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

نوع مقاله : علمی پژوهشی

نویسندگان

1 کارشناس‌ارشد اصلاح‌نباتات، دانشکده کشاورزی، دانشگاه ارومیه، ارومیه، ایران

2 استادیار، بخش تحقیقات علوم زراعی و باغی، مرکز تحقیقات و آموزش کشاورزی و منابع طبیعی آذربایجان غربی، سازمان تحقیقات، آموزش و ترویج کشاورزی، ارومیه، ایران

3 دانشیار گروه اصلاح‌نباتات و بیوتکنولوژی گیاهی، دانشکده کشاورزی دانشگاه ارومیه، ارومیه، ایران

چکیده

هشت ژنوم دیپلوئید شامل ژنوم‌های A، B، C، D، E، F، G و K در جنس گوسیپیوم Gossypium شناسایی شده اند. ژنوم A فقط به دو گونه herbaceum و arboreum پنبه های دنیای قدیم محدود شده است و این ژنوم از G. herbaceumبه گونه‌های دیگر انتقال پیدا کرده است. به منظور توالی یابی ژنوم کلروپلاست G. herbaceum (A1) و مقایسه آن با دو گونه G. hirsutum (AD1) و G. barbadense (AD2) توالی‌های ژنوم سه گونه از سایت مرکز ملی اطلاعات بیوتکنولوژی برداشت شده است. موقعیت هر کدام از ژن‌ها، تعداد نوکلئوتید‌ها، نواحی بین ژنی و اینترون‌ها مشخص گردید. ژنوم کلروپلاست G. herbaceum دارای 160140 جفت‌‌باز بوده و ساختمان چهاربعدی حفاظت شده دارد. نواحی تک نسخه‌ای ژنوم کلروپلاست، توسط دو ناحیه‌ تکرار معکوس از هم جدا شده که ناحیه‌ تک نسخه‎‌ای بزرگ دارای 88709 جفت ‌باز، ناحیه‌ تک نسخه‌ای کوچک 20221 جفت ‌باز بوده و هر ناحیه‌ تکرار معکوس 25605 جفت باز دارد. ژنوم پلاستیدی 114 ژن تک نسخه‌ای و 19 ژن دو نسخه‌ای دارد که ژن‌های تک نسخه‌ای شامل 79 ژن رمزکننده‌ پروتئین، 4 ژن rRNA ریبوزومی و 31 ژن tRNA است. نتایج نشان داد میان ژن‌های پلاستیدی فقط 18 ژن دارای 2-1 اینترون هستند که در مقایسه با ژنوم کلروپلاست دو گونه آلوتتراپلوئیدی ژن ycf15 تنها ژن دو


نسخه‌ای موجود در G. herbaceum بود. در G. herbaceum و G. barbadense ژن rpl22 وجود داشت ولی ژن ycf15 در


G. barbadense، ژن های rpl22 و ycf15 در G. hirsutum از دست رفته اند. با وجود میزان بالای حفاظت SSRها در ژنوم کلروپلاست این SSRها به دلیل بازده بالا در مقابل SSR ژنومی برای آنالیز تنوع ژنتیکی مفید هستند.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

Comparative bioinformatics analyses of the chloroplast genome of a diploid Cotton (G. herbaceum) with two allotetraploid species

نویسندگان [English]

  • Hajar Nasrollahi 1
  • Farshid Talat 2
  • Iraj Bernousi 3
  • Mehdi Badri Anarjan 1

1 Former M.Sc. Student of Plant Breeding, Urmia University, Urmia, Iran

2 Assistant Professor, Seed and Plant Improvement Research Department, West Azarbaijan Agricultural and Natural Resources Research and Education Center, AREEO, Urmia, Iran.

3 Associate Professor, Department of Plant Breeding and Plant Biotechnology, Faculty of Agriculture, Urmia University, Urmia, Iran

چکیده [English]

Diploid genome contains 8 genomes designated as A, B, C, D, E, F, G and K which have been identified in the genus Gossypium. The genome of A is limited only in two species as G. herbaceum and G.arboreum, and it is transferred from G. herbaceum to other species. The chloroplast genome (CP) of G. herbaceum has 160,140 bp lengths with protected quadripartite structure. Single copy regions of chloroplast genome are separated by two inverted repeat regions with a large copy region with 88,709 bp also the single copy region and each small inverted repeat regions have 20,221 and 25,605bp. The plastidic' s genome has 113 single copy genes and 19 duplicated copy genes. Single copy genes are encoding of 79 genes for protein production, four ribosomal RNA genes and 31 transfer RNA genes. Result showed that among all plastid genes only 18 genes appeared to have 1-2 intron/s and when compared with chloroplast genome of two allotetraploid species. Ycf15 gene as the only duplicated gene, rpl22 was in G. herbaceum and in the two species has studied G. herbaceum, G. barbadense. But ycf15 gene in G. barbadense and both ycf15 and rpl22 genes were lost in G. barbadense and G. hirsutum. Though the high level of SSR protection in the chloroplast genome. SSRs are useful for genetic variation analysis since they have high efficiency against genomic SSRs.

کلیدواژه‌ها [English]

  • Gossypium herbaceum
  • Chloroplast Genome
  • sequencing
Bausher M, Singh ND, Lee SB, Jansen RK, Daneill H (2006) The complete chloroplast genome sequence of Citrus sinesis (L.) obsek var Ridye pinapple organization and phylogenetic relationships to the angiosperms. J. BMC. Plant. Bio. doi: 10.1186/1471-2229-6-21.
Blenda A, Scheffler J, Scheffler B, Palmer M, Lacap JM, Yu JZ, Jesudurai C, Jung S, Muthukumar S, Yellambalase P, Ficklin S, Staton M, Eshelman R, Ulloa M, Saha S, Burr B, Liu S, Zhang T, Fang D (2006) A cotton microsatellite database resource for Gossypium genomics. BMC. Gen. 7:132-142.        
Chan CX, Grass J, Yoon HS, Bhattacharya D (2011) Plastid origin and evolution: new models provide insights into old problems. Plant. Phys. doi: 10.1104/pp.111.173500
Chatterjee A, Pakrashi SC (2006) The treatise on Indian medicinal plants. National Institue of Science Communication and Information Resources, New Delhi. 
Choudhury MN, Uddin A, Chakraborty S (2017) Nucleotide composition and codon usage bias of SRY gene. J. Andr. doi: 10.1111/and.12787
Daniell H, Lee SB, Grerich J, Saski C, Quesada-Varges T, Guda C, Tomkins J, Jansen RK (2006) Complete chloroplast genome sequences of Solanum bulbacastanum, Solanum lycopersicum and comparative analysis with other Solanaceae genomes. Theor. Appl. Genet. 112:1503-1518.
Daniell H, Wurdack KJ, Kanagaraj A, Lee SB, Saski Ch, Jansen RK (2008) The complete nucleotide sequence of the cassava (Manihot esculenta) chloroplast genome and the evolution of atpF in Malpighiales: RNA editing and multiple losses of a group II intron. Theor. Appl. Genet. doi: 10.1007/s00122-007-0706-y
Goremykin V, Hirsch-Ernest K, Wolf S, Hellwig F (2003) Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborella is not a basal angiosperm. Mol. Bio. Evo. doi: 10.1093/mobev/msg159
Gray JC, Hird SM, Dyer TA (1990) Nucleotide sequence of a wheat chloroplast gene encoding the proteolytic sub nit of an ATP-dependent protease. Plant. Mol. Bio. 15:947-950.
Greiner S, Rauwolf U, Meurer J, Herrmann RG (2011) The role of plastids in plant speciation. Mol. Eco. 20:671-691.
Hirao T, Watanabe A, Kurita M, Kondo T, Takata K (2008) Complete nucleotide sequence of the Cryptomeria japonica D. Don. Chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species. BMC. Plant. Biol. doi: 10.1186/1471-2229-8-70
Ibrahim RIH, Azuma JI, Sakamoto M (2006) Complete nucleotide sequence of the cotton (Gossypium barbadense L.) chloroplast genome with a comparative analysis of sequences among 9 dicot plants. Gene. Genet. Syst. 81:311-321.
Lee SB, Kaittanis C, Jansen RK, Hostetler JB, Tallon LJ (2006) The complete chloroplast genome sequence of Gossypium hirsutum organization and phylogenetic relationship to other angiosperms. BMC. Gen. 7:61.
Leebens-Mack J, Raubenson LA, Cui L, Kuehl J, Fourcade M, Chumley T, Boore JL, Jansen RK, Pamphilis CW (2005) Identifying the basal angiosperms in chloroplast genome phylogenetic: sampling one’s way out of the Felsenstein zone. Mol. Bio. Evo. 22:1948-1963.
Leseberg CH, Duvall MR (2009) The complete chloroplast genome of Coixlacryma jobi and a comparative molecular evolutionary analysis of plastomes in cereals. J. Mol. Evo. 69:311-318.
Lin CHP, Huang JP, Wu CHSH, Hsu CHY, Chaw SHM (2010) Comparative chloroplast genomics reveals the evolution of Pinaceae genera and Subfamilies. Gen. Bio. Evo. doi: 10.1093/gbe/evq036
Nguyen TB, Giband M, Brottier P, Risterucci AM, Lacape JM (2004) Wide coverage of the tetraploid cotton genome using newly developed microsatellite markers. Theor. Appl. Genet. 109:167-175.
Palmer JD (1991) Plastid chromosomes, structure and evolution in the molecular biology of plastids edited by (Bogorad L, Vasil K, San Diego). Academic Press, USA.
Raubeson LA, Peery RH, Chumley TW, Dziubek Ch, Fourcade HM, Boore JL, Jansen RK (2007) Comprative chloroplast genome: analyses including new sequences from the angiosperm Nuphar advena and Ranunculus macranthus. BMC. Geno. doi: 10.1186/1471-2164-8-174
Rebeiro MM, Mariette S, Vendramin GG, Szmidt AE, Plomin C, Kremer A (2002) Comparison of genetic diversity estimates within and among populations of Maritime pine using chloroplast simple-sequence repeat and amplified fragment length polymorphism data. Mol. Eco. doi: 10.1046/j.1365-294X.2002.01490.x
Sharma PC, Yenle MB, Dennis TJ (2005) Data base of medicinal plants used in Ayurveda. Central council for research in Ayurveda and siddha, India.
Soltis DE, Albert VA, Savolainen V, Hilu K, Qiu YQ, Chase MW, Foris JS, Stefanovic S, Rice DW, Palmer JD, Solits PS (2004) Genome-scale data, angiosperm relationships, and ‘ending incongruence’. Tren. Plant. Sci. 9:477-483.
Soltis DE, Soltis PS (2004) Amborella not a “basal angiosperm”? No so fast. J. Botan. doi:10.3732/ajb.91.997
Sugiura M, Hirose T, Sugita M (1998) Evolution and mechanism of translation in chloroplasts. Ann. Rev. Genet. 32:437-459.
Talat F, Wang K (2014) Chloroplast genome study, new tool in plant biotechnology Gossypium spp. as a model crop. J. curr. Rese. Sci. 838-850.
Talat F, Wang K (2015) Comparative bioinformatics analysis of the chloroplast genome of a wild diploid Gossypium and two cultivated allotetraploid species. J. Biotech. doi:10.15171/ijb.1231
Turmel M, Gagnon MC, O’kelly CJ, Otis C, Lemieux C (2009) The chloroplast genome of the green Algae pyramimona, Monomostix and Pycnococous shed new light on the evolutionary history of prasinophytes and the origin of the secondary chloroplast of Euglenids. Mol. Bio. Evo. 26: 631-648.
Turmel M, Otis C, Lemieux C (2009) The chloroplast genome of the green Algae pedinomonas minor, Parachlorella kessleri and Oocystis solitaria reveal a shared ancestry between the chlorellales. Mol. Bio. Evo. 26: 2317-2331.
Walker JF, Michael JZ, Nancy CE (2014) Correction to comparative analysis of complete chloroplast genome sequence and inversion variation in Lasthenia burkei (Medieae, asteraceae). Amer. J. Botan. doi:10.3732/ajb.1400049
Wendel JF, Brubaker C, Alvarez I, Cronn R, Stewart JM (2009) Evolution and natural history of the cotton genus. Crop. Model. 3:3-22.
Wilson C A (2004) Phylogeny of Iris based on chloroplast matK gene and trnK intron sequence data. Mol. Phylo. Evo. doi: 10.1016/j.ympev.2004.06.013
Wu FH, Kan DP, Lee SB, Daniell H, Lee YW, Lin CC, Lin NS, Lin CS (2009) Complete nucleotide sequence of Dendrocalamus latiflorus and Bambusa oldhamii chloroplast genomes. Tree. physiol. doi: 10.1093/ treephys/tpp015.