Science assignment help on: Genomes
Introduction
Since the last four years, there has been shift from the process of practising of Sanger sequencing for analysis of genome. Earlier, for twenty years, this automated method invented by Sanger has dominated ,and there has been large number of accomplishment .There has been quite a lot of improvement technically in this era, and due to the limitations of technology developed by Sanger, there has been a need of improved and new technology for sequencing the human genomes. There has been the development of methods, due to the effort, and new advance technology has been developed.( 9Metzker, M. L,2005; 5Hutchison,2007).The automated method by Sanger is known as first generation technology and new methods are known by next generation sequencing technology. The various strategies have been constituted in a newer technology, and it is based on the imaging, sequencing, and preparation. The automated Sanger method is considered as a ‘first-generation’ technology, and newer methods are referred to as next-generation sequencing (NGS). These newer technologies constitute various strategies that rely on ion of templates, assembly methods and genome allignment.Comming of new generation sequencing technology in the market has changed the way of approach scientifically in applied, clinical and basic research. The advantage of the next generation sequencing technology is that it produces large volume of data in a cheap rate, in few cases in excess of billions. The chain terminating technology which has been created by Frederick Sanger, and his co-workers, in 1970s, has act as a workhorse for molecular biology for many years. The basis of this technology is to separate the extended DNA fragment by adding di-deoxynucleotides. Since there is a absence of 3’-hydroxy group, these nucleotides are different from the standard deoxynucleotide. So, we can say there has been a saturation of a chain termination technology as there has been improvement ,for an example ,inculcation of di-deoxynucleotides, tagged fluorescently, read length has been improved up to bases ,thousands in numbers, introduction of capillary electrophoresis, increase in automation, all these have allow these technique in projects of genome ,and also act as a tool in molecular biology.There has been a desire for an increase of bases sequence at a low cost. Due to this reason, there has been a development of new theories in 19990s.Thus there has been a development of next generation sequencing technology.
Advantages of ‘Next Generation’ sequencing technologies over conventional chain terminator technologies
The next generation sequencing technology, or NGS has a great impact both at the research and economic Level, there has been an increase in the production of data’s and reduction of the cost. This technology has allowed the sequencing of genomes from microbes to human and almost thousand in numbers, and they has lead to the way of new enquiries, biologically, and there has been an investigation of genomes of disease of human, identification and characterization of etiological agents. The application of this field can be categories into three major components the first one is related to the task of genome that is assembly of genomes, variations in structure, the second component is transciptome analysis that is prediction of genes and some problems related to genetics. The challenges are being offered in management and analysis of data, design of the experiment by the new technologies. Particularly it is very important that analysis should be keep in pace with the production of data, and thus there has been the development of the new bioinformatics tool. For DNA sequencing read production, there are three platforms available, which are being used widely .these platforms are the Roche /454, the Applied Biological Solid TM system, and the last platform is the Illumina or Solexa Genome Analyser.There are lot of advantages of the next generation sequencing technologies, if compare to conventional first generation sequencing technology, or we can say sequencing demonstrated by Sanger. The conventional termination technology has remained a choice to detect the change in the genome of the human, genetically so that therapy could be properly guided both in the lung cancer. ( 6Kobayashi S, Boggon TJ, Dayaram T, Jänne PA, Kocher O, Meyerson M, et al.,2005) and other diseases ( 11 Monzon FA, Ogino S, Hammond ME, Halling KC, Bloom KJ, Nikiforova MN,2009). The conventional sequencing by Sanger has been used to detect the genetic change in NSCL, or we can say patient who are having non small cell lung cancer to decide the therapy that must be targeted to cure them. In a similar way, to detect the EML4-ALK translocations, there has been used of fluorescence in situ hybridisation. The convention chain termination method demonstrated by Sanger’s chain termination method of DNA sequencing ( 15Sanger F, Coulson AR,1975)is based on a process in which sequence of nucleotide, which are being fluorescence labelled are being detected.. The elongation of DNA occurs with single stranded templates of DNA and is stop by inculcation of fluorescent di deoxynucleotide chain terminators. Capillary electrophoresis is being used to detect the sequence of DNA of increased length. The structural change is not being detected by this technique. Next generation sequencing technology is suitable for sequencing of gene on the large scale, and is also comparatively less costly that the traditional techniques of sequencing. The SOLIDTM techniques and the illumine has been able to give ten millions of read and several hundreds and thousands of reads have been yielded by Roche platform compare with the traditional method which yield only 96 reads. The cost of single base is comparatively low, but the cost of single test is more in case of next generation sequencing technology ,when compare to the traditional sequencing method. For frequent acquisition of image, longer time is required for next generation sequencing technology, compare to the chain terminating technologies and shorter reads are being yielded. ( 14Ross JS, Cronin M.2011). The applications of these techniques are important for the study of exomes, along with the genomes. ( 18Sjöblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD, et al,2006 ), transciptome ( 24Yassour M, Kaplan T, Fraser HB, Levin JZ, Pfiffner J, Adiconis X, et,2009 ), and epigenetic ( 10Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, et al,2007) for the discovery scientifically, the scope has been extended ( 8Mardis ER,2008).There has been a high demand for the sequencing at the lower cost that has led to the development of throughput sequencing or the next generation sequencing technology that has at once produced the millions and thousands of sequences ( 4 Hall N May 2007; 1Church GM ,January 2006) The cost of sequencing of DNA has been lowered with the high throughput sequencing technology, which is also done by the dye terminator methods. ( 17Schuster Stephan C., January 2008) Parallel five lakhs sequencing synthesis operation may be run In ultra-high-throughput sequencing ( 3Gilbert Kalb, Robert Moxley , 1992 ; 19Ten Bosch, J. R.; Grody, W. W,2008; 21Tucker, T.; Marra, M.; Friedman, J. M,2009).Luciferase has been used by the technology of pyrosequencing.It has been used for generating light for detecting the nucleotides, which are being added to the nascent DNA, and sequences read outs are being generated by the combined data. This technology has provided read of intermediate length and lower price per base compare to the chain terminating technology on one side, and on the other side when compare to the Solid and Solexa technology. The development of the Polony sequencing method took place in the lab of George Church, which is in Harvard. This sequencing method is amongst the method which has been developed in the next generation sequencing technology in the beginning and in 2005,it has been used for sequencing the full genome. It has done the sequencing of the genome of the E.coli with an accuracy of more than 99.99 % and the cost is one tenth that has been used by Sanger sequencing. The major advantage of the next generation sequencing technology approach ,when compare with the traditional technology is that in a single run, it is possible to obtain hundred and thousands of the sequence, the information data has been generated with the larger magnitude. ( 2Engelbrektson A, Kunin V, Wrighton KC, Zvenigorodsky N, Chen F, Ochman H, et al.,2010) The cost per base is less in case of pyrosequencing.It has helped to increase the utilization of sequencing approach..This pyrosequencing.It method has also avoided the inheritance of the biases in the procedure of the cloning. There can be an identification of sequences from different samples by using the approach of bar-coding multiplex in a same run. ( 20Tringe SG, Hugenholtz P., 2008). The efficiency has been increased and the cost has been reduced through this multiplex approach. ( 12Parameswaran P, Jalili R, Tao L, Shokralla S, Gharizadeh B, Ronaghi M, et al.,2007 ).The technology has an impact on the depth and the breadth of the sampling. The greater depth of sampling gives a better coverage to an individual sample and the probability become more to detect the species which are rare. The greater breadth in sampling allows examining large numbers of subjects and samples. New generation sequencing technologies are being often used for examining large number of samples, rather than examining sample in depth. ( 7 Kuczynski J, Costello EK, Nemergut DR, Zaneveld J, Lauber CL, Knights D, et al ,2010). The large volume of sequence data have been produced due to the next generation sequencing technology compare with the chain termination technology. The data of high resolution and less noise has been generated by this new sequencing technology. The qualification and characterisation of transciptome are being possible with this NGS technology. This NGS technique acts a powerful vehicle for studying the complexity of the bacterial genome, which has been used for designing the synthetic genome. There has been a great impact of generation sequencing at biological level. There are three major advantage of next generation sequencing technology over chain terminator technology, firstly is amplification and construction clonally, secondly the array based on sequencing gives the degree of parallelism to the high extent and finally less quantity of reagent are being used that cut the cost to the extent.
. Potential impact of technologies on crop improvement
It has been a long history of human to use artificial selection to bring change in the character of agricultural species. The reference genomes have been obtained in the past years for species which include rice, maize, arabidopis, medicago and brachpodium.These references are being used as a base to study and comparing species and it act as a tool for large number of genomic approaches. There are also projects which provides sequences for genomes to understand the variation intraspecificaly.[ 25Zhang Q, Li J, Xue Y, et al ,2020;23 Weigel D, Mott R ,2009]. With the adventure of the next generation sequencing technology, there has been a higher access to the genome variation and sequence. The impact of the next generation sequencing technology over the crop improvement, it has affected it in a positive manner. ( 22 Varshney RK, Nayak SN, May GD, Jackson SA, 2009; 8Mardis ER, 2008) .next generation sequencing technology act as a vehicle, which has lead to the discovery of genes in plants, crops and their relatives. By the knowledge of new generation sequencing technology, we can facilitate the domestication of new species of plants as crops. The sequencing of genotypes again can be used for an identification of low diversity regions. By whole genome shot gun sequencing, from related species, the specific data’s related to species can be obtained. This sequencing is being used for designing specific PCR, or polymers chain primers. The example, where the recent application of new generation sequencing technology for improvement in crops are sugarcane, eucalypts and rice. the crop plant that is known as bread wheat (Poaceae,triticum aestivum) has a major in the world of crops, since almost two percent of the daily food to the world is provided by intake of it and it provide calorie similar to the calorie which is intake by the rice. There has been rise in the yield of the wheat that is within four years, it has been double due to the combination of improved germplasm and advanced agronomic practise. According to recent survey, the growth in the yield is less dramatic and there has been requirement for the improvement in the production of wheat, if the demand has to be met for growing population. Next generation sequencing technology are kind of revolution in biology and critical issues can be address by applying this technology in plant biology. The draft sequence of genomes is being produced by this technology which leads to the reduction in the cost and time as compare with the chain terminating technologies. The assessment of the structure of gene are done by the new generation sequencing technologies, and identification of heritable variation related to genes are being obtain using this technology. There has been advancement in technology of DNA sequencing and this advancement has a major impact for the improvement of the crops. The next generation sequencing technology has been used for sequencing the genomes of cereals crops like sorghum, maize and rice. There has been production of quality sequence of the rice that has covered the 95% of the 389 Mb genome. There has been an as semblance of the genome that is the sorghum bicolour (L) genome which has the size of seven thirty mega base and having 98% of genes in the context of the chromosomes. ( 13Paterson, A.H.; Bowers, J.E.; Bruggmann, R.; Dubchak, I.; Grimwood, J.; Gundlach, H.;Haberer, G.; Hellsten, U.; Mitros, T.; Poliakov, A.; et al.,2009).There has been improvement of the genome of the maize.(16 P.S.; Ware, D.; Fulton, R.S.; Stein, J.C.; Wei, F.S.; Pasternak, S.; Liang, C.Z.;Zhang, J.W.; Fulton, L.; Graves, T.A.; et al.,2009).there has been improvement in the sequencing technologies and as a result ,goals can be achieved and the cost and complexities can be overcome and there has been also improvement in the bioinformatics capabilities. The target should not be achieved for the moment; rather advancement in technology must be done so that the researchers may provide information to the breeders and biologists that can lead to the high crop genome information. The strategy will be required for the complex and large genome so that the profit from the new generation sequencing technology become high and not only quality, high quality is achieved. The funding should not be over after the realest of the first draft of the genome, since in various phases, this project of genome sequencing can be developed.
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