Analyzing Simple Sequence Repeats Derived from Expressed Sequence Tags in Dromedary Camels
محورهای موضوعی : Camelا. برازنده 1 , م. مختاری 2 , م. مقبلی دامنه 3 , ز. رودباری 4
1 - Department of Animal Science, Faculty of Agriculture, University of Jiroft, Jiroft, Iran
2 - Department of Animal Science, Faculty of Agriculture, University of Jiroft, Jiroft, Iran
3 - Department of Animal Science, Faculty of Agriculture, University of Jiroft, Jiroft, Iran
4 - Department of Animal Science, Faculty of Agriculture, University of Jiroft, Jiroft, Iran
کلید واژه: camel, SSR, Molecular marker, genomic, EST, gene ontology,
چکیده مقاله :
The objective of the current research was to make a character description of simple sequence repeats (SSR) derived from expressed sequence TAGs (EST) markers of dromedary camels (EST-SSR markers) and to conduct a practical analysis of these sequences for their application in comparative genomics and molecular genetics studies. A complete of 862 SSRs were discovered from 17155 EST sequences using the SSR Locator software. 827 EST out of 17155 EST had SSRs, that 794 (96%), 31 (3.8%) and 2 (0.2%) of them contained 1, 2 and 3 SSRs, respectively. The dimeric motifs were the most abundant SSRs (38.86%), followed by 27.15%, 21.46%, 6.96%, and 5.57% for tri-, hexa-, tetra- and pentameric motifs. The most plentiful dimer, trimer, tetramer, pentamer and hexamer motif were AC/TG (54%), GCC/GGC (19.2%), TTTA (13.3%), AAAAG (10.4%) and AACCAC (67.6 %), respectively. BLASTX was used to examine the final non-redundant EST-SSRs. Almost all of EST-SSRs were found out to be protected in the macromolecule catabolic process and RNA processing and splicing. EST-SSR markers might be applied as a novel resource of useful markers in the biological survey. Also, these markers may be a valuable source for further molecular genetics and genomics research of camels and related species.
هدف از تحقیق حاضر بررسی ویژگی های توالی های تکراری ساده مشتق شده از توالی های بیان شده برچسب دار (نشانگرهای EST-SSR) در شتر تک کوهانه و همچنین تجزیه و تحلیل عملکردی این نشانگرها جهت استفاده در مطالعات مولکولی و ژنومی بود. از 17155 توالی EST با استفاده از نرم افزارSSR Locator تعداد 862 توالی تکراری ساده (SSRs) بدست آمد. به طورکلی تعداد 827 توالی EST دارای SSR بوده که 794 (96 درصد)، 31 (8/3 درصد) و 2 (2/0 درصد) تا از آنها به ترتیب حاوی 1، 2 و 3 توالی SSR بودند. موتیفهای دایمری فراوانترین نوع SSR بودند و پس از آنها به ترتیب موتیفهای تری، هگزا، تترا و پنتامری با 27.15، 21.46، 6.96 و 5.57 درصد قرار گرفتند. فراوانترین موتیف های دایمر، تریمر، تترامر، پنتامر و هگزامر به ترتیب AC/TG (54 درصد)، GCC/GGC (19.2 درصد)، TTTA (13.3 درصد)، AAAAG (10.4 درصد) و AACCAC (67.6 درصد) بودند. نشانگرهای EST-SSR نهایی با استفاده از BLASTX بررسی شدند. تقریباً اکثر این نشانگرها در فرایندهای کاتابولیک ماکرومولکول ها و پردازش و اسپلایسینگ RNA مشارکت داشتند. میتوان از نشانگرهای EST-SSR به عنوان نشانگرهای جدید مفید در بررسیهای بیولوژیکی استفاده نمود. همچنین این نشانگرها یک منبع ارزشمند جهت مطالعات مولکولی و ژنومی شتر و گونه های مرتبط با آن هستند.
Abe H. and Gemmell N.J. (2014). Abundance, arrangement, and function of sequence motifs in the chicken promoters. BMC Genom. 15, 900-912.
Al-Swailem A.M., Shehata M.M., Abu-Duhier F.M., Al-Yamani E.J., Al-Busadah K.A., Al-Arawi M.S., Al-Khider A.Y., Al-Muhaimeed A.N., Al-Qahtani F.H., Manee M.M., Al-Shomrani B.M., Al-Qhtani S.M., Al-Harthi A.S., Akdemir K.C., Inan M.S. and Otu H.H. (2010). Sequencing, analysis, and annotation of expressed sequence tags for Camelus dromedarius. PLoS One. 5, e10720.
Altaher Y. and Kandeel M. (2015). Molecular analysis of some camel cytochrome P450 enzymes reveals lower evolution and drug-binding properties. J. Biomol. Struct. Dyn. 33, 1-10.
Asadi A.A. and Rashidi Monfared S. (2014). Characterization of EST-SSR markers in durum wheat EST library and functional analysis of SSR-containing EST fragments. Mol. Genet. Genom. 289, 625-640.
Bai J.Y., Pang Y.Z., Qi Y.X., Zhang X.H. and Yun X.Y. (2016). Development and application of EST-SSR markers in quails. Rev. Bras. Ciênc. Avíc. 18, 27-32.
Bakhtiarizadeh M.R., Ebrahimi M. and Ebrahimie E. (2011). Discovery of EST-SSRs in lung cancer: Tagged ESTs with SSRs lead to differential amino acid and protein expression patterns in cancerous tissues. PLoS One. 6, e27118.
Bakhtiarizadeh M.R., Arefnejad B., Ebrahimie E. and Ebrahimi M. (2012). Application of functional genomic information to develop efficient EST-SSRs for the chicken (Gallus gallus). Genet. Mol. Res. 11, 1558-1574.
Cai K., Zhu L., Zhang K., Li L., Zhao Z. and Zeng W. (2019). Development and characterization of EST-SSR markers from RNA-Seq data in Phyllostachys violascens. Front. Plant Sci. 10, 1-9.
Consortium G.O. (2008). The gene ontology project in 2008. Nucleic Acids Res. 36, 440-444.
Du J., Zhang Z., Zhang H. and Junhong T. (2017). EST-SSR marker development and transcriptome sequencing analysis of different tissues of Korean pine. Biotechnol. Biotechnol. Equip. 31, 679-689.
Durand J., Bodénès C., Chancerel E., Frigerio J.M., Vendramin G., Sebastiani F., Buonamici A., Gailing O., Koelewijn H.P., Villani F., Mattioni C., Cherubini M., Goicoechea P.G., Herrán A., Ikaran Z., Cabané C., Ueno S., Alberto F., Dumoulin P.Y., Guichoux E., de Daruvar A., Kremer A. and Plomion C. (2010). A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study. BMC Genom. 11, 570-581.
Ellis J.R. and Burke J.M. (2007). EST-SSRs as a resource for population genetic analyses. Heredity. 99, 125-132.
Feng B., Yi S. V., Zhang M. and Zhou X. (2018). Development of novel EST-SSR markers for ploidy identification based on de novo transcriptome assembly for Misgurnus anguillicaudatus. PLoS One. 13, 1-15.
Guzinski J., Mauger S., Cock J.M. and Valero M. (2016). Characterization of newly developed expressed sequence tag-derived microsatellite markers revealed low genetic diversity within and low connectivity between European Saccharina latissima populations. J. Appl. Phycol. 28, 3057-3070.
Huang D.W., Sherman B.T. and Lempicki R.A. (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57.
Jiao S., Sun Y., Zhang D., Gao Q., Jin Y., Liu H., Ma Y., Yang Y., Porth I. and Mao J. (2019). Development of novel EST- SSR markers for Ephedraceae (Ephedra sinica) by transcriptome database mining. Appl. Plant Sci. 7, 3-7.
Jirimutu Wang Z., Ding G., Chen G., Sun Y., Sun Z., Zhang H., Wang L., Hasi S., Zhang Y., Li J., Shi Y., Xu Z., He C., Yu S., Li S., Zhang W., Batmunkh M., Ts B., Narenbatu U., Bat-Ireedui S., Gao H., Baysgalan B., Li Q., Jia Z., Turigenbayila S., Narenmanduhu W.Z., Wang J., Pan L., Chen Y., Ganerdene Y., Dabxilt E., Altansha A., Liu T., Cao M., Aruuntsever B., Hosblig H.F., Zha-ti A., Zheng G., Qiu F., Sun Z., Zhao L., Zhao W., Liu B., Li C., Chen Y., Tang X., Guo C., Liu W., Ming L., Temuulen C.A., Li Y., Gao J., Li J., Wurentaodi N.S., Sun T., Zhai Z., Zhang M., Chen C., Baldan T., Bayaer T., Li Y. and Meng H. (2012). Genome sequences of wild and domestic bactrian camels. Nat. Commun. 3, 1202-1209.
Joshi R.K., Kuanar A., Mohanty S., Subudhi E. and Nayak S. (2010). Mining and characterization of EST derived microsatellites in Curcuma longa. Bioinformation. 5, 128-131.
Ju Z., Wells M.C., Martinez A., Hazlewood L. and Walter R.B. (2005). An in silico mining for simple sequence repeats from expressed sequence tags of zebrafish, medaka, Fundulus, and Xiphophorus. In Silico Biol. 5, 439-463.
Kastelic D., Frkovic-Grazio S., Baty D., Truan G., Komel R. and Pompon D. (2009). A single-step procedure of recombinant library construction for the selection of efficiently produced llama VH binders directed against cancer markers. J. Immunol. Methods. 350, 54-62.
Khimoun A., Ollivier A., Faivre B. and Garnier S. (2017). Level of genetic differentiation affects relative performances of expressed sequence tag and genomic SSRs. Mol. Ecol. Resour. 17, 893-903.
Kim B.Y., ParK H.S., Lee J.H., KwaK M. and Kim aNd Y. (2017). Development of microsatellite markers baseD on expresseD sequence tags in AspArAgus cochinchinensis (asparagaceae). Appl. Plant Sci. 5, 1-5.
Kim K.S., Ratcliffe S.T., French B.W., Liu L. and Sappington T.W. (2008). The utility of EST-derived SSRs as population genetics markers in a beetle. J. Hered. 99, 112-124.
Kumar B., Kumar U. and Yadav H.K. (2015). Identification of EST–SSRs and molecular diversity analysis in Mentha piperita. Crop J. 3, 335-342.
Li B., Xia Q., Lu C., Zhou Z. and Xiang Z. (2004a). Analysis on frequency and density of microsatellites in coding sequences of several eukaryotic genomes. Genom. Proteom. Bioinf. 2, 24-31.
Li Y.C., Korol A.B., Fahima T. and Nevo E. (2004b). Microsatellites within genes: Structure, function, and evolution. Mol. Biol. Evol. 21, 991-1007.
Maia L.C.D., Palmieri D.A., Souza V.Q.D, Kopp M.M., Carvalho F.I.F.D. and Costa de Oliveira A. (2008). SSR locator: Tool for simple sequence repeat discovery integrated with primer design and PCR simulation. Int. J. Plant Genom. 2008, 412696.
Mbwana J., Bölin I., Lyamuya E., Mhalu F. and Lagergård T. (2006). Molecular characterization of Haemophilus ducreyi isolates from different geographical locations. J. Clin. Microbiol. 44, 132-137.
Mirkin S.M. (2006). DNA structures, repeat expansions and human hereditary disorders. Curr. Opin. Struct. Biol. 16, 351-358.
Nguyen V.K., Hamers R., Wyns L. and Muyldermans S. (2000). Camel heavy-chain antibodies: Diverse germline V(H)H and specific mechanisms enlarge the antigen-binding repertoire. EMBO J. 19, 921-30.
Nirapathpongporn K., Kongsawadworakul P., Viboonjun U., Teerawattanasuk K., Chrestin H., Segiun M., Clément-Dement A. and Narangajavana J. (2016). Development and mapping of functional expressed sequence tag-derived simple sequence repeat markers in a rubber tree. Mol. Breed. 36, 39-45.
Peakall R., Gilmore S., Keys W., Morgante M. and Rafalski A. (1998). Cross-species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: implications for the transferability of SSRs in plants. Mol. Biol. Evol. 15, 1275-1287.
Pérez F., Ortiz J., Zhinaula M., Gonzabay C., Calderón J. and Volckaert F.A.M.J. (2005). Development of EST-SSR markers by data mining in three species of shrimp: Litopenaeus vannamei, Litopenaeus stylirostris, and Trachypenaeus birdy. Mar. Biotechnol. 7, 554-569.
Qin Z., Wang Y., Wang Q., Li A., Hou F. and Zhang L. (2015). Evolution analysis of simple sequence repeats in plant genome. PLoS One. 10, e0144108.
Reddy M.P., Sarla N. and Siddiq E.A. (2002). Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica. 128, 9-17.
Reed K.M. and Chaves L.D. (2008). Simple sequence repeats for genetic studies of Alpaca. Anim. Biotechnol. 19, 243-309.
Sadder M., Migdadi H., Al-haidary A. and Okab A. (2015). Identification of simple sequence repeat markers in the dromedary (Camelus dromedarius) genome by next-generation sequencing. 39, 218-228.
Saiki R.K., Scharf S., Faloona F., Mullis K.B., Horn G.T., Erlich H.A. and Arnheim N. (1985). Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science. 230, 1350-1354.
Serapion J., Kucuktas H., Feng J. and Liu Z. (2004). Bioinformatic mining of type I microsatellites from expressed sequence tags of channel catfish (Ictalurus punctatus). Mar. Biotechnol. 6, 364-377.
Singh S., Gupta S., Mani A. and Chaturvedi A. (2012). Mining and gene ontology based annotation of SSR markers from expressed sequence tags of Humulus lupulus. Bioinformation. 8, 114-22.
Slate J., Hale M.C. and Birkhead T.R. (2007). Simple sequence repeats in zebra finch (Taeniopygia guttata) expressed sequence tags: A new resource for evolutionary genetic studies of passerines. BMC Genom. 8, 52-60.
Taheri S., Abdullah T.L., Yusop M.R., Hanafi M.M., Sahebi M., Azizi P. and Shamshiri R.R. (2018). Mining and development of novel SSR markers using next generation sequencing (NGS). Molecules. 23, 399-406.
Toth G., Gaspari Z. and Jurka J. (2000). Microsatellites in different eukaryotic genomes : Survey and analysis. Genome Res. 10, 967-981.
Varshney R.K., Thiel T., Stein N., Langridge P. and Graner A. (2002). In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell. Mol. Biol. Lett. 7, 537-546.
Vekemans X., Beauwens T., Lemaire M. and Roldan Ruiz I. (2002). Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Mol. Ecol. 11, 139-151.
Vieira M.L.C., Santini L., Diniz A.L. and Munhoz C. de F. (2016). Microsatellite markers : What they mean and why they are so useful. Genet. Mol. Biol. 39, 312-328.
Wang B.H., Rong P., Cai X.X., Wang W., Zhu X.Y., Chen C.J., Xu Y.Y., Huang X.J., Zhuang Z.M. and Wang C.B. (2015). Development of EST-SSR markers related to disease resistance and their application in genetic diversity and evolution analysis in Gossypium. Genet. Mol. Res. 14, 10630-10644.
Wang P., Yang L., Zhang E., Qin Z., Wang H., Liao Y., Wang X. and Gao L. (2017). Characterization and development of EST-SSR markers from a cold-stressed transcriptome of centipedegrass by illumina paired-end sequencing. Plant Mol. Biol. Report. 35, 215-223.
Wu H., Guang X., Al-Fageeh M.B., Cao J., Pan S., Zhou H., Zhang L., Abutarboush M.H., Xing Y., Xie Z., Alshanqeeti A.S., Zhang Y., Yao Q., Al-Shomrani B.M., Zhang D., Li J., Manee M.M., Yang Z., Yang L., Liu Y., Zhang J., Altammami M.A., Wang S., Yu L., Zhang W., Liu S., Ba L., Liu C., Yang X., Meng F., Wang S., Li L., Li E., Li X., Wu K., Zhang S., Wang J., Yin Y., Yang H., Al-Swailem A.M. and Wang J. (2014). Camelid genomes reveal evolution and adaptation to desert environments. Nat. Commun. 5, 5188-5199.
Yan Q., Zhang Y., Li H., Wei C., Niu L. and Guan S. (2008). Identification of microsatellites in cattle unigenes. J. Genet. Genom. 35, 261-266.
Zane L., Patarnello T., Bargelloni L. and Patarnello T. (2002). Strategies for microsatellite isolation: A review. Mol. Ecol. 11, 1-16.
Zhang W., Wang Z., Zhao Z., Zeng X., Wu H. and Yu P. (2010). Using bioinformcotics methods to develop EST-SSR makers from sheep’s ESTs. J. Anim. Vet. Adv. 9, 2759-2762.
Zheng X., Kuang Y., Lü W., Cao D. and Sun X. (2014). Transcriptome-derived EST–SSR markers and their correlations with growth traits in crucian carp Carassius auratus. Fish Sci. 80, 977-984.
Zhou Q., Luo D., Ma L., Xie W., Wang Y., Wang Y. and Liu Z. (2016). Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus) using Illumina sequencing. Sci. Rep. 6, 20549-20559.
