با همکاری مشترک دانشگاه پیام نور و انجمن بیوتکنولوژی جمهوری اسلامی ایران

نوع مقاله : علمی پژوهشی

نویسندگان

دکتری، گروه اصلاح نباتات، واحد علوم و تحقیقات، دانشگاه آزاد اسلامی، تهران، ایران.

چکیده

گیاه زراعی Brassica napus به‌عنوان یک دانه روغنی مهم، پس از هیبریداسیون بین گونه‌ای اجدادش تحت بازسازی گسترده ژنوم قرار گرفته است. به‌منظور تبیین ساز و کارهای تکاملی زمینه‌سازِ تنوع متابولیت‌های ثانویه، تحلیل مقایسه‌ای این‌سیلیکو ژن‌های افتراقی بین سه گونه براسیکا انجام شد. بعد از هم‌گذاری توالی اولیه EST کتابخانه‌ها با استفاده از نرم‌افزار EGassembler، کانتیگ‌ها به‌وسیله جستجوگر بلاست X توسط نرم‌افزار CLC Protein Workbench در مقابل پروتئین‌های غیر تکراری بانک ژن واکاوی شدند. نرم‌افزار IDEG6 و آماره Audic-Claverie برای تعیین بیان افتراقی ژن‌ها استفاده شد. برای شناسایی ارتولوگ‌ها و پارالوگ‌ها، از تارنمای Ensembl Plants استفاده شد و هم ردیفی دو به دو برای هر جفت پروتئین توسط CLUSTALW انجام شد. کشف موتیف DNA یک گام اولیه در بسیاری از سیستم‌ها برای مطالعه عملکرد ژن است، بنابراین وب سایت MEME و وب ابزار STAMP برای کاوش موتیف اتصال به DNA و تعیین شباهت توالی‌های موتیف پارالوگ‌ها استفاده شد. نتایج، تفاوت معنی‌داری را بین 18 ژن درگروه‌های کارکردی متابولیسم ثانویه و تنظیم رونویسی نشان داد. اکثر ژن‌های دخیل در تنوع گلوکوزینولات‌ها در B. napus دارای ژن‌های ارتولوگ در گونه‌های اجدادی و آرابیدوپسیس بودند که طی فرایندهای تکاملی واگرا شده‌اند. درحالی‌که بیشتر ژن‌های تنظیم رونویسی شامل MYB28 و bHLH دارای ژن‌های پارالوگ بودند که در درون گونه B. napus و در نتیجه تکثیر و جهش، به دنبال تغییرات حاصل از آلو پلی‌پلوئیدی تغییر عملکرد یافته‌اند. ژنوم اجداد B. napus، منابع ارزشمندی برای تحلیل این‌سیلیکو در درک پیامدهای ژنتیکی پلی‌پلوئیدی، تکامل و اصلاح B. napus فراهم می‌کند.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

Evolutionary mechanisms underlying secondary metabolite diversity of the three Brassica species using insilico comparative analysis of the related genes

نویسندگان [English]

  • Shadi Heidari
  • Peivand Heidari

Ph. D, Department of Plant Breeding, Science and Research Branch, Islamic Azad University, Tehran, Iran

چکیده [English]

Brassica napus field plant, as an important oilseed, has undergone extensive genome reconstruction after interspecies hybridization of its ancestors. To elucidate the evolutionary mechanisms underlying the diversity of secondary metabolites, insilico comparative analysis of different genes between three Brasica species was performed. After assembling the preliminary EST sequence of libraries using EGassembler software, the contigs were analyzed by X-blast using CLC Protein Workbench software against non-redundant proteins databank. IDEG6 software and Audic-Claverie statistics were used to determine the differential expression of genes. To identify orthologs and paralogs, the Ensembl Plants website and CLUSTALW were used for a pairwise alignment for each pair of proteins. The discovery of the DNA motif is a first step in many systems to study gene function, so the MEME website and STAMP webtool were used to explore the DNA binding motif and determine the similarity of the motif sequences of the paralogs. The results showed a significant difference between 18 genes in the functional groups of secondary metabolism and transcriptional regulation. Most of the genes involved in the glucosinolate diversity in B. napus have ortholog genes in the ancestral species and Arabidopsis, which have diverged during evolutionary processes. While most transcriptional regulatory genes, including MYB28 and bHLH, have paralog genes that have been functionally altered within B. napus as a result of duplication and mutation following changes in allopolyploidy. The ancestral genome of B. napus provides valuable resources for insilico analysis in understanding the genetic consequences of polyploidy, evolution and breeding of B. napus.

کلیدواژه‌ها [English]

  • Allopolyploidy
  • Brassica napus
  • Comparative analysis of insilico
  • EST
  • Ortholog groups and paralog genes
Bassel, G. W., Glaab, E., Marquez, J. & Bacardit, J. (2011). Functional Network Construction in Arabidopsis Using Rule-Based Machine Learning on Large-Scale Data Sets. Plant Cell, 23 (9), 3101-3116. Bisht, N.C., Gupta, V., Ramchiary, N., Sodhi, Y.S., Mukhopadhyay, A., Arumugam, N., Pental, D. & Pradhan, A. (2009). Fine mapping of loci involved with glucosinolate biosynthesis in oilseed mustard (Brassica juncea) using genomic information from allied species. Theoretical and Applied Genetics, 118 (3), 413-421. FAO (2020). Oilseeds oils and meals to contribute to world food security. America, New York. Friedt, W. & Snowdon, R. (2009). Oilseed rape in Oil Crops. New York, Vollmann press. Gigolashvili, T., Engqvist, M., Yatusevich, R., Muller, C. & Flugge, U. I. (2007). The transcription factor HIG1/MYB51 regulates indolic glucosinolate biosynthesis in Arabidopsis thaliana. Plant Journal, 50 (5), 886-901. Harper, A.L., Trick, M., Higgins, J., Fraser, F., Clissold, L., Wells, R., Werner, P. & Bancroft, I. (2012). Associative transcriptomics of traits in the polyploid crop species Brassica napus. Nature Biotechnology, 30, 798-802. Hayes, J.D., Kelleher, M.O. & Eggleston, I.M. (2008). The cancer chemopreventive actions of phytochemicals derived from glucosinolates. European Journal of Nutrition, 47 (2), 73-88. Heidary, P., Maleki Zanjani, B. & Heidary, S. (2012). A study of gene expression and functional genomics of wheat, rice, cotton and festuca plants under drought stress by analyzing expressed sequence tags (EST). Modern Genetics Journal, 7(2 (29)), 129-140. (in Persian). Heidari, Sh., Azizinezhad, R., Haghparast, R. & Heidari, P. (2019). Evaluation of the association among yield and contributing characters through path coefficient analysis in advanced lines of durum wheat under diverse conditions. Journal of Animal and Plant Sciences, 29 (5), 1325-1335. Heidari, Sh., Heidari, P., Azizinezhad, R., Etminan, A. & Khosroshahli, M. (2020). Assessment of variability heritability and genetic advance for agro-morphological and some in-vitro related-traits in durum wheat. Bulgarian Journal of Agricultural Science, 26(1), 120-127. Ke, Y. Z., Wu, Y. W. & Zhou, H. J. (2020). Genome-wide survey of the bHLH super gene family in Brassica napus. BMC Plant Biology, 20, 115. Kliebenstein, D. J., Kroymann, J., Brown, P., Figuth, A., Pedersen, D., Gershenzon, J. & Mitchell-Olds, T. (2001). Genetic control of natural variation in Arabidopsis glucosinolate accumulation. Plant Physiology, 126(2), 811-825. Koonin, E. V., Mushegian, A. R. & Bork, P. (1996). Non-orthologous gene displacement. Trends in Genetics, 12(9), 334-336. Kumar, R., Lee, S. G., Augustine, R., Reichelt, M., Vassão, D. G., Palavalli, M. H., Allen, A., Gershenzon, J., Jez, J. M. & Bisht, N. C. (2019). Molecular Basis of the Evolution of Methylthioalkylmalate Synthase and the Diversity of Methionine-Derived Glucosinolates. The Plant Cell, 31(7), 1633-1647. Li, X., Chen, L., Hong, M., Zhang, Y., Zu, F., Yi, B., Shen, J., Tu, J. & Fu, T. (2012). A large insertion in bHLH transcription factor BrTT8 resulting in yellow seed coat in Brassica rapa. PloS One, 7(9), e44145. Lysak, M. A., Koch, M. A., Pecinka, A. & Schubert, I. (2005). Chromosome triplication found across the tribe Brassiceae. Genome Research, 15 (4), 516-525. Mahony, S. & Benos, P. V. (2007). STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Research, 35, W253-W258. Masoudi Nejad, A., Tonomura, K., Kawashima, Sh., Moriya, Y., Suzuki, M., Itoh, M., Kanehisa, M., Endo, T. & Goto, S. (2006). EGassembler: online bioinformatics service for large-scale processing clustering and assembling ESTs and genomic DNA fragments. Nucleic Acids Research, 34, 459-462. Mcginnis, S. & Madden, T. L. (2004). BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Research, 32: 20-25. Neerincx, P. & Leunissen, J. (2005). Evolution of web service in bioinformatics. Briefings in Bioinformatics, 6 (2), 178-188. Nugroho, A.B., Han, N. & Pervitasari, A.N. (2020). Differential expression of major genes involved in the biosynthesis of aliphatic glucosinolates in intergeneric Baemoochae (Brassicaceae) and its parents during development. Plant Molecular Biology, 102, 569. Panjabi, P., Jagannath, A., Bisht, N. C., Padmaja, K. L., Sharma, S., Gupta, V., Pradhan, A. K. & Pental, D. (2008). Comparative mapping of Brassica juncea and Arabidopsis thaliana using Intron Polymorphism (IP) markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genomes. BMC Genomics, 9, 113. Pérez-Bercoff, A., Makino, T. & McLysaght, A. (2010). Duplicability of self-interacting human genes. BMC Evolutionary Biology, 28(10), 160. Ramsak, Z., Baebler, S., Rotter, A., Korbar, M., Mozetic, I., Usadel, B. & Gruden, K. (2014). GoMapMan: integration consolidation and visualization of plant gene annotations within the MapMan ontology. Nucleic Acids Research, 42(1), D1167-D1175. Ren, Y., Zhang, N., Li, R., Ma, X. & Zhang, L. (2021). Comparative transcriptome and flavonoids components analysis reveal the structural genes responsible for the yellow seed coat color of Brassica rapa L. PeerJ, 9, e10770. Romualdi, C., Bortoluzzi, S. & Danieli, G. A. (2003). IDEG6: a web tool for detection of differentially expressed genes in multiple tag sampling experiments. Physiological Genomics, 12, 159-162. Sharma, M., Mukhopadhyay, A., Gupta, V., Pental, D. & Pradhan, A. K. (2016). BjuB.CYP79F1 Regulates Synthesis of Propyl Fraction of Aliphatic Glucosinolates in Oilseed Mustard Brassica juncea: Functional Validation through Genetic and Transgenic Approaches. PloS One, 11(2), e0150060. Singh, P., Arf, Y., Bajuz, A. & Hayt, S. (2021). The role of quercetin in plant. Plant Physiology, 166, 10-19 Sinha, S. & Tompa, M. (2003). YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Research, 31(13), 3586-3588. Sønderby, I. E., Burow, M., Rowe, H. C., Kliebenstein, D. J. & Halkier, B. A. (2010). A Complex Interplay of Three R2R3 MYB Transcription Factors Determines the Profile of Aliphatic Glucosinolates in Arabidopsis. Plant Physiology, 153 (1), 348-363. Town, C.D., Cheung, F., Maiti, R., Crabtree, J., Haas, B. J., Wortman, J. R., Hine, E. E., Althoff, R., Arbogast, T. S., Tallon, L. J., Vigouroux, M. T., Rick, M. & Bancroft, I. (2006). Comparative Genomics of Brassica oleracea and Arabidopsis thaliana Reveal Gene Loss, Fragmentation, and Dispersal after Polyploidy. The Plant Cell, 18(6), 1348-1359. Udall, J. A., Swanson, J. M., Nettleton, D., Percifield, R. J. & Wendel, J. F. (2006). A novel approach for characterizing expression levels of genes duplicated by polyploidy. Genetics, 173, 1823-1827. Vassilev, D. J., Leunissen, A., Atanassov, A., Nenov, A. & G, Dimov. (2005). Application of bioinformatics in plant breeding. Biotechnology and Biotechnological Equipment, 19, 139-152. Wood, T., Takebayashi, N., Barker, M., Mayrose, I., Greenspoon, P. & Rieseberg, L.H. (2009). The frequency of polyploid speciation in vascular plants. Proceedings of the National Academy of Sciences, 106 (33), 13875-13879. Yonekura, K. & Saito, K. (2009). Functional genomics for plant natural product biosynthesis. Natural Product Reports, 26 (11), 1466-1487. Zang, Y. X., Kim, H. U. & Kim, J. A. (2009). Genome-wide identification of glucosinolate synthesis genes in Brassica rapa. The FEBS Journal, 276 (13), 3559-3574.