Fol. Biol. 2023, 69, 99-106

https://doi.org/10.14712/fb2023069030099

De novo Transcriptome Analysis and Gene Expression Profiling of Corylus Species

Salih Ulu1, Zehra Omeroglu Ulu1,2, Aysun Akar3, Nehir Ozdemir Ozgenturk1

1Department of Molecular Biology and Genetics, Faculty of Art and Science, Yildiz Technical University, Istanbul, Turkey
2Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
3Hazelnut Research Institution, Ministry of Food, Agriculture and Livestock, Giresun, Turkey

Received July 2023
Accepted November 2023

References

1. Andrews, S., Krueger, F., Segonds-Pichon, A. et al. (2012) FastQC. Babraham Institute, Babraham, UK.
2. Ayan, S., Aydınözü, D., Yer, E. N. et al. (2016) Turkish Filbert (Corylus colurna L.): a new distribution area in Northwestern Anatolia Forests (Provinces of Müsellimler, Tunuslar in Ağlı, Kastamonu/Turkey). Biol. Divers. Conserv. 9, 128-135. (in Turkish)
3. Ayan, S., Ünalan, E., İslam, A. et al. (2018) Kastamonu yöresinde yetişen Türk fındığının (Corylus colurna L.) yağ ve protein içeriği. Artvin Çoruh Üniversitesi Orman Fakültesi Dergisi 19, 1-7. (in Turkish) <https://doi.org/10.17474/artvinofd.296580>
4. Ban, Y.-W., Roy, N. S., Yang, H. et al. (2019) Comparative transcriptome analysis reveals higher expression of stress and defense responsive genes in dwarf soybeans obtained from the crossing of G. max and G. soja. Genes Genomics 41, 1315-1327. <https://doi.org/10.1007/s13258-019-00846-2>
5. Beier, S., Thiel, T., Münch, T. et al. (2017) MISA-web: a web server for microsatellite prediction. Bioinformatics 33, 2583-2585. <https://doi.org/10.1093/bioinformatics/btx198>
6. Benov, L., Georgiev, N. (1994) The antioxidant activity of flavonoids isolated from Corylus colurna. Phythother. Res. 8, 92-94. <https://doi.org/10.1002/ptr.2650080208>
7. Boccacci, P., Akkak, A., Botta, R. (2006) DNA typing and genetic relations among European hazelnut (Corylus avellana L.) cultivars using microsatellite markers. Genome 49, 598-611. <https://doi.org/10.1139/g06-017>
8. FAO (2020) Global Forest Resources Assessment 2020 Main Report. Available at: https://www.fao.org/3/ca9825en/ca9825en.pdf
9. Fu, L., Niu, B., Zhu, Z. et al. (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150-3152. <https://doi.org/10.1093/bioinformatics/bts565>
10. Haas, B. J., Papanicolaou, A., Yassour, M. et al. (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat. Protoc. 8, 1494-1512. <https://doi.org/10.1038/nprot.2013.084>
11. Han, Y., Gao, S., Muegge, K. et al. (2015) Advanced applications of RNA sequencing and challenges. Bioinform. Biol. Insights 9 (Suppl. 1), BBI.S28991. <https://doi.org/10.4137/BBI.S28991>
12. İslam, A. (2020) Fındık ıslahında gelişmeler. Akademik Ziraat Dergisi. 8, 167-174. (in Turkish) <https://doi.org/10.29278/azd.667662>
13. Jo, Y., Lian, S., Cho, J. K. et al. (2015) De novo transcriptome assembly of two different Prunus salicina cultivars. Genom. Data 6, 262-263. <https://doi.org/10.1016/j.gdata.2015.10.015>
14. Kahraman, K., Lucas, S. J. (2019) Comparison of different annotation tools for characterization of the complete chloroplast genome of Corylus avellana cv Tombul. BMC Genomics 20, 874. <https://doi.org/10.1186/s12864-019-6253-5>
15. Kavas, M., Kurt Kızıldoğan, A., Balık, H. İ. (2019) Gene expression analysis of bud burst process in European hazelnut (Corylus avellana L.) using RNA-Seq. Physiol. Mol. Biol. Plants 25, 13-29. <https://doi.org/10.1007/s12298-018-0588-2>
16. Li, Q., Zhao, T., Liang, L. et al. (2020) Molecular cloning and expression analysis of hybrid hazelnut (Corylus heterophylla × Corylus avellana) ChaSRK1/2 genes and their homologs from other cultivars and species. Gene 756, 144917. <https://doi.org/10.1016/j.gene.2020.144917>
17. Livak, K. J., Schmittgen, T. D. (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25, 402-408. <https://doi.org/10.1006/meth.2001.1262>
18. Lucas, S. J., Kahraman, K., Avşar, B. et al. (2021) A chromosome‐scale genome assembly of European hazel (Corylus avellana L.) reveals targets for crop improvement. Plant J. 105, 1413-1430. <https://doi.org/10.1111/tpj.15099>
19. McGarvey, P., Huang, J., McCoy, M. et al. (2020) De novo assembly and annotation of transcriptomes from two cultivars of Cannabis sativa with different cannabinoid profiles. Gene 762, 145026. <https://doi.org/10.1016/j.gene.2020.145026>
20. Peona, V., Weissensteiner, M. H., Suh, A. (2018) How complete are “complete” genome assemblies? An avian perspective. Mol. Ecol. Resour. 18, 1188-1195. <https://doi.org/10.1111/1755-0998.12933>
21. Raghavan, V., Kraft, L., Mesny, F. et al. (2022) A simple guide to de novo transcriptome assembly and annotation. Brief. Bioinform. 23, 1-30. <https://doi.org/10.1093/bib/bbab563>
22. Riethmüller, E., Tóth, G., Alberti, A. et al. (2014) Antioxidant activity and phenolic composition of Corylus colurna. Nat. Prod. Commun. 9, 679-682.
23. Rowley, E. R., Fox, S. E., Bryant, D. W. et al. (2012) Assembly and characterization of the European hazelnut “Jefferson” transcriptome. Crop Sci. 52, 2679-2686. <https://doi.org/10.2135/cropsci2012.02.0065>
24. Rowley, E. R., VanBuren, R., Bryant, D. W. et al. (2018) A draft genome and high-density genetic map of European hazelnut (Corylus avellana L.). bioRxiv. <https://doi.org/10.1101/469015>
25. Sullivan, G. T., Ozman-Sullivan, S. K., Akbasli, O. et al. (2014) A tribute to the hazelnut plant (Corylus spp.) – the multiple uses of nature’s magnificent gifts. Acta Hortic. 1052, 371-376. <https://doi.org/10.17660/ActaHortic.2014.1052.51>
26. Tanhuanpää, P., Heinonen, M., Bitz, L. et al. (2019) Genetic diversity and structure in the northern populations of European hazelnut (Corylus avellana L.). Genome 62, 537-548. <https://doi.org/10.1139/gen-2018-0193>
27. Thakur, O., Randhawa, G. S. (2018) Identification and characterization of SSR, SNP and InDel molecular markers from RNA-Seq data of guar (Cyamopsis tetragonoloba, L. Taub.) roots. BMC Genomics 19, 951. <https://doi.org/10.1186/s12864-018-5205-9>
28. Thole, V., Bassard, J.-E., Ramírez-González, R. et al. (2019) RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics. BMC Genomics 20, 995. <https://doi.org/10.1186/s12864-019-6183-2>
29. Van Bel, M., Proost, S., Van Neste, C. et al. (2013) TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes. Genome Biol. 14, R134. <https://doi.org/10.1186/gb-2013-14-12-r134>
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