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PvTLP genlerinin genom çaplı tespit ve karakterizasyonu

Yıl 2022, Sayı: 34, 676 - 684, 31.03.2022
https://doi.org/10.31590/ejosat.1083519

Öz

TUBBY-like proteinleri (TLP) C terminal bölgede TUB domaini ve ilave olarak N terminal bölgede F-Box domaini içeren çok işlevli bir proteindir. Memelilerde nöronal gelişme ve farklılaşmada rol oynarken bitkilerde strese karşı yanıtta, sinyal iletimi ve hücre döngüsünün kontrolü gibi birçok işleve sahiptir. Bitkiler sesil organizmalar olduğu için çevresel streslerden kaçamazlar. Bu yüzden strese karşı savunma mekanizmalarını aktifleştirmektedirler. Bu savunma mekanizmalarından biri de çeşitli gen ya da gen ailelerinin ifade seviyelerinin artırılması ya da azaltılmasıdır. TLP genleri ilk olarak obez farelerde tanımlanmış olup ardından diğer ökaryotik hücrelerde de tanımlanmaya başlamıştır. Fakat Phaseolus vulgaris genomunda TUBBY-like proteinlerinin karakterizasyonu henüz yapılmamıştır. Bu çalışmanın amacı P. vulgaris genomundaki TLP genlerini tespit ve karakterize ederek çeşitli biyoinformatik araçlarla genom bazında analizini gerçekleştirmektir. P. vulgaris genomunda 10 adet TLP geni belirlenmiştir. PvTLP7 geni hariç diğer PvTLP genleri F-Box domaini içermekte ve tüm PvTLP genleri TUB domainini barındırmaktadır. PvTLP proteinlerinin amino asit sayıları 360-431, moleküler ağırlıkları 40,46-48,12 kDa ve teorik izoelektrik noktası 9,09-9,71 arasında olup PvTLP proteinleri bazik özellik göstermektedir. Arabidopsis thaliana, Glycine max ve P. vulgaris TLP genleri arasındaki filogentik ilişkiler tespit edilmiş olup 3 ana gruba ayrıldığı bulunmuştur. Kuraklık ve tuz stresi altındaki PvTLP genlerinin ifade seviyeleri in siliko olarak incelenmiş olup PvTLP1 ve PvTLP7 genlerinin ifade seviyelerinde farklılıklar gözlemlenmiştir. Bu çalışmadan elde edilen bilgiler ışığında TLP genlerinin fasulyedeki işlevi aydınlatılarak gelecekte yapılacak olan fonksiyonel çalışmalara zemin oluşturacaktır.

Kaynakça

  • Bailey TL, Williams N, Misleh C, Li WW (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34:W369-W373. https://doi.org/10.1093/nar/gkl198
  • Bao Y, Song W-M, Jin Y-L, Jiang C-M, Yang Y, Li B, Huang W-J, Liu H, Zhang H-X. 2014. Characterization of Arabidopsis Tubby-like proteins and redundant function of AtTLP3 and AtTLP9 in plant response to ABA and osmotic stress. Plant Molecular Biology 86:471–483 DOI 10.1007/s11103-014-0241-6.
  • Boggon TJ, Shan WS, Santagata S, Myers SC, Shapiro L. 2000. Implication of tubby proteins as transcription factors by structure-based functional analysis. Acta Crystallographica Section A Foundations of Crystallography 56:s263–s263 DOI 10.1107/S0108767300025642.
  • Cai, M., Qiu, D., Yuan, T., Ding, X., Li, H., Duan, L., et al. (2008). Identification of novel pathogen-responsive cis-elements and their binding proteins in the promoter of OsWRKY13, a gene regulating rice disease resistance. Plant Cell Environ. 31, 86–96.
  • Cannon, S. B., Mitra, A., Baumgarten, A., Young, N. D., & May, G. (2004). The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC plant biology, 4(1), 1-21.
  • Chen, C., Chen, H., Zhang, Y., Thomas, H. R., Frank, M. H., He, Y., and Xia, R. (2020). TBtools: an integrative toolkit developed for interactive analyses of big biological data. Molecular plant, 13(8), 1194-1202.
  • Gagne, J. M., Downes, B. P., Shiu, S. H., Durski, A. M., & Vierstra, R. D. (2002). The F-box subunit of the SCF E3 complex is encoded by a diverse superfamily of genes in Arabidopsis. Proceedings of the national academy of sciences, 99(17), 11519-11524.
  • Guo Y, Qiao DH, Yang C, Chen J, Li Y, Liang SH, Lin KQ, Chen ZW (2020) Genome-wide identification and expression analysis of SABATH methyltransferases in tea plant (Camellia sinensis): insights into their roles in plant defense responses. Plant Signal Behav 15(10). https://doi.org/10.1080/15592324.2020.1804684
  • Hanada, K., Zou, C., Lehti-Shiu, M. D., Shinozaki, K., and Shiu, S. (2008) Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol. 148, 993–1003.
  • Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res 35:W585-W587. https://doi.org/10.1093/nar/gkm259
  • Ikeda, A., Nishina, P. M., and Naggert, J. K. (2002) The tubby-like proteins, a family with roles in neuronal development and function. J. Cell Sci. 115, 9–14.
  • Jain, M., Nijhawan, A., Arora, R., Agarwal, P., Ray, S., Sharma, P., Kapoor, S., Tyagi, A. K., and Khurana, J. P. (2007) F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol. 143, 1467–1483.
  • KASAPOĞLU, A. G., İLHAN, E., KIZILKAYA, D., POUR, A. H., and HALİLOĞLU, K. (2020). Sorgum (Sorghum bicolor (L.) Moench) Genomunda BES1 Transkripsiyon Faktör Ailesinin Genom Çaplı Analizi. Türkiye Tarımsal Araştırmalar Dergisi, 7(1), 85-95.
  • Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJE (2015) The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 10(6):845-858. https://doi.org/10.1038/nprot.2015.053
  • Kırıcı A. Fasulye (Phaseolus vulgaris L.) bitkisinde Yabby ve Dof genlerinin kuraklık stresi ile olan ilişkilerinin salisilik asit etkisiyle karşılaştırmalı olarak gen ifadesi düzeyinde incelenmesi. 2019. M. thesis, Ankara Üniversitesi Fen Bilimleri Enstitüsü, Ankara, Türkiye.
  • KIZILKAYA, D., KASAPOĞLU, A. G., HOSSEİNPOUR, A., HALİLOĞLU, K., MUSLU, S., and İLHAN, E. (2020) Sorghum bicolor L. CAMTA Transkripsiyon Faktörlerinin Genom Çaplı Analizi. Atatürk Üniversitesi Ziraat Fakültesi Dergisi, 51(3), 267-278.
  • Kim S, Sung HJ, Lee JW, Kim YH, Oh Y-S, Yoon K-A, Heo K, Suh P-G. 2017. C-terminally mutated tubby protein accumulates in aggresomes. BMB Reports 50:37–42 DOI 10.5483/BMBRep.2017.50.1.140.
  • Korkmaz, H., & Durmaz, A. (2017). Bitkilerin Abiyotik Stres Faktörlerine Karşı Geliştirilen Cevaplar. Gümüşhane Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 7(2), 192-207.
  • Kou, Y., Qiu, D., Wang, L., Li, X., and Wang, S. (2009). Molecular analyses of the rice tubby-like protein gene family and their response to bacterial infection. Plant Cell Rep. 28, 113–121. doi: 10.1007/s00299-008-0620-z
  • Kumar S, Stecher G, and Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33:1870-1874
  • Lai C-P, Lee C-L, Chen P-H, Wu S-H, Yang C-C, Shaw J-F. 2004. Molecular analyses of the Arabidopsis TUBBY-like protein gene family. Plant Physiology 134:1586–1597 DOI 10.1104/pp.103.037820.
  • Lai, C. P., Chen, P. H., Huang, J. P., Tzeng, Y. H., Chaw, S. M., and Shaw, J. F. (2012) Functional diversification of the Tubby-like protein gene families (TULPs) during eukaryotic evolution. Biocatal. Agric. Biotechnol. 1, 2–8.
  • 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. https://doi.org/10.1093/nar/gkr1090
  • 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 Res 39:W475-W478. https://doi.org/10.1093/nar/gkr201
  • Liu, Q. (2008). Identification of rice TUBBY‐like genes and their evolution. The FEBS Journal, 275(1), 163-171.
  • Mortazavi A, Williams BA, Mccue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5(7):621-628. https://doi.org/10.1038/nmeth.1226
  • Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005) InterProScan: protein domains identifier. Nucleic Acids Res 33:W116-W120. https://doi.org/10.1093/nar/gki442
  • Schmutz, J., Cannon, S. B., Schlueter, J., Ma, J., Mitros, T., Nelson, W., Jackson, S. A. (2010). Genome sequence of the palaeopolyploid soybean. Nature, 463(7278), 178–183. https://doi.org/10.1038/nature08670
  • SİRAT, Abdulveli. "Yerel Kuru Fasulye (Phaseolus vulgaris L.) Genotiplerinin Tane Verimi, Verim Unsurları ve Bazı Kalite Özelliklerinin Belirlenmesi." Adnan Menderes Üniversitesi Ziraat Fakültesi Dergisi 17.2 (2020): 245-254.
  • Suyama M, Torrents D, Bork P (2006) PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 34:W609-W612. https://doi.org/10.1093/nar/gkl315
  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25(24):4876-4882. https://doi.org/10.1093/nar/25.24.4876
  • Valliyodan, B., Cannon, S. B., Bayer, P. E., Shu, S., Brown, A. V., Ren, L., ... & Nguyen, H. T. (2019). Construction and comparison of three reference‐quality genome assemblies for soybean. The Plant Journal, 100(5), 1066-1082.
  • Voorrips RE (2002) MapChart: Software for the graphical presentation of linkage maps and QTLs. J Hered 93(1):77-78. https://doi.org/10.1093/jhered/93.1.77
  • Wang, K., Cheng, Y., Yi, L., He, H., Zhan, S., & Yang, P. (2021). Genome-wide identification of the Tubby-Like Protein (TLPs) family in medicinal model plant Salvia miltiorrhiza. PeerJ, 9, e11403.
  • Wang, M., Xu, Z., & Kong, Y. (2018). The tubby-like proteins kingdom in animals and plants. Gene, 642, 16-25.
  • Wang, Tong, et al. "Identification, evolution and expression analyses of whole genome-wide TLP gene family in Brassica napus." BMC genomics 21.1 (2020): 1-14.
  • Wang, Y., You, F. M., Lazo, G. R., Luo, M. C., Thilmony, R., Gordon, S., ... & Gu, Y. Q. (2013). PIECE: a database for plant gene structure comparison and evolution. Nucleic acids research, 41(D1), D1159-D1166.
  • Wang, Yupeng, et al. "MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity." Nucleic acids research 40.7 (2012): e49-e49.
  • Wardhan V, Jahan K, Gupta S, Chennareddy S, Datta A, Chakraborty S, Chakraborty N. 2012. Overexpression of CaTLP1, a putative transcription factor in chickpea (Cicer arietinum L.), promotes stress tolerance. Plant Molecular Biology 79:479–493 DOI 10.1007/s11103-012-9925-y.
  • Xu J, Xing S, Sun Q, Zhan C, Liu X, Zhang S, Wang X. 2019. The expression of a tubby-like protein from Malus domestica (MdTLP7) enhances abiotic stress tolerance in Arabidopsis. BMC Plant Biology 19:60 DOI 10.1186/s12870-019-1662-9.
  • Xu, Jia-Ning, et al. "Genome-wide identification and expression analysis of the tubby-like protein family in the Malus domestica genome." Frontiers in Plant Science 7 (2016): 1693.
  • Yang ZH (2007) PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 24(8):1586-1591. https://doi.org/10.1093/molbev/msm088
  • Yang, Z., Zhou, Y., Wang, X., Gu, S., Yu, J., Liang, G., ... & Xu, C. (2008). Genomewide comparative phylogenetic and molecular evolutionary analysis of tubby-like protein family in Arabidopsis, rice, and poplar. Genomics, 92(4), 246-253.
  • Yulong, C., Wei, D., Baoming, S., Yang, Z., and Qing, M. (2016). Genome-wide identification and comparative analysis of the TUBBY-like protein gene family in maize. Genes Genom. 38, 25–36. doi: 10.1007/s13258-015-0338-6
  • Zhang L, Wu B, Zhao D, Li C, Shao F, Lu S. 2014. Genome-wide analysis and molecular dissection of the SPL gene family in Salvia miltiorrhiza: the SPL gene family in Salvia miltiorrhiza. Journal of Integrative Plant Biology 56:38–50 DOI 10.1111/jipb.12111.

Genome-wide characterization and identification of PvTLP genes

Yıl 2022, Sayı: 34, 676 - 684, 31.03.2022
https://doi.org/10.31590/ejosat.1083519

Öz

TUBBY-like proteins (TLP) are multifunctional proteins that contain a TUB domain in the C-terminal region and an additional F-Box domain in the N-terminal region. While it plays a role in neuronal development and differentiation in mammals, it has many functions such as the response to stress, signal transduction and cell cycle control in plants. Since plants are sessile organisms, they cannot escape from environmental stresses. Therefore, they activate their defense mechanisms against stress. One of these defense mechanisms is to increase or decrease the expression levels of various genes or gene families. TLP genes were first identified in obese mice and then began to be expressed in other eukaryotic cells. However, characterization of TUBBY-like proteins in the Phaseolus vulgaris genome has not yet been performed. The purpose of this study is to detect and recognize TLP genes in the P. vulgaris genome, as well as to analyze them using various bioinformatics tools across the genome. Ten TLP genes were identified in the P. vulgaris genome. Except for the PvTLP7 gene, other PvTLP genes contain the F-Box domain and all PvTLP genes contain the TUB domain. PvTLP proteins have an amino acid number of 360-431, a molecular weight of 40.46-48.12 kDa, and a theoretical isoelectric point of 9.09-9.71, and PvTLP proteins show basic properties. Phylogenetic relationships between Arabidopsis thaliana, Glycine max and P. vulgaris TLP genes were determined and they were found to be divided into 3 main groups. Expression levels of PvTLP genes under drought and salt stress were examined in silico, and differences in expression levels of PvTLP1 and PvTLP7 genes were observed. In the light of the information obtained from this study, the function of TLP genes in beans will be clarified and will form the basis for future functional studies.

Kaynakça

  • Bailey TL, Williams N, Misleh C, Li WW (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34:W369-W373. https://doi.org/10.1093/nar/gkl198
  • Bao Y, Song W-M, Jin Y-L, Jiang C-M, Yang Y, Li B, Huang W-J, Liu H, Zhang H-X. 2014. Characterization of Arabidopsis Tubby-like proteins and redundant function of AtTLP3 and AtTLP9 in plant response to ABA and osmotic stress. Plant Molecular Biology 86:471–483 DOI 10.1007/s11103-014-0241-6.
  • Boggon TJ, Shan WS, Santagata S, Myers SC, Shapiro L. 2000. Implication of tubby proteins as transcription factors by structure-based functional analysis. Acta Crystallographica Section A Foundations of Crystallography 56:s263–s263 DOI 10.1107/S0108767300025642.
  • Cai, M., Qiu, D., Yuan, T., Ding, X., Li, H., Duan, L., et al. (2008). Identification of novel pathogen-responsive cis-elements and their binding proteins in the promoter of OsWRKY13, a gene regulating rice disease resistance. Plant Cell Environ. 31, 86–96.
  • Cannon, S. B., Mitra, A., Baumgarten, A., Young, N. D., & May, G. (2004). The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC plant biology, 4(1), 1-21.
  • Chen, C., Chen, H., Zhang, Y., Thomas, H. R., Frank, M. H., He, Y., and Xia, R. (2020). TBtools: an integrative toolkit developed for interactive analyses of big biological data. Molecular plant, 13(8), 1194-1202.
  • Gagne, J. M., Downes, B. P., Shiu, S. H., Durski, A. M., & Vierstra, R. D. (2002). The F-box subunit of the SCF E3 complex is encoded by a diverse superfamily of genes in Arabidopsis. Proceedings of the national academy of sciences, 99(17), 11519-11524.
  • Guo Y, Qiao DH, Yang C, Chen J, Li Y, Liang SH, Lin KQ, Chen ZW (2020) Genome-wide identification and expression analysis of SABATH methyltransferases in tea plant (Camellia sinensis): insights into their roles in plant defense responses. Plant Signal Behav 15(10). https://doi.org/10.1080/15592324.2020.1804684
  • Hanada, K., Zou, C., Lehti-Shiu, M. D., Shinozaki, K., and Shiu, S. (2008) Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol. 148, 993–1003.
  • Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res 35:W585-W587. https://doi.org/10.1093/nar/gkm259
  • Ikeda, A., Nishina, P. M., and Naggert, J. K. (2002) The tubby-like proteins, a family with roles in neuronal development and function. J. Cell Sci. 115, 9–14.
  • Jain, M., Nijhawan, A., Arora, R., Agarwal, P., Ray, S., Sharma, P., Kapoor, S., Tyagi, A. K., and Khurana, J. P. (2007) F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol. 143, 1467–1483.
  • KASAPOĞLU, A. G., İLHAN, E., KIZILKAYA, D., POUR, A. H., and HALİLOĞLU, K. (2020). Sorgum (Sorghum bicolor (L.) Moench) Genomunda BES1 Transkripsiyon Faktör Ailesinin Genom Çaplı Analizi. Türkiye Tarımsal Araştırmalar Dergisi, 7(1), 85-95.
  • Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJE (2015) The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 10(6):845-858. https://doi.org/10.1038/nprot.2015.053
  • Kırıcı A. Fasulye (Phaseolus vulgaris L.) bitkisinde Yabby ve Dof genlerinin kuraklık stresi ile olan ilişkilerinin salisilik asit etkisiyle karşılaştırmalı olarak gen ifadesi düzeyinde incelenmesi. 2019. M. thesis, Ankara Üniversitesi Fen Bilimleri Enstitüsü, Ankara, Türkiye.
  • KIZILKAYA, D., KASAPOĞLU, A. G., HOSSEİNPOUR, A., HALİLOĞLU, K., MUSLU, S., and İLHAN, E. (2020) Sorghum bicolor L. CAMTA Transkripsiyon Faktörlerinin Genom Çaplı Analizi. Atatürk Üniversitesi Ziraat Fakültesi Dergisi, 51(3), 267-278.
  • Kim S, Sung HJ, Lee JW, Kim YH, Oh Y-S, Yoon K-A, Heo K, Suh P-G. 2017. C-terminally mutated tubby protein accumulates in aggresomes. BMB Reports 50:37–42 DOI 10.5483/BMBRep.2017.50.1.140.
  • Korkmaz, H., & Durmaz, A. (2017). Bitkilerin Abiyotik Stres Faktörlerine Karşı Geliştirilen Cevaplar. Gümüşhane Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 7(2), 192-207.
  • Kou, Y., Qiu, D., Wang, L., Li, X., and Wang, S. (2009). Molecular analyses of the rice tubby-like protein gene family and their response to bacterial infection. Plant Cell Rep. 28, 113–121. doi: 10.1007/s00299-008-0620-z
  • Kumar S, Stecher G, and Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33:1870-1874
  • Lai C-P, Lee C-L, Chen P-H, Wu S-H, Yang C-C, Shaw J-F. 2004. Molecular analyses of the Arabidopsis TUBBY-like protein gene family. Plant Physiology 134:1586–1597 DOI 10.1104/pp.103.037820.
  • Lai, C. P., Chen, P. H., Huang, J. P., Tzeng, Y. H., Chaw, S. M., and Shaw, J. F. (2012) Functional diversification of the Tubby-like protein gene families (TULPs) during eukaryotic evolution. Biocatal. Agric. Biotechnol. 1, 2–8.
  • 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. https://doi.org/10.1093/nar/gkr1090
  • 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 Res 39:W475-W478. https://doi.org/10.1093/nar/gkr201
  • Liu, Q. (2008). Identification of rice TUBBY‐like genes and their evolution. The FEBS Journal, 275(1), 163-171.
  • Mortazavi A, Williams BA, Mccue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5(7):621-628. https://doi.org/10.1038/nmeth.1226
  • Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005) InterProScan: protein domains identifier. Nucleic Acids Res 33:W116-W120. https://doi.org/10.1093/nar/gki442
  • Schmutz, J., Cannon, S. B., Schlueter, J., Ma, J., Mitros, T., Nelson, W., Jackson, S. A. (2010). Genome sequence of the palaeopolyploid soybean. Nature, 463(7278), 178–183. https://doi.org/10.1038/nature08670
  • SİRAT, Abdulveli. "Yerel Kuru Fasulye (Phaseolus vulgaris L.) Genotiplerinin Tane Verimi, Verim Unsurları ve Bazı Kalite Özelliklerinin Belirlenmesi." Adnan Menderes Üniversitesi Ziraat Fakültesi Dergisi 17.2 (2020): 245-254.
  • Suyama M, Torrents D, Bork P (2006) PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 34:W609-W612. https://doi.org/10.1093/nar/gkl315
  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25(24):4876-4882. https://doi.org/10.1093/nar/25.24.4876
  • Valliyodan, B., Cannon, S. B., Bayer, P. E., Shu, S., Brown, A. V., Ren, L., ... & Nguyen, H. T. (2019). Construction and comparison of three reference‐quality genome assemblies for soybean. The Plant Journal, 100(5), 1066-1082.
  • Voorrips RE (2002) MapChart: Software for the graphical presentation of linkage maps and QTLs. J Hered 93(1):77-78. https://doi.org/10.1093/jhered/93.1.77
  • Wang, K., Cheng, Y., Yi, L., He, H., Zhan, S., & Yang, P. (2021). Genome-wide identification of the Tubby-Like Protein (TLPs) family in medicinal model plant Salvia miltiorrhiza. PeerJ, 9, e11403.
  • Wang, M., Xu, Z., & Kong, Y. (2018). The tubby-like proteins kingdom in animals and plants. Gene, 642, 16-25.
  • Wang, Tong, et al. "Identification, evolution and expression analyses of whole genome-wide TLP gene family in Brassica napus." BMC genomics 21.1 (2020): 1-14.
  • Wang, Y., You, F. M., Lazo, G. R., Luo, M. C., Thilmony, R., Gordon, S., ... & Gu, Y. Q. (2013). PIECE: a database for plant gene structure comparison and evolution. Nucleic acids research, 41(D1), D1159-D1166.
  • Wang, Yupeng, et al. "MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity." Nucleic acids research 40.7 (2012): e49-e49.
  • Wardhan V, Jahan K, Gupta S, Chennareddy S, Datta A, Chakraborty S, Chakraborty N. 2012. Overexpression of CaTLP1, a putative transcription factor in chickpea (Cicer arietinum L.), promotes stress tolerance. Plant Molecular Biology 79:479–493 DOI 10.1007/s11103-012-9925-y.
  • Xu J, Xing S, Sun Q, Zhan C, Liu X, Zhang S, Wang X. 2019. The expression of a tubby-like protein from Malus domestica (MdTLP7) enhances abiotic stress tolerance in Arabidopsis. BMC Plant Biology 19:60 DOI 10.1186/s12870-019-1662-9.
  • Xu, Jia-Ning, et al. "Genome-wide identification and expression analysis of the tubby-like protein family in the Malus domestica genome." Frontiers in Plant Science 7 (2016): 1693.
  • Yang ZH (2007) PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 24(8):1586-1591. https://doi.org/10.1093/molbev/msm088
  • Yang, Z., Zhou, Y., Wang, X., Gu, S., Yu, J., Liang, G., ... & Xu, C. (2008). Genomewide comparative phylogenetic and molecular evolutionary analysis of tubby-like protein family in Arabidopsis, rice, and poplar. Genomics, 92(4), 246-253.
  • Yulong, C., Wei, D., Baoming, S., Yang, Z., and Qing, M. (2016). Genome-wide identification and comparative analysis of the TUBBY-like protein gene family in maize. Genes Genom. 38, 25–36. doi: 10.1007/s13258-015-0338-6
  • Zhang L, Wu B, Zhao D, Li C, Shao F, Lu S. 2014. Genome-wide analysis and molecular dissection of the SPL gene family in Salvia miltiorrhiza: the SPL gene family in Salvia miltiorrhiza. Journal of Integrative Plant Biology 56:38–50 DOI 10.1111/jipb.12111.
Toplam 46 adet kaynakça vardır.

Ayrıntılar

Birincil Dil Türkçe
Konular Mühendislik
Bölüm Makaleler
Yazarlar

Ayşe Gül Kasapoğlu 0000-0002-6447-4921

Ahmed Sidar Aygören 0000-0002-6264-9935

Selman Muslu 0000-0003-4777-0726

Burak Muhammed Öner 0000-0003-2785-2089

Murat Isıyel 0000-0003-4157-2729

Esra Yaprak 0000-0002-8753-494X

Sümeyra Uçar 0000-0002-7629-0206

Recep Aydınyurt 0000-0003-3743-1835

Büşra Uzun 0000-0002-5682-6739

Emre İlhan 0000-0002-8404-7900

Murat Aydın 0000-0003-1091-0609

Erken Görünüm Tarihi 30 Ocak 2022
Yayımlanma Tarihi 31 Mart 2022
Yayımlandığı Sayı Yıl 2022 Sayı: 34

Kaynak Göster

APA Kasapoğlu, A. G., Aygören, A. S., Muslu, S., Öner, B. M., vd. (2022). PvTLP genlerinin genom çaplı tespit ve karakterizasyonu. Avrupa Bilim Ve Teknoloji Dergisi(34), 676-684. https://doi.org/10.31590/ejosat.1083519