Published November 5, 2021 | Version 1
Dataset Open

FASTA file containing the MYB encoding gene An2-like and Ant1 coding sequences corresponding to wild and cultivated tomato accessions

Authors/Creators

  • 1. The Ohio State University, Department of Horticulture and Crop Science

Description

The coding sequence (CDS) of the MYB encoding genes Ant1 and An2-like. Sequences were retrieved from regions corresponding to the Aft locus from Solanum galapagense accession LA1141, S. lycopersicum variety OH8245, and  84 tomato accessions published as part of The 100 Tomato Genome Sequencing Consortium (The 100 Tomato Genome Sequencing Consortium et al., 2014). Sequences were compared to available CDS available from the Sol genomics network (SGN) and the National Center for Biotechnology Information. The CDS was retrieved from S. lycopersicum variety Indigo Rose [MN433087 (Yan et al., 2020)], S. lycopersicum accession LA1996 [MN242011.1, EF433417.1( Sapir et al., 2008; Colanero et al., 2020)], and S. chilense accession LA1930 [MN242012.1 (Colanero et al., 2020)], The orthologous CDS corresponding to the Aft MYB encoding genes from Solanum tuberosum L. Group Phureja clone DM1-3 genome (PGSC DM v4.03 Pseudomolecules) was retrieved from the Potato Genome Sequence Consortium (PGSC: Potato Genome Sequencing Consortium et al., 2011), and the Capsicum annum cv. CM334 genome was retrieved from Capsicum annuum cv CM334 genome chromosome release 1.55 (Hulse-Kemp et al. 2018). These CDS were obtained using the Basic Local Alignment Search Tool (BLAST) tool available from the Sol Genomics Network (SGN) (available at https://solgenomics.net/tools/blast/). Comparison of syntenic chromosomal regions using known positions of tomato, potato, and pepper markers with comparative map viewer from  SGN: (available at https://solgenomics.net/cview) on chromosome 10, was used as a quality check for S. tuberosom and C. annuum. Orthologous CDS corresponding to Salvia miltiorrhiza, Arabidopsis thaliana, [NM_105308.2, NM_105310.4 (Teng et al., 2005, Cominelli et al., 2008; Beradini et al., 2015)] were chosen based on tomato Aft sequence homology and gene annotations of positive R2R3 MYB regulation of anthocyanin. The CDS corresponding to the Aft genes were retrieved from the CDS reference genomes available from the Sol Genomics Network SGN: Tomato Genome CDS (ITAG release 4.0), Potato PGSC DM v3.4 CDS sequences, Capsicum annuum cv CM334 Genome CDS (release 1.55), or from the National Center for Biotechnology Information (NCBI: https://www.ncbi.nlm.nih.gov) reference sequences (RefSeq) section of the Genbank records. When accessed from Genank records, the CDS sequence was extracted from the “features” section and exported as a FASTA file.

Notes

Raw FASTA file

Files

Files (136.5 kB)

Name Size Download all
md5:cd7045f405ca98cd58b6ae5fac4cb030
136.5 kB Download

Additional details

References

  • Berardini T Z, Reiser L, Li D, Mezheritsky Y, Muller R, Strait E, Huala E. 2015. The Arabidopsis information resource: making and mining the "gold standard" annotated reference plant genome. Genesis 53, 474-485.
  • Colanero, S., Tagliani, A., Perata, P., & Gonzali, S. (2020). Alternative splicing in the anthocyanin fruit gene encoding an R2R3 MYB transcription factor affects anthocyanin biosynthesis in tomato fruits. Plant communications, 1(1), 100006.
  • Cominelli E, Gusmaroli G, Allegra D, Galbiati M, Wade HK, Jenkins GI, Tonelli C. 2008. Expression analysis of anthocyanin regulatory genes in response to different light qualities in Arabidopsis thaliana. Journal of plant physiology 165, 886-894.
  • Hosmani, P. S., Flores-Gonzalez, M., van de Geest, H., Maumus, F., Bakker, L. V., Schijlen, E., ... & Saha, S. (2019). An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps. BioRxiv, 767764.
  • Hulse-Kemp AM, Maheshwari S, Stoffel K, et al. 2018. Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library. Horticulture research 5, 1-13.
  • Li C, Lu S. 2014. Genome-wide characterization and comparative analysis of R2R3-MYB transcription factors shows the complexity of MYB-associated regulatory networks in Salvia miltiorrhiza. BMC genomics 15, 1-12.
  • PGS Consortium. 2011. Genome sequence and analysis of the tuber crop potato. Nature 475, 189-195.
  • Sapir M, Oren-Shamir M, Ovadia R, Reuveni M, Evenor D, Tadmor Y, Nahon S, Shlomo H, Chen L, Meir A, Levin I. 2008. Molecular aspects of Anthocyanin fruit tomato in relation to high pigment-1. Journal of Heredity 99, 292-303.
  • Teng S, Keurentjes J, Bentsink L, Koornneef M, Smeekens S. 2005. Sucrose-specific induction of anthocyanin biosynthesis in Arabidopsis requires the MYB75/PAP1 gene. Plant physiology 139, 1840- 1852.
  • Yan, S., Chen, N., Huang, Z., Li, D., Zhi, J., Yu, B., ... & Qiu, Z. (2020). Anthocyanin Fruit encodes an R2R3‐MYB transcription factor, SlAN2‐like, activating the transcription of SlMYBATV to fine‐tune anthocyanin content in tomato fruit. New Phytologist, 225(5), 2048-2063.
  • 100 Tomato Genome Sequencing Consortium, Aflitos, S., Schijlen, E., de Jong, H., de Ridder, D., Smit, S., ... & Peters, S. (2014). Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole‐genome sequencing. The Plant Journal, 80(1), 136-148.