explanation of the sample names can be found in the 'Sample Tables' section of the 'Download' page. And the expression values are TPM. The table of the tissue-enriched genes has an extra column called 'EnrichedStage'. This column shows the stages at which the genes are specifically expressed in a tissue.

Gene Tables:

Include the BLAST, OrthoFinder and consensus network results

Expression Tables:

Include the gene expression values (TPM)

Sample Tables:

Include the sample description

Red raspberry (Rubus idaeus) genome files:

Include the genome assembly FASTA file, genome annotation GFF file, transcript FASTA file, and protein FASTA file

Note:

The genomes of the four Rosaceae species can be found in GDR: Prunus persica v2.0.a1 , Malus domestica GDDH13 v1.1 , Fragaria vesca v4.0.a2 , and Rubus idaeus Joan J Genome v2.0

Orthogroup Table:

Include the ortholog information from 6 species (peach, apple, strawberry, red raspberry, black raspberry, and arabidopsis). All the data on the website are from red raspberry. Black raspberry is only used to help with the ortholog identification by OrthoFinder.

References

• Hollender, C. A., Geretz, A. C., Slovin, J. P., & Liu, Z. (2012). Flower and early fruit development in a diploid strawberry, Fragaria vesca. Planta, 235, 1123-1139.


• Kang, C., Darwish, O., Geretz, A., Shahan, R., Alkharouf, N., & Liu, Z. (2013). Genome-scale transcriptomic insights into early-stage fruit development in woodland strawberry Fragaria vesca. The Plant Cell, 25(6), 1960-1978.


• Li, M., Galimba, K., Xiao, Y., Dardick, C., Mount, S. M., Callahan, A., & Liu, Z. (2022). Comparative transcriptomic analysis of apple and peach fruits: insights into fruit type specification. The Plant Journal, 109(6), 1614-1629.


• Liu, Z., Ma, H., Jung, S., Main, D., & Guo, L. (2020). Developmental mechanisms of fleshy fruit diversity in Rosaceae. Annual review of plant biology, 71, 547-573.


• Zhou, J., Li, M., Li, Y., Xiao, Y., Luo, X., Gao, S., Sadowski, N., Timp, W., Callahan, A., Mount, S. M., & Liu, Z. (2023) Comparative analyses of red raspberry and strawberry fruit development reveal diverse mechanisms for different fruit types. Plant Physiology (accepted)

Q & A

1. What reference transcriptomes were used for gene expression quantification?

RNA-Seq data of the four Rosaceae species were mapped against Prunus persica v2.0.a1 , Malus domestica GDDH13 v1.1 , Fragaria vesca v4.0.a2 , and Rubus idaeus Joan J Genome v2.0 reference transcriptomes.

How-To Videos

1. How to identify the Rosaceae orthologs of an Arabidopsis gene?

Please cite the following reference if you use the ROFT database

• Li, M., Mount, S. M., & Liu, Z. (2023). Rosaceae Fruit Transcriptome Database (ROFT)-a useful genomic resource for comparing fruits of apple, peach, strawberry, and raspberry. Horticulture Research, uhad240.

The RNA-Seq data were collected from the following papers

• Kang, C., Darwish, O., Geretz, A., Shahan, R., Alkharouf, N., & Liu, Z. (2013). Genome-scale transcriptomic insights into early-stage fruit development in woodland strawberry Fragaria vesca. The Plant Cell, 25(6), 1960-1978.


• Li, M., Galimba, K., Xiao, Y., Dardick, C., Mount, S. M., Callahan, A., & Liu, Z. (2022). Comparative transcriptomic analysis of apple and peach fruits: insights into fruit type specification. The Plant Journal, 109(6), 1614-1629.


• Zhou, J., Li, M., Li, Y., Xiao, Y., Luo, X., Gao, S., ... & Liu, Z. (2023). Comparison of red raspberry and wild strawberry fruits reveals mechanisms of fruit type specification. Plant Physiology, 193(2), 1016-1035.

Other recent related papers

• Shahan, R., Zawora, C., Wight, H., Sittmann, J., Wang, W., Mount, S. M., & Liu, Z. (2018). Consensus coexpression network analysis identifies key regulators of flower and fruit development in wild strawberry. Plant physiology, 178(1), 202-216.


• Galimba, K. D., Bullock, D. G., Dardick, C., Liu, Z., & Callahan, A. M. (2019). Gibberellic acid induced parthenocarpic 'Honeycrisp'apples (Malus domestica) exhibit reduced ovary width and lower acidity. Horticulture research, 6.


• Shahan, R., Li, D., & Liu, Z. (2019). Identification of genes preferentially expressed in wild strawberry receptacle fruit and demonstration of their promoter activities. Horticulture Research, 6.


• Li, Y., Pi, M., Gao, Q., Liu, Z., & Kang, C. (2019). Updated annotation of the wild strawberry Fragaria vesca V4 genome. Horticulture research, 6.


• Zhou, J., Li, D., Wang, G., Wang, F., Kunjal, M., Joldersma, D., & Liu, Z. (2020). Application and future perspective of CRISPR/Cas9 genome editing in fruit crops. Journal of integrative plant biology, 62(3), 269-286.


• Zhou, J., Sittmann, J., Guo, L., Xiao, Y., Huang, X., Pulapaka, A., & Liu, Z. (2021). Gibberellin and auxin signaling genes RGA1 and ARF8 repress accessory fruit initiation in diploid strawberry. Plant Physiology, 185(3), 1059-1075.


• Liu, Z., Ma, H., Jung, S., Main, D., & Guo, L. (2020). Developmental mechanisms of fleshy fruit diversity in Rosaceae. Annual review of plant biology, 71, 547-573.


• Li, M., Xiao, Y., Mount, S., & Liu, Z. (2021). An atlas of genomic resources for studying Rosaceae fruits and ornamentals. Frontiers in Plant Science, 12, 644881.


• Liu, T., Li, M., Liu, Z., Ai, X., & Li, Y. (2021). Reannotation of the cultivated strawberry genome and establishment of a strawberry genome database. Horticulture research, 8.


• Alger, E. I., Platts, A. E., Deb, S. K., Luo, X., Ou, S., Cao, Y., ... & Edger, P. P. (2021). Chromosome-Scale genome for a Red-Fruited, perpetual flowering and runnerless woodland strawberry (Fragaria vesca). Frontiers in genetics, 12, 671371.


• Joldersma, D., Sadowski, N., Timp, W., & Liu, Z. (2022). Assembly and annotation of Fragaria vesca'Yellow Wonder'genome, a model diploid strawberry for molecular genetic research. Fruit Research, 2(1), 1-5.


• Guo, L., Luo, X., Li, M., Joldersma, D., Plunkert, M., & Liu, Z. (2022). Mechanism of fertilization-induced auxin synthesis in the endosperm for seed and fruit development. Nature Communications, 13(1), 3985.


• Luo, X., Plunkert, M., Teng, Z., Mackenzie, K., Guo, L., Luo, Y., ... & Liu, Z. (2023). Two MYB activators of anthocyanin biosynthesis exhibit specialized activities in petiole and fruit of diploid strawberry. Journal of Experimental Botany, 74(5), 1517-1531.


• Liu, Z., Liang, T., & Kang, C. (2023) Fruit quality regulation in strawberry: advances, challenges, and opportunities. Plant Physiology (revision under review)

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