Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data
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Accurate detection of polymorphisms with a next generation sequencer data is an important element of current genetic analysis. However, there is still no detection pipeline that is completely reliable.We demonstrate two new detection methods of polymorphisms focusing on the Polymorphic Edge (PED). In the matching between two homologous sequences, the first mismatched base to appear is the SNP, or the edge of the structural variation. The first method is based on k-mers from short reads and detects polymorphic edges with k-mers for which there is no match between target and control, making it possible to detect SNPs by direct comparison of short-reads in two datasets (target and control) without a reference genome sequence. The second method is based on bidirectional alignment to detect polymorphic edges, not only SNPs but also insertions, deletions, inversions and translocations. Using these two methods, we succeed in making a high-quality comparison map between rice cultivars showing good match to the theoretical value of introgression, and in detecting specific large deletions across cultivars.Using Polymorphic Edge Detection (PED), the k-mer method is able to detect SNPs by direct comparison of short-reads in two datasets without genomic alignment step, and the bidirectional alignment method is able to detect SNPs and structural variations from even single-end short-reads. The PED is an efficient tool to obtain accurate data for both SNPs and structural variations.The PED software is available at: https://github.com/akiomiyao/ped .Bacterial genome size
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Gene density
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Білім берy қоғaмның экономикaлық дaмyының негізі, әлеyметтік тұрaқтылықтың фaкторлaрының бірі, хaлықтың рyхaни-aдaмгершілік әлеyетінің және интеллектyaлдық өсyінің қaйнaр көзі ретінде бaрлық yaқыттaрдa тaптырмaс құндылық болып есептеліп келеді. Aл қaзіргідей aдaм кaпитaлын қaлыптaстырy мен дaмытy мәселесін шешy негізгі міндет ретінде қaрaстырылaтын зaмaндa хaлықтың білімдік қaжеттіліктері өсіп, жоғaры, ортa aрнayлы, кәсіби қосымшa білім aлyғa үміткерлер сaны aртa түсyде. Бұғaн жayaп ретінде білім берy ұйымдaрының сaлaлaнyы aртып, әртүрлі типтегі оқy орындaрының сaны aртyдa, білім берyдің инфрaқұрылымы, бaсқaрy формaлaры, әдістемелік, ғылыми қызмет түрлері дaмyдa. Олaрды білім aлyшылaрдың жеке сұрaныстaры мен мүмкіндіктеріне бaғыттay күшейтілyде. Осығaн орaй білімнің сaпaсынa қойылaтын тaлaптaр aртып, бұл сaлaның әлеyметпен өзaрa әрекеттестігіне негізделген құрылымдық – қызметтік дaмyының көкейтестілігі aртyдa. Мaқaлaдa «серіктестік», «әлеyметтік серіктестік», «білімдегі әлеyметтік серіктестік» ұғым- дaрының мәні aшылып, олaрдың қaлыптaсy және дaмy үрдісіне шолy жaсaлaды, жоғaры оқy орындaрындa педaгогтaрды дaярлayдa әлеyметтік серіктестердің әлеyетін пaйдaлaнyдa бaсшылыққa aлынaтын ұстaнымдaр мен тиімді жолдaры сипaттaлaды. Түйін сөздер: серіктестік, әлеyметтік серіктестік, білімдегі әлеyметтік серіктестік, бірлескен әрекет ұстaнымдaры, әлеуметтік серіктестік әлеуеті. Обрaзовaние является основой экономического рaзвития обществa, одним из фaкторов социaль- ной стaбильности, источником дyховно-нрaвственного потенциaлa и интеллектyaльного ростa людей и во все временa считaлось незaменимой ценностью. И в нaстоящее время, когдa решение проблемы формировaния и рaзвития человеческого кaпитaлa рaссмaтривaется кaк основнaя зaдaчa, рaстyт обрaзовaтельные потребности людей, yвеличивaется количество желaющих полyчить высшее, среднее, специaльное, профессионaльное дополнительное обрaзовaние. В ответ нa это yсиливaется рaзветвленность обрaзовaтельных оргaнизaций, yвеличивaется количество обрaзовaтельных оргaни- зaций рaзличного типa, рaзвивaются инфрaстрyктyрa обрaзовaния, формы yпрaвления, методическaя и нayчнaя деятельность. Yсиливaется их ориентaция нa индивидyaльные потребности и возможности обyчaющихся. В связи с этим повышaются требовaния к кaчествy обрaзовaния, возрaстaет знaчение стрyктyрно-фyнкционaльного рaзвития этой сферы нa основе взaимодействия с обществом. В стaтье рaскрывaется знaчение понятий «пaртнерство», «социaльное пaртнерство», «социaльное пaртнерство в обрaзовaнии», рaссмaтривaется процесс их стaновления и рaзвития, описывaются рyко- водящие принципы и эффективные способы использовaния потенциaлa социaльных пaртнеров в подготовке педaгогических кaдров в высших yчебных зaведениях. Ключевые словa: партнерство, социaльное пaртнерство, социaльное пaртнерство в обрaзовaнии, принципы совместного действия, поненциал социального партнерство. Education is the basis of the economic development of society, one of the factors of social stability, a source of spiritual and moral potential and intellectual growth of people and has always been considered an irreplaceable value. And at the present time, when the solution of the problem of the formation and development of human capital is considered as the main task, the educational needs of people are growing, the number of people wishing to receive higher, secondary, special, professional additional education is increasing. In response to this, the branching of educational organizations is increasing, the number of educational organizations of various types is increasing, the infrastructure of education, forms of management, methodological and scientific activities are developing. Their focus on the individual needs and capabilities of students is increasing. In this regard, the requirements for the quality of education are increasing, the importance of the structural and functional development of this sphere on the basis of interaction with society is increasing. The article reveals the meaning of the concepts of "partnership", "social partnership", "social partnership in education", examines the process of their formation and development, describes the guidelines and effective ways to use the potential of social partners in the training of teachers in higher educational institutions. Keywords: partnership, social partnership, social partnership in education, principles of joint action, the potential of social partnership.
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Objective:To detect single nucleotide polymorphisms(SNPs) existing in 5′-regulatory region of β2-adrenoceptor(β2-AR) gene and to investigate association of the identified SNPs with essential hypertension in Uighur of Xinjiang.Methods:Single nucleotide polymorphisms(SNPs)in the position-654G/A and-1429T/A of β2-AR gene were tested with MALDI-TOF-MS and Genotypes of the SNP were typed by MassARRAY iPLEXTMmethod.Results:Two SNPs were identified at position-654 with G→A substitution and-1429 with T→A substitution.The frequency of genotype of the two SNPs complied well with the Hardy-Weinberg equilibrium in normal group Distribution of genotype AA,GA,GG of the SNPs at locus-654 in hypertension group was no significantly different from that in normal group(P0.05),No significant difference was observed in distribution of geno-types of the SNPs at locus-1429 between the two groups(P0.05).Conclusion:These results indicate that the SNPs at locus-654 and-1429 of β2-AR gene were the SNPs position but not linked to hypertension.
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الجين المعني بالدراسة والمعروف اختصارًا (BMPR2) هو الجين المسئول عن توازن ضغط الدم في الشريان الرئوي في جسم الإنسان، كما أن له دور كبير في تنظيم نمو الخلايا. ولما يكون هنالك عطب في هذا الجين لا يتمكن جسم الإنسان من أداء دوره بصورة طبيعية، فيصاب عندها بضغط الدم وتحديداً في الشريان الرئوي كما يتأثر نمو الخلايا سلباً. في هذه الدراسة استخدمنا برمجيات حاسوبية عالية الدقة في تحديد الجزء من الجين والذي تحدث فيه هذه الإشكالات وقمنا بتحديدها. وفي الدراسات السابقة كان هذا الجين هو المتهم أيضاً بهذه المشكلة. لكن لم يتم تحديد الجزء داخل الجين المسؤول عن هذه المشكلة، بالرغم من ظهور بعض هذه الأجزاء في دراسات سابقة. من مميزات هذه الدراسة استخدام عدد من الخوازميات الحديثة، توفر الجهد والوقت والمال للعمل فقط على جزء معين من الجين وليس كله.
BMPR2
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Carcass weight (CW) is one of the most important economic traits in pigs, directly affecting the income of farmers. In this study, a genome wide association study was performed to detect significant single nucleotide polymorphisms (SNPs) affecting CW in pigs derived from a $F_2$ intercross between Landrace and Korean native pig (KNP). Using high-density porcine SNP chips, highly significant SNPs were identified on SSC12. Two candidate genes, LOC100523510 and LOC100621652, were subsequently selected within this region and further investigated. Within these candidate genes, five SNPs were identified and genotyped using the VeraCode GoldenGate assay. The results revealed that one SNP in the LOC100621652 gene and four SNPs in the LOC100523510 gene are highly associated with CW. These SNP markers can thus have significant applications for improving CW in KNP. However, the functions of these candidate genes are not fully understood and require further study.
SNP
Candidate gene
SNP genotyping
SNP array
Tag SNP
Genome-wide Association Study
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SNP
SNP genotyping
Tag SNP
dbSNP
Nonsynonymous substitution
Genetic Association
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Induced autotetraploids of Triticum uniaristatum, T. tauschii, and T. umbellulatum were used to study the genomes of the polyploid species T. ventricosum, T. neglecta, and T. recta. The N genome in T. ventricosum is homologous to the N genome in the putative diploid donor T. uniaristatum and has undergone little modification. The D genome in T. ventricosum is also essentially unmodified. The U genome of T. neglecta appears to be unchanged from the U genome of T. umbellulatum. Two of the genomes of T. recta are the same as the genomes in T. neglecta (U and a presumed modified M genome). The presence of a U genome in T. recta has also been independently confirmed. The origin of the third genome in T. recta has not been confirmed.Key words: chromosomes, meiosis, genome analysis, wheat.
Polyploid
Genome size
Genomic Organization
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ポストシークエンスの時代に入り, 複数の遺伝子と環境因子が関与して発症する多因子性疾患の危険因子の探求が注目されるようになってきた。'ありふれた病気'の一つである歯周炎の発症および進行には, 口腔内環境や生体の免疫応答が関与していると考えられ, 歯周炎についての遺伝子学的検索が求められている。本研究では, 一塩基多型 (SNPs) 解析により歯周炎の関連因子の検討を行った。SNPsは, DNA配列中に見られる多型のうちもっともよく見られる多型で, SNPs解析は多くの遺伝子の解析が可能である。被検者は, 早期発症型歯周炎患者 (EOP) 13人, 成人性歯周炎患者 (AP) 9人, 健常者19人とした。本研究は, インターロイキン1 (IL1), 腫瘍壊死因子α (TNFα) 等の歯周炎候補遺伝子の一塩基多型 (Single Nucleotide Polymorphisms: SNPs) 計59について, TaqMan PCR法により, 歯周炎との関連について検討すること目的とした。また, SNPsの選択には, 連鎖不平衡を考慮した。その結果, 早期発症型歯周炎群とコントロール群では, カテプシンG (CTSG) と腫瘍壊死因子レセプター関連因子1 (TRAF1) において有意差 (P<0.05) が認められた。成人性歯周炎群とコントロール群では, インターロイキン10レセプターβ (IL10RB) とマトリックスメタロプロテアーゼ9 (MMP9) において有意差が認められた。また, 早期発症型歯周炎群と成人性歯周炎群では, インターフェロンγ (IFNG) において有意差が認められた。以上のことから, 早期発症型歯周炎においては, CTSGの関与が推測された。成人性歯周炎においては, IL10RBとMMP9の関与が推測された。さらに, 早期発症型歯周炎と成人性歯周炎においては, IFNGの関与に相違があるものと推測された。本研究より, 今後日本人の標準SNPsのデータベースであるJSNPに登録されているSNPsのさらなる解析により, 日本人における歯周炎の遺伝子学的な関連因子の解明につながる可能性が示唆された。
TaqMan
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In cells simultaneously infected with any two of the three reovirus serotypes ST1, ST2, and ST3, up to 15% of the yields are intertypic reassortants that contain all possible combinations of parental genome segments. We have now found that not all genome segments in reassortants are wild type. In reassortants that possess more ST1 than ST3 genome segments, all ST1 genome segments appear to be wild type, but the incoming ST3 genome segments possess mutations that make them more similar to the ST1 genome segments that they replace. In reassortants resulting from crosses of the more distantly related ST3 and ST2 viruses that possess a majority of ST3 genome segments, all incoming ST2 genome segments are wild type, but the ST3 S4 genome segment possesses two mutations, G74 to A and G624 to A, that function as acceptance signals. Recognition of these signals has far-reaching implications for the construction of reoviruses with novel properties and functions.
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