Identification and Characterization of the COBRA-Like Gene Family in the Spinacia oleracea L. Genome

Ayşe Gül Kasapoğlu

doi:10.19159/tutad.1769142

TR EN

Identification and Characterization of the COBRA-Like Gene Family in the Spinacia oleracea L. Genome

Öz

COBL genes play an important role in the biosynthesis of cellulose, the main component of the cell wall. This study aimed to identify and characterize members of the COBL gene family that have not been characterized in the spinach genome. Eleven COBL members carrying the COBRA and/or COBL domains were found in the spinach genome. Among the So-COBL proteins, So-COBL1 and So-COBL2 are unstable. All So-COBL proteins are hydrophilic and, with aliphatic indices below 100, are not heat-stable. Both tandem and segmental duplications have occurred during the evolution of So-COBL genes. Because the Ka/Ks ratio is less than one, they have been subjected to purifying selection throughout evolution, eliminating deleterious variants. So-COBL genes contain cis elements in their promoter region that respond to many environmental stimuli, particularly hormone and light responses. Phylogeny analysis of spinach, Arabidopsis, and quinoa COBL genes revealed two groups, COBRA and COBL7-like. The intron-exon organization, motif, and domain structure of the genes grouped in the same group are similar. Synteny analysis revealed further orthology between quinoa and spinach. This study highlights the importance of COBL genes for future studies.

Anahtar Kelimeler

Identification and Characterization of the COBRA-Like Gene Family in the Spinacia oleracea L. Genome

Öz

COBL genes play an important role in the biosynthesis of cellulose, the main component of the cell wall. This study aimed to identify and characterize members of the COBL gene family that have not been characterized in the spinach genome. Eleven COBL members carrying the COBRA and/or COBL domains were found in the spinach genome. Among the So-COBL proteins, So-COBL1 and So-COBL2 are unstable. All So-COBL proteins are hydrophilic and, with aliphatic indices below 100, are not heat-stable. Both tandem and segmental duplications have occurred during the evolution of So-COBL genes. Because the Ka/Ks ratio is less than one, they have been subjected to purifying selection throughout evolution, eliminating deleterious variants. So-COBL genes contain cis elements in their promoter region that respond to many environmental stimuli, particularly hormone and light responses. Phylogeny analysis of spinach, Arabidopsis, and quinoa COBL genes revealed two groups, COBRA and COBL7-like. The intron-exon organization, motif, and domain structure of the genes grouped in the same group are similar. Synteny analysis revealed further orthology between quinoa and spinach. This study highlights the importance of COBL genes for future studies.

Anahtar Kelimeler

Kaynakça

Bailey, T.L., Johnson, J., Grant, C.E., Noble, W.S., 2015. The MEME suite. Nucleic Acids Research, 43(W1): W39-W49.
Ben‐Tov, D., Idan‐Molakandov, A., Hugger, A., Ben‐Shlush, I., Günl, M., Yang, B., Harpaz‐Saad, S., 2018. The role of COBRA‐LIKE 2 function, as part of the complex network of interacting pathways regulating Arabidopsis seed mucilage polysaccharide matrix organization. The Plant Journal, 94(3): 497-512.
Blum, M., Andreeva, A., Florentino, L.C., Chuguransky, S.R., Grego, T., Hobbs, E., Bateman, A., 2025. InterPro: The protein sequence classification resource in 2025. Nucleic Acids Research, 53(D1): D444-D456.
Borner, G.H., Lilley, K.S., Stevens, T.J., Dupree, P., 2003. Identification of glycosylphosphatidylinositol-anchored proteins in Arabidopsis: A proteomic and genomic analysis. Plant Physiology, 132(2): 568-577.
Brady, S.M., Song, S., Dhugga, K.S., Rafalski, J.A., Benfey, P.N., 2007. Combining expression and comparative evolutionary analysis: The COBRA gene family. Plant Physiology, 143(1): 172-187.
Brinkjost, T., Ehrt, C., Koch, O., Mutzel, P., 2020. SCOT: Rethinking the classification of secondary structure elements. Bioinformatics, 36(8): 2417-2428.
Brown, D.M., Zeef, L.A., Ellis, J., Goodacre, R., Turner, S.R., 2005. Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. The Plant Cell, 17(8): 2281-2295.
Cao, Y., Tang, X., Giovannoni, J., Xiao, F., Liu, Y., 2012. Functional characterization of a tomato COBRA-like gene functioning in fruit development and ripening. BMC Plant Biology, 12(1): 211.

Chen, C., Wu, Y., Li, J., Wang, X., Zeng, Z., Xu, J., Xia, R., 2023. TBtools-II: A “one for all, all for one” bioinformatics platform for biological big-data mining. Molecular Plant, 16(11): 1733-1742.
Combet, C., Blanchet, C., Geourjon, C., Deleage, G., 2000. NPS@: Network protein sequence analysis. Trends in Biochemical Sciences, 25(3): 147-150.
Cosgrove, D.J., 2016. Plant cell wall extensibility: Connecting plant cell growth with cell wall structure, mechanics, and the action of wall-modifying enzymes. Journal of Experimental Botany, 67(2): 463-476.
Dai, X., You, C., Wang, L., Chen, G., Zhang, Q., Wu, C., 2009. Molecular characterization, expression pattern, and function analysis of the OsBC1L family in rice. Plant Molecular Biology, 71(4): 469.
Dauda, A., Abbaya, H.Y., Abare, E.A., James, A.K., 2017. Insilico analysis of mycobacterium caprae protein sequence. Journal Animal Production Research, 29(1): 128-135.
Gamage, D.G., Gunaratne, A., Periyannan, G.R., Russell, T.G., 2019. Applicability of instability index for in vitro protein stability prediction. Protein and Peptide Letters, 26(5): 339-347.
Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S.E., Wilkins, M.R., Appel, R.D., Bairoch, A., 2005. Protein identification and analysis tools on the ExPASy server. In: J.M. Walker (Eds.), The Proteomics Protocols Handbook, Springer Protocols Handbooks, Humana Press, Totowa, pp. 571-607.
Geourjon, C., Deleage, G., 1995. SOPMA: Significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Bioinformatics, 11(6): 681-684.
Goodstein, D.M., Shu, S., Howson, R., Neupane, R., Hayes, R.D., Fazo, J., Rokhsar, D.S., 2012. Phytozome: A comparative platform for green plant genomics. Nucleic Acids Research, 40(D1): D1178-D1186.
Guindon, S., Dufayard, J.F., Lefort, V., Anisimova, M., Hordijk, W., Gascuel, O., 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Systematic Biology, 59(3): 307-321.
Guruprasad, K., Reddy, B.B., Pandit, M.W., 1990. Correlation between stability of a protein and its dipeptide composition: A novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Engineering, Design and Selection, 4(2): 155-161.
Handakumbura, P.P., Hazen, S.P., 2012. Transcriptional regulation of grass secondary cell wall biosynthesis: playing catch-up with Arabidopsis thaliana. Frontiers in Plant Science, 3: 74.
Hassler, M., 2021. World Plants: Synonymic Checklists of the Vascular Plants of the World (Version 2021-03-17). Species 2000 & ITIS Catalogue of Life. (https://www.catalogueoflife.org/annual-checklist/2018).
Huerta-Cepas, J., Serra, F., Bork, P., 2016. ETE 3: Reconstruction, analysis, and visualization of phylogenomic data. Molecular Biology and Evolution, 33(6): 1635-1638.
Hulse‐Kemp, A.M., Bostan, H., Chen, S., Ashrafi, H., Stoffel, K., Sanseverino, W., Van Deynze, A., 2021. An anchored chromosome‐scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids. The Plant Genome, 14(2): e20101.
Jarvis, D.E., Ho, Y.S., Lightfoot, D.J., Schmöckel, S.M., Li, B., Borm, T.J.A., Tester, M., 2017. The genome of Chenopodium quinoa. Nature, 542(7641): 307-312.
Khrustalev, V.V., Khrustaleva, T.A., Barkovsky, E.V., 2013. Random coil structures in bacterial proteins. Relationships of their amino acid compositions to flanking structures and corresponding genic base compositions. Biochimie, 95(9): 1745-1754.
Korkuć, P., Schippers, J.H., Walther, D., 2014. Characterization and identification of cis-regulatory elements in Arabidopsis based on single-nucleotide polymorphism information. Plant Physiology, 164(1): 181-200.
Lamesch, P., Berardini, T.Z., Li, D., Swarbreck, D., Wilks, C., Sasidharan, R., Huala, E., 2011. The Arabidopsis Information Resource (TAIR): Improved gene annotation and new tools. Nucleic Acids Research, 40(D1): D1202-D1210.
Lescot, M., Déhais, P., Thijs, G., Marchal, K., Moreau, Y., van de Peer, Y., Rombauts, S., 2002. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Research, 30(1): 325-327.
Letunic I., Bork P., 2011. Interactive tree of life v2: Online annotation and display of phylogenetic trees made easy. Nucleic Acids Research 39: W475-W478.
Li, S., Ge, F.R., Xu, M., Zhao, X.Y., Huang, G.Q., Zhou, L.Z., Zhang, Y., 2013. Arabidopsis COBRA‐LIKE 10, a GPI‐anchored protein, mediates directional growth of pollen tubes. The Plant Journal, 74(3): 486-497.
Li, Y., Qian, Q., Zhou, Y., Yan, M., Sun, L., Zhang, M., Li, J., 2003. BRITTLE CULM1, which encodes a COBRA-like protein, affects the mechanical properties of rice plants. The Plant Cell, 15(9): 2020-2031.
Liu, D., Hunt, M., Tsai, I.J., 2018. Inferring synteny between genome assemblies: A systematic evaluation. BMC Bioinformatics, 19(1): 26.
Liu, J., Wu, J., Silaiyiman, S., Ouyang, L., Cao, Z., Shen, C., 2025. Comparative genomics reveals gene duplication and evolution in 26 Aurantioideae species. Horticulturae, 11(2): 209.
Liu, L., Shang-Guan, K., Zhang, B., Liu, X., Yan, M., Zhang, L., Zhou, Y., 2013. Brittle Culm1, a COBRA-like protein, functions in cellulose assembly through binding cellulose microfibrils. PLoS genetics, 9(8): e1003704.
MacMillan, C.P., Mansfield, S.D., Stachurski, Z.H., Evans, R., Southerton, S.G., 2010. Fasciclin‐like arabinogalactan proteins: specialization for stem biomechanics and cell wall architecture in Arabidopsis and Eucalyptus. The Plant Journal, 62(4): 689-703.
Maughan, P.J., Bonifacio, A., Coleman, C.E., Jellen, E.N., Stevens, M.R., Fairbanks, D.J., 2007. Quinoa (Chenopodium quinoa). In: C. Kole (Eds.), Pulses, Sugar and Tuber Crops, Genome Mapping and Molecular Breeding in Plants, Vol 3, Springer, Berlin, Heidelberg, pp. 147-158.
Morelock, T.E., Correll, J.C. 2008. Spinach. In: J. Prohens and F. Nuez (Eds.), Handbook of Plant Breeding, Vegetables I.: Asteraceae, Brassicaceae, Chenopodicaceae, and Cucurbitaceae, Springer, New York, NY, pp. 189-218.
Niu, E., Shang, X., Cheng, C., Bao, J., Zeng, Y., Cai, C., Guo, W., 2015. Comprehensive analysis of the COBRA-like (COBL) gene family in gossypium identifies two COBL s potentially associated with fiber quality. PloS One, 10(12): e0145725.
Peters, J., Jin, C., Luczak, A., Lyons, B., Kalyanaraman, R., 2025. Machine learning enabled protein secondary structure characterization using drop-coating deposition Raman spectroscopy. Journal of Pharmaceutical and Biomedical Analysis, 259: 116762.
Ramaiyan, B., Kour, J., Nayik, G.A., Anand, N., Alam, M.S., 2020. Spinach (Spinacia oleracea L.). In: G.A. Nayik and A. Gull (Eds.), Antioxidants in Vegetables and Nuts - Properties and Health Benefits, Springer, Singapore, pp. 159-173.
Rao, J., Huang, Z., Chen, Z., Liu, H., Zhang, X., Cen, X., Ren, Y., 2023. Identification and expression profiles of xylogen-like arabinogalactan protein (XYLP) gene family in Phyllostachys edulis in different developmental tissues and under various abiotic stresses. International Journal of Biological Macromolecules, 227: 1098-1118.
Ren, P., Ma, L., Bao, W., Wang, J., 2024. Genome-wide ıdentification and hormone response analysis of the cobl gene family in barley. Genes, 15(5): 612.
Roudier, F., Fernandez, A.G., Fujita, M., Himmelspach, R., Borner, G.H., Schindelman, G., Benfey, P.N., 2005. COBRA, an Arabidopsis extracellular glycosyl-phosphatidyl inositol-anchored protein, specifically controls highly anisotropic expansion through its involvement in cellulose microfibril orientation. The Plant Cell, 17(6): 1749-1763.
Roudier, F., Schindelman, G., DeSalle, R., Benfey, P.N., 2002. The COBRA family of putative GPI-anchored proteins in Arabidopsis. A new fellowship in expansion. Plant Physiology, 130(2): 538-548.
Sajjad, M., Ahmad, A., Riaz, M.W., Hussain, Q., Yasir, M., Lu, M.Z., 2023. Recent genome resequencing paraded COBRA-Like gene family roles in abiotic stress and wood formation in Poplar. Frontiers in Plant Science, 14: 1242836.
Sangi, S., Araújo, P.M., Coelho, F.S., Gazara, R.K., Almeida-Silva, F., Venancio, T.M., Grativol, C., 2021. Genome-wide analysis of the cobra-like gene family supports gene expansion through whole-genome duplication in soybean (Glycine max). Plants, 10(1): 167.
Szklarczyk, D., Kirsch, R., Koutrouli, M., Nastou, K., Mehryary, F., Hachilif, R., Von Mering, C., 2023. The STRING database in 2023: Protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Research, 51(D1): D638-D646.
Urry, D.W., 2004. The change in Gibbs free energy for hydrophobic association: Derivation and evaluation by means of inverse temperature transitions. Chemical Physics Letters, 399(1-3): 177-183.
Vaahtera, L., Schulz, J., Hamann, T., 2019. Cell wall integrity maintenance during plant development and interaction with the environment. Nature Plants, 5(9): 924-932.
Wallin, E., Heijne, G.V., 1998. Genome‐wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Science, 7(4): 1029-1038.
Wang, J., Chitsaz, F., Derbyshire, M.K., Gonzales, N.R., Gwadz, M., Lu, S., Marchler-Bauer, A., 2023. The conserved domain database in 2023. Nucleic Acids Research, 51(D1): D384-D388.
Wang, Y., Tang, H., DeBarry, J.D., Tan, X., Li, J., Wang, X., Paterson, A.H., 2012. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Research, 40(7): e49-e49.
Wright, P.E., Dyson, H.J., 2015. Intrinsically disordered proteins in cellular signalling and regulation. Nature reviews Molecular Cell Biology, 16(1): 18-29.
Yang, Q., Wang, S., Chen, H., You, L., Liu, F., Liu, Z., 2021. Genome-wide identification and expression profiling of the COBRA-like genes reveal likely roles in stem strength in rapeseed (Brassica napus L.). PloS One, 16(11): e0260268.
Zaheer, M., Rehman, S.U., Khan, S.H., Shahid, S., Rasheed, A., Naz, R., Sajjad, M., 2022. Characterization of new COBRA like (COBL) genes in wheat (Triticum aestivum) and their expression analysis under drought stress. Molecular Biology Reports, 49(2): 1379-1387.
Zhang, Z., 2022. KaKs_Calculator 3.0: Calculating selective pressure on coding and non-coding sequences. Genomics, Proteomics and Bioinformatics, 20(3): 536-540.
Zhao, T., Schranz, M.E., 2017. Network approaches for plant phylogenomic synteny analysis. Current opinion in plant biology, 36: 129-134.

Ayrıntılar

Birincil Dil

İngilizce

Konular

Bitki Biyoteknolojisi

Bölüm

Araştırma Makalesi

Yazarlar

Ayşe Gül Kasapoğlu ^*
0000-0002-6447-4921
Türkiye

Yayımlanma Tarihi

31 Ekim 2025

Gönderilme Tarihi

20 Ağustos 2025

Kabul Tarihi

29 Ekim 2025

Yayımlandığı Sayı

Yıl 2025 Cilt: 12 Sayı: 3

DOI

https://doi.org/10.19159/tutad.1769142

IZ

https://izlik.org/JA54TT63DN

Kaynak Göster

RIS / Bibtex

APA

Kasapoğlu, A. G. (2025). Identification and Characterization of the COBRA-Like Gene Family in the Spinacia oleracea L. Genome. Türkiye Tarımsal Araştırmalar Dergisi, 12(3), 320-333. https://doi.org/10.19159/tutad.1769142

AMA

1.Kasapoğlu AG. Identification and Characterization of the COBRA-Like Gene Family in the Spinacia oleracea L. Genome. TÜTAD. 2025;12(3):320-333. doi:10.19159/tutad.1769142

Chicago

Kasapoğlu, Ayşe Gül. 2025. “Identification and Characterization of the COBRA-Like Gene Family in the Spinacia oleracea L. Genome”. Türkiye Tarımsal Araştırmalar Dergisi 12 (3): 320-33. https://doi.org/10.19159/tutad.1769142.

EndNote

Kasapoğlu AG (01 Ekim 2025) Identification and Characterization of the COBRA-Like Gene Family in the Spinacia oleracea L. Genome. Türkiye Tarımsal Araştırmalar Dergisi 12 3 320–333.

IEEE

[1]A. G. Kasapoğlu, “Identification and Characterization of the COBRA-Like Gene Family in the Spinacia oleracea L. Genome”, TÜTAD, c. 12, sy 3, ss. 320–333, Eki. 2025, doi: 10.19159/tutad.1769142.

ISNAD

Kasapoğlu, Ayşe Gül. “Identification and Characterization of the COBRA-Like Gene Family in the Spinacia oleracea L. Genome”. Türkiye Tarımsal Araştırmalar Dergisi 12/3 (01 Ekim 2025): 320-333. https://doi.org/10.19159/tutad.1769142.

JAMA

1.Kasapoğlu AG. Identification and Characterization of the COBRA-Like Gene Family in the Spinacia oleracea L. Genome. TÜTAD. 2025;12:320–333.

MLA

Kasapoğlu, Ayşe Gül. “Identification and Characterization of the COBRA-Like Gene Family in the Spinacia oleracea L. Genome”. Türkiye Tarımsal Araştırmalar Dergisi, c. 12, sy 3, Ekim 2025, ss. 320-33, doi:10.19159/tutad.1769142.

Vancouver

1.Ayşe Gül Kasapoğlu. Identification and Characterization of the COBRA-Like Gene Family in the Spinacia oleracea L. Genome. TÜTAD. 01 Ekim 2025;12(3):320-33. doi:10.19159/tutad.1769142