118
Views
0
CrossRef citations to date
0
Altmetric
Short Communication

Genome survey and identification of key genes associated with freezing tolerance in genomic draft of hexaploid wild Camellia oleifera

, , , & ORCID Icon
Pages 326-335 | Received 09 Aug 2023, Accepted 05 Oct 2023, Published online: 05 Nov 2023

References

  • Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403–410. https://doi.org/10.1016/s0022-2836(05)80360-2
  • Beier, S., Thiel, T., Munch, T., Scholz, U., Mascher, M., & Valencia, A. (2017). MISA-web: A web server for microsatellite prediction. Bioinformatics, 33(16), 2583–2585. https://doi.org/10.1093/bioinformatics/btx198
  • Bohra, A., Kilian, B., Sivasankar, S., Caccamo, M., Mba, C., McCouch, S. R., & Varshney, R. K. (2022). Reap the crop wild relatives for breeding future crops. Trends in Biotechnology, 40(4), 412–431. https://doi.org/10.1016/j.tibtech.2021.08.009
  • Cantalapiedra, C. P., Hernández-Plaza, A., Letunic, I., Bork, P., Huerta-Cepas, J., & Tamura, K. (2021). eggNOG-mapper v2: Functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Molecular Biology and Evolution, 38(12), 5825–5829. https://doi.org/10.1093/molbev/msab293
  • Chatterjee, R., & Vinson, C. (2012). CpG methylation recruits sequence specific transcription factors essential for tissue specific gene expression. Biochimica Et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 1819(7), 763–770. https://doi.org/10.1016/j.bbagrm.2012.02.014
  • Chen, Y. X., Chen, Y. S., Shi, C. M., Huang, Z. B., Zhang, Y., Li, S. K., Li, Y., Ye, J., Yu, C., Li, Z., Zhang, X. Q., Wang, J., Yang, H. M., Fang, L., & Chen, Q. (2017). Soapnuke: A MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. GigaScience, 7(1), 1–6. https://doi.org/10.1093/gigascience/gix120
  • Cui, X. Y., Li, C. H., Qin, S. Y., Huang, Z. B., Gan, B., Jiang, Z. W., Huang, X. M., Yang, X. Q., Li, Q., Xiang, X. G., Chen, J. K., Zhao, Y., & Rong, J. (2022). High-throughput sequencing-based microsatellite genotyping for polyploids to resolve allele dosage uncertainty and improve analyses of genetic diversity, structure and differentiation: A case study of the hexaploid camellia oleifera. Molecular Ecology Resources, 22(1), 199–211. https://doi.org/10.1111/1755-0998.13469
  • Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S. A., Davies, R. M., & Li, H. (2021). Twelve years of SAMtools and BCFtools. GigaScience, 10(2), 1–4. https://doi.org/10.1093/gigascience/giab008
  • Gong, W., Xiao, S., Wang, L., Liao, Z., Chang, Y., Mo, W., Hu, G., Li, W., Zhao, G., Zhu, H., Hu, X., Ji, K., Xiang, X., Song, Q., Yuan, D., Jin, S., & Zhang, L. (2022). Chromosome-level genome of Camellia lanceoleosa provides a valuable resource for understanding genome evolution and self-incompatibility. The Plant Journal: For Cell and Molecular Biology, 110(3), 881–898. https://doi.org/10.1111/tpj.15739
  • Gremme, G., Brendel, V., Sparks, M. E., & Kurtz, S. (2005). Engineering a software tool for gene structure prediction in higher organisms. Information and Software Technology, 47(15), 965–978. https://doi.org/10.1016/j.infsof.2005.09.005
  • Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013). QUAST: Quality assessment tool for genome assemblies. Bioinformatics, 29(8), 1072–1075. https://doi.org/10.1093/bioinformatics/btt086
  • Haas, B. J., Salzberg, S. L., Zhu, W., Pertea, M., Allen, J. E., Orvis, J., White, O., Buell, C. R., & Wortman, J. R. (2008). Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biology, 9(1), R7. https://doi.org/10.1186/gb-2008-9-1-r7
  • Huang, X., Chen, J., Yang, X., Duan, S., Long, C., Ge, G., & Rong, J. (2018). Low genetic differentiation among altitudes in wild camellia oleifera, a subtropical evergreen hexaploid plant. Tree Genetics & Genomes, 14(2), 21. https://doi.org/10.1007/s11295-018-1234-4
  • Ke, C. (2019). Main nutrient composition and health function of tea oil. Modern Food, 13, 105–108. https://doi.org/10.16736/j.cnki.cn41-1434/ts.2019.13.033
  • Keilwagen, J., Wenk, M., Erickson, J. L., Schattat, M. H., Grau, J., & Hartung, F. (2016). Using intron position conservation for homology-based gene prediction. Nucleic Acids Research, 44(9), e89–e89. https://doi.org/10.1093/nar/gkw092
  • Keller, O., Kollmar, M., Stanke, M., & Waack, S. (2011). A novel hybrid gene prediction method employing protein multiple sequence alignments. Bioinformatics, 27(6), 757–763. https://doi.org/10.1093/bioinformatics/btr010
  • Kokot, M., Długosz, M., Deorowicz, S., & Berger, B. (2017). KMC 3: Counting and manipulating k-mer statistics. Bioinformatics, 33(17), 2759–2761. https://doi.org/10.1093/bioinformatics/btx304
  • Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv: Genomics. https://doi.org/10.48550/arXiv.1303.3997
  • Lin, P., Wang, K., Wang, Y., Hu, Z., Yan, C., Huang, H., Ma, X., Cao, Y., Long, W., Liu, W., Li, X., Fan, Z., Li, J., Ye, N., Ren, H., Yao, X., & Yin, H. (2022). The genome of oil-Camellia and population genomics analysis provide insights into seed oil domestication. Genome Biology, 23(1), 14. https://doi.org/10.1186/s13059-021-02599-2
  • Luo, R. B., Liu, B. H., Xie, Y. L., Li, Z. Y., Huang, W. H., Yuan, J. Y., He, G. Z., Chen, Y. X., Pan, Q., Liu, Y. J., Tang, J. B., Wu, G. X., Zhang, H., Shi, Y. J., Liu, Y., Yu, C., Wang, B., Lu, Y. , and Wang, J. (2012). SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler. GigaScience, 1(1), 18. https://doi.org/10.1186/2047-217x-1-18
  • Ma, L., Wang, X., Yan, M., Liu, F., Zhang, S., & Wang, X. (2022). Genome survey sequencing of common vetch (Vicia sativa L.) and genetic diversity analysis of Chinese germplasm with genomic SSR markers. Molecular Biology Reports, 49(1), 313–320. https://doi.org/10.1007/s11033-021-06875-z
  • Ma, J. L., Ye, H., Rui, Y. K., Chen, G. C., & Zhang, N. Y. (2011). Fatty acid composition of Camellia oleifera oil. Journal Fur Verbraucherschutz Und Lebensmittelsicherheit-Journal of Consumer Protection and Food Safety, 6(1), 9–12. https://doi.org/10.1007/s00003-010-0581-3
  • Meyers, L. A., & Levin, D. A. (2006). On the ABUNDANCE of POLYPLOIDS in FLOWERING PLANTS. Evolution, 60(6), 1198–1206. https://doi.org/10.1111/j.0014-3820.2006.tb01198.x
  • Paliwal, R., Singh, R., Choudhury, D. R., Tiwari, G., Kumar, A., Bhat, K. C., & Singh, R. (2022). Molecular characterization of tinospora cordifolia (Willd.) Miers using novel g-SSR markers and their comparison with EST-SSR and SCoT markers for genetic diversity study. Genes, 13(11), 2042. https://doi.org/10.3390/genes13112042
  • Qin, S. Y., Chen, K., Zhang, W. J., Xiang, X. G., Zuo, Z. Y., Guo, C., Zhao, Y., Li, L. F., Wang, Y. G., Song, Z. P., Yang, J., Yang, X. Q., Zhang, J., Jin, W. T., Wen, Q., Zhao, S. Z., Chen, J. K., Li, D. Z., & Rong, J. (2023). Phylogenomic insights into the reticulate evolution of Camellia sect. Paracamellia Sealy (Theaceae). Journal of Systematics and Evolution. https://doi.org/10.1111/jse.12948
  • Qin, S. Y., Rong, J., Zhang, W. J., & Chen, J. K. (2018). Cultivation history of Camellia oleifera and genetic resources in the Yangtze River Basin. Biodiversity Science, 26(4), 384–395. https://doi.org/10.17520/biods.2017254
  • Ranallo-Benavidez, T. R., Jaron, K. S., & Schatz, M. C. (2020). GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nature Communications, 11(1), 1432. https://doi.org/10.1038/s41467-020-14998-3
  • Ranty, B., Aldon, D., Cotelle, V., Galaud, J. P., Thuleau, P., & Mazars, C. (2016). Calcium sensors as key hubs in plant responses to biotic and abiotic stresses. Frontiers in Plant Science, 7, 327. https://doi.org/10.3389/fpls.2016.00327
  • Salgotra, R. K., & Chauhan, B. S. (2023). Genetic diversity, conservation, and utilization of plant genetic Resources. Genes, 14(1), 174. https://doi.org/10.3390/genes14010174
  • Shen, T.-F., Huang, B., Xu, M., Zhou, P.-Y., Ni, Z.-X., Gong, C., Wen, Q., Cao, F.-L., & Xu, L.-A. (2022). The reference genome of Camellia chekiangoleosa provides insights into Camellia evolution and tea oil biosynthesis. Horticulture Research, 9, uhab083. https://doi.org/10.1093/hr/uhab083
  • Song, Y., Liu, L., Feng, Y., Wei, Y., Yue, X., He, W., Zhang, H., An, L., & Lu, W.-J. (2015). Chilling- and freezing- induced alterations in cytosine methylation and its association with the cold tolerance of an alpine subnival plant, chorispora bungeana. PLoS ONE, 10(8), e0135485. https://doi.org/10.1371/journal.pone.0135485
  • Tan, X. (2023). Advances in the molecular breeding of Camellia oleifera. Journal of Central South University of Forestry & Technology, 43(1), 1–24. https://doi.org/10.14067/j.cnki.1673-923x.2023.01.001
  • van Dijk, E. L., Auger, H., Jaszczyszyn, Y., & Thermes, C. (2014). Ten Years of next-generation sequencing technology. Trends in Genetics, 30(9), 418–426. https://doi.org/10.1016/j.tig.2014.07.001
  • Vurture, G. W., Sedlazeck, F. J., Nattestad, M., Underwood, C. J., Fang, H., Gurtowski, J., Schatz, M. C., & Berger, B. (2017). GenomeScope: Fast reference-free genome profiling from short reads. Bioinformatics, 33(14), 2202–2204. https://doi.org/10.1093/bioinformatics/btx153
  • Wang, R., & Chen, Y. (2015). Development status and promotion ideas of Camellia oleifera industry in China. Journal of Forestry Engineering, 29(4), 6–10. https://doi.org/10.13360/j.issn.1000-8101.2015.04.002
  • Wang, X.-D., Li, X.-H., Zhang, Z.-W., & Wang, K.-J. (2019). Genetic diversity and genetic structure of natural populations in an extremely narrowly distributed perennial species glycine tabacina (Labill.) Benth. On the southeast islands in China. Genetic Resources and Crop Evolution, 66(5), 989–1008. https://doi.org/10.1007/s10722-019-00764-y
  • Xie, H. X., Zhang, J., Cheng, J. Y., Zhao, S. Z., Wen, Q., Kong, P., Zhao, Y., Xiang, X. G., & Rong, J. (2023). Field plus lab experiments help identify freezing tolerance and associated genes in subtropical evergreen broadleaf trees: A case study of Camellia oleifera. Frontiers in Plant Science, 14, 1113125. https://doi.org/10.3389/fpls.2023.1113125
  • Yu, X., Wang, P., Li, J., Zhao, Q., Ji, C., Zhu, Z., Zhai, Y., Qin, X., Zhou, J., Yu, H., Cheng, X., Isshiki, S., Jahn, M., Doyle, J. J., Ottosen, C.-O., Bai, Y., Cai, Q., Cheng, C. … Chen, J. (2021). Whole-genome sequence of synthesized allopolyploids in Cucumis reveals insights into the genome evolution of allopolyploidization. Advanced Science, 8(9), 2004222. https://doi.org/10.1002/advs.202004222
  • Zalapa, J. E., Cuevas, H., Zhu, H. Y., Steffan, S., Senalik, D., Zeldin, E., McCown, B., Harbut, R., & Simon, P. (2012). Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. American Journal of Botany, 99(2), 193–208. https://doi.org/10.3732/ajb.1100394
  • Zhang, Q., Qi, Y., Pan, H., Tang, H., Wang, G., Hua, X., Wang, Y., Lin, L., Li, Z., Li, Y., Yu, F., Yu, Z., Huang, Y., Wang, T., Ma, P., Dou, M., Sun, Z., Wang, Y. … Zhang, J. (2022). Genomic insights into the recent chromosome reduction of autopolyploid sugarcane saccharum spontaneum. Nature Genetics, 54(6), 885–896. https://doi.org/10.1038/s41588-022-01084-1
  • Zhang, Z., Zhang, J., Yang, Q., Li, B., Zhou, W., & Wang, Z. (2021). Genome survey sequencing and genetic diversity of cultivated akebia trifoliata assessed via phenotypes and SSR markers. Molecular Biology Reports, 48(1), 241–250. https://doi.org/10.1007/s11033-020-06042-w
  • Zhou, P., Zhang, Q., Li, J., Li, F., Huang, J., & Zhang, M. (2023). A first insight into the genomic background of ilex pubescens (Aquifoliaceae) by flow cytometry and genome survey sequencing. BMC Genomics, 24(1), 270. https://doi.org/10.1186/s12864-023-09359-5
  • Zhuang, R. L. (2008). Oil-tea camellia in China (2nd ed.). China Forestry Publishing House. ISBN 978-7-5038-5163-6.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.