發(fā)布時(shí)間：2018-04-13 18:13

  本文選題：驢 + 全基因組��； 參考：《山東師范大學(xué)》2017年碩士論文

【摘要】：驢(Equus asinus)作為役用家畜,具有抗病力強(qiáng)、體質(zhì)強(qiáng)健、耐粗飼和適應(yīng)力強(qiáng)等特點(diǎn)。如今它在交通不便的地區(qū)仍是主要的交通工具,其肉、奶、皮均具有較高的營(yíng)養(yǎng)價(jià)值�？勺兗羟袑�(duì)于真核生物的分化、生長(zhǎng)、信號(hào)轉(zhuǎn)導(dǎo)等多種生物學(xué)現(xiàn)象有著較為重要的意義。當(dāng)前國(guó)內(nèi)外對(duì)于家畜的可變剪切的研究主要集中在毛色、體尺等表型性狀和抗病性狀及產(chǎn)奶產(chǎn)肉等經(jīng)濟(jì)性狀方面,但迄今仍未見(jiàn)驢全基因組可變剪切的報(bào)道。驢皮作為阿膠的原材料,目前對(duì)其研究主要集中在驢皮的蛋白水平和微量元素的鑒定及阿膠的真?zhèn)舞b定上,而對(duì)其轉(zhuǎn)錄組水平的研究比較少。鑒于此,本課題擬在前期驢基因組測(cè)序、組裝基礎(chǔ)上,通過(guò)對(duì)44個(gè)組織的轉(zhuǎn)錄組數(shù)據(jù)分析,對(duì)驢進(jìn)行全基因組范圍內(nèi)的可變剪切的研究;同時(shí)深入對(duì)比研究了德州驢和新疆驢的驢皮轉(zhuǎn)錄組數(shù)據(jù),旨在解析驢皮的免疫保護(hù)、特殊功效的分子機(jī)制。首先是利用Illumina Hiseq 2000測(cè)序平臺(tái)對(duì)德州驢和新疆驢兩個(gè)品種的15個(gè)驢皮組織進(jìn)行了RNA-seq測(cè)序。經(jīng)皮爾森相關(guān)性分析后去除2個(gè)組織樣品,從13個(gè)驢皮組織中共鑒定出35429個(gè)轉(zhuǎn)錄本。前100的高表達(dá)基因功能主要富集在維持生命活動(dòng)的各個(gè)通路及抗病免疫相關(guān)的代謝通路中。通過(guò)cuffcompare評(píng)估、蛋白功能預(yù)測(cè)、與其他數(shù)據(jù)庫(kù)比對(duì)以及與參考注釋文件比較,共獲得379個(gè)新轉(zhuǎn)錄本,其中363個(gè)轉(zhuǎn)錄本在KEGG中有注釋結(jié)果,功能富集顯示這些新轉(zhuǎn)錄本主要集中在蛋白質(zhì)、免疫抗病相關(guān)功能上。鑒定的新轉(zhuǎn)錄本可用來(lái)補(bǔ)充驢基因組的注釋。通過(guò)對(duì)lncRNA常規(guī)篩選及四種蛋白編碼能力預(yù)測(cè)軟件的預(yù)測(cè),共檢測(cè)出1148個(gè)linc RNAs,同時(shí)發(fā)現(xiàn)這些linc RNAs的功能主要集中在氨基酸合成代謝相關(guān)的通路中。從德州驢和新疆驢兩個(gè)品種皮中共鑒定出6008個(gè)發(fā)生可變剪切的轉(zhuǎn)錄本,功能主要富集在抗病、代謝相關(guān)的通路上。進(jìn)一步對(duì)兩個(gè)品種對(duì)應(yīng)部位的驢皮組織的轉(zhuǎn)錄組數(shù)據(jù)進(jìn)行比較分析,發(fā)現(xiàn)222個(gè)表達(dá)差異基因,且這些基因功能多集中在免疫代謝通路中。最后利用同源基因?qū)ⅢH和其他物種進(jìn)行比較,發(fā)現(xiàn)了皮組織中驢特異性表達(dá)的基因,其功能富集主要集中在能量代謝、免疫和抗病性上。對(duì)驢皮轉(zhuǎn)錄組水平的研究將會(huì)為驢皮功效、驢地方品種的形成及環(huán)境適應(yīng)性提供分子遺傳基礎(chǔ)資料。驢全基因組范圍內(nèi)可變剪切的研究。利用astalavista-3.2對(duì)RNA測(cè)序所得的15種組織44個(gè)樣品進(jìn)行可變剪切的鑒定,發(fā)現(xiàn)驢全基因組范圍內(nèi)有50.73%的基因發(fā)生了可變剪切,且外顯子跳躍為主要可變剪切模式,發(fā)生可變剪切事件的基因主要參與抗病、免疫及能量代謝相關(guān)的通路。對(duì)15種組織進(jìn)行組織間剪切事件的比較分析,發(fā)現(xiàn)肉和血液兩個(gè)組織發(fā)生可變剪切事件數(shù)目少于其他組織;在44個(gè)組織中只有130個(gè)基因均發(fā)生了AS事件,它們的功能主要集中在維持生命活動(dòng)的各個(gè)通路中;還發(fā)現(xiàn)在130個(gè)保守剪切基因中42個(gè)基因的剪切模式完全一致。比較分析了發(fā)生可變剪切的基因和未發(fā)生可變剪切的基因結(jié)構(gòu),發(fā)現(xiàn)此兩種類型的基因在基因長(zhǎng)度、外顯子長(zhǎng)度和數(shù)目、表達(dá)量等方面均存在顯著差異,表明兩種類型的基因在基因結(jié)構(gòu)上存在顯著差異。為研究發(fā)生可變剪切體基因的組織特異性,對(duì)驢、牛、山羊、綿羊及馬五個(gè)物種通過(guò)同源基因進(jìn)行比較分析,獲得了五個(gè)物種間各個(gè)組織保守的剪切基因及驢特異于其他物種的剪切基因。綜上所述,本研究運(yùn)用高通量測(cè)序及生物信息學(xué)的方法,首次對(duì)驢進(jìn)行了全基因組范圍內(nèi)的可變剪切圖譜鑒定、可變剪切的基因組織特異性分析及不同食草性物種間可變剪切比較分析;同時(shí)對(duì)德州驢和新疆驢兩個(gè)品種的驢皮組織從可變剪切、表達(dá)量等方面進(jìn)行了分析,并預(yù)測(cè)出了新轉(zhuǎn)錄本和linc RNAs,豐富了驢的全基因組注釋結(jié)果。
[Abstract]:The donkey (Equus asinus) as working animals, with strong disease resistance, strong physique, strong adaptability and resistance characteristics of forage. It is now in inaccessible areas is still the main means of transport, the nutritional value of meat, milk, skin have high differentiation., alternative splicing for eukaryotic growth, has the important significance of signal transduction and other biological phenomena. The research on variable shear livestock at home and abroad mainly focus on the hair color, body size and other phenotypic traits and disease resistance traits and milk production of meat and other economic traits, but so far no donkey genome reported. The variable shear donkey skin as a raw material gelatin the authenticity of the identification and identification of gelatin protein levels and trace elements of its current research mainly focus on the donkey skin, but little research on the transcriptional level. In view of this, this article in the early donkey genome sequencing The assembly, on the basis of the transcriptome data of 44 tissue analysis, study alternative splicing in genomic region of donkey donkey skin; transcriptome data and in-depth comparative study of Dezhou and Xinjiang donkey, immune protection aims to reveal the molecular mechanism of donkey skin, special effects. The first is the use of Illumina Hiseq 2000 Dezhou and Xinjiang donkey sequencing platform of two varieties of 15 donkey skin tissue were analyzed by RNA-seq sequencing. The Pearson correlation analysis after removal of 2 tissue samples from 13 donkey skin tissue identified 35429 transcripts. The high expression of gene function is mainly concentrated in the top 100 of each pathway and life sustaining activities immune disease related metabolic pathways. Through cuffcompare evaluation, prediction of protein function, and other database and compared with the reference annotation file, received a total of 379 new transcripts, 363 of them turn This book in the KEGG annotation results show that these new functional enrichment transcripts mainly concentrated in protein, immune related functions. The identification of new transcription annotation can be used to supplement the donkey genome. The lncRNA routine screening and four protein encoding capacity prediction software prediction, detected a total of 1148 Linc RNAs at the same time, found that these Linc RNAs mainly focuses on the synthesis of amino acid metabolism pathway. From Dezhou and Xinjiang donkey skin two varieties identified 6008 transcripts have variable shear function, mainly enriched in disease resistance, metabolic pathway. The transcriptome data of two varieties of the corresponding part Lvpi organization to carry on the comparative analysis, found 222 differentially expressed genes, and these genes are more concentrated in the immune metabolism. The homologous genes and other species than Is found in skin tissue, the expression of donkey specific gene, the functional enrichment focuses on energy metabolism, immunity and disease resistance. The research will be on the donkey skin transcriptome level for skin effect, formation and environmental adaptability of donkey breeds to provide molecular genetic basis. The research of donkey genome wide variable shear. The identification of 44 samples of 15 kinds of tissues by astalavista-3.2 RNA sequencing of the variable shear, found a variable shear donkey genome-wide 50.73% gene and exon skipping is the main variable shear mode, variable shear events occur mainly involved in disease resistance gene, immune and metabolic pathway related. Comparative analysis of 15 kinds of shear event organization organization, found that the flesh and blood of two groups of variable shear events number less than other organizations; only 1 in 44 tissues 30 genes have undergone AS events, each path of their functions mainly focus on life sustaining activities; also found in shear mode 130 conserved gene shear 42 genes are identical. A comparative analysis of the occurrence of alternative splicing genes and no variable shear gene structure, found that the two types of the genes in the gene exon length, length and number, expression etc. there were significant differences, indicating two types of genes have significant differences in gene structure. For tissue specificity, of variable shear body gene on donkeys, cattle, goats, sheep and horse five species by homologous gene comparative analysis of shear gene obtained five species each organization conservative shear gene and other species specific to the donkey. In summary, this study used high-throughput sequencing and bioinformatics method, for the first time The donkey was spliced identification of genome wide comparative analysis, analysis of species specific gene organization and different herbivorous variable shear between the variable shear; while the Dezhou donkey and Xinjiang donkey two varieties of donkey skin tissue from the variable shear, expression and other aspects of the analysis, and to predict new RNAs and Linc transcripts, enrich the whole genome annotation results of a donkey.

【學(xué)位授予單位】：山東師范大學(xué)
【學(xué)位級(jí)別】：碩士
【學(xué)位授予年份】：2017
【分類號(hào)】：S822

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