本文選題：基因組 + 轉(zhuǎn)錄組　； 參考：《內(nèi)蒙古大學(xué)》2016年博士論文

【摘要】：自人類基因組計(jì)劃啟動(dòng)以來,基因組學(xué)逐漸成為研究人員關(guān)注的焦點(diǎn)。隨著第二代測序技術(shù)的誕生,高通量、高深度的基因組測序被用于越來越多的非模式生物。就鳥類而言,2004年雞基因組測序草圖的完成,標(biāo)志著禽類基因組時(shí)代的來臨,圍繞著鳥類基因組層面的進(jìn)化關(guān)系研究也由此展開。鳥類羽毛顏色豐富多彩,從多種方面賦予鳥類獨(dú)特而重要的優(yōu)勢,是研究脊椎動(dòng)物顏色形成的理想模型,因此從鳥類基因組層面研究羽毛色素的調(diào)控機(jī)制具有極為重要的意義。紅腹錦雞(Chrysolophus pictus)是原產(chǎn)于中國西部的著名觀賞雉類。本研究結(jié)合紅腹錦雞基因組、轉(zhuǎn)錄組測序及羽毛色素成分的分析,對羽毛中黑色素和類胡蘿卜素的合成和沉積機(jī)理進(jìn)行了探索。利用二代測序技術(shù),測得了紅腹錦雞全基因組序列和錦雞羽毛毛囊組織轉(zhuǎn)錄組序列,并進(jìn)行了組裝,其中基因組大小為1.029 Gb,注釋到16,088個(gè)蛋白編碼基因,10個(gè)樣本的轉(zhuǎn)錄組組裝序列57.66 Gb,注釋得到15,118個(gè)基因。經(jīng)過進(jìn)一步的物種間全基因組比較分析和不同顏色羽毛間的轉(zhuǎn)錄組表達(dá)分析,以及結(jié)合不同顏色羽毛中色素成分的鑒定結(jié)果,發(fā)現(xiàn)了一系列參與紅腹錦雞羽毛黑色素和類胡蘿卜素調(diào)控的因子,為開展色素相關(guān)基因的功能研究奠定了基礎(chǔ)。1.紅腹錦雞與其它鳥類的全基因組比較首先利用由紅腹錦雞基因組序列注釋到的單拷貝同源基因構(gòu)建了系統(tǒng)發(fā)育樹,表明紅腹錦雞在系統(tǒng)發(fā)育地位上與雞形目中火雞親緣關(guān)系最近,原雞次之。然后以斑胸草雀為外群,對雞、火雞、紅腹錦雞的全基因組進(jìn)行了比較分析。在基因拷貝數(shù)方面,紅腹錦雞有44個(gè)物種特異的基因家族和200個(gè)擴(kuò)張的基因家族,其中的POU家族、涉及脂類代謝的家族和p角蛋白亞家族被認(rèn)為與黑色素和脂色素的合成和積累有關(guān)。在基因共線性方面,紅腹錦雞假染色體中共有58個(gè)scaffold基因順序發(fā)生了變化,包括3個(gè)大的基因組重排區(qū),受基因組重排影響的基因包括15和黑色素相關(guān)基因和24個(gè)Hox基因,這些基因直接或間接地參與紅腹錦雞色素的調(diào)控。2.紅腹錦雞與白腹錦雞羽毛色素成分的鑒定利用光譜和色譜的技術(shù)對錦雞不同顏色羽毛的色素成分進(jìn)行了鑒定。首先進(jìn)行了拉曼光譜的測定,結(jié)果顯示紅腹錦雞紅、橙、黃色羽毛的羽枝部分和綠色羽毛的羽干部分檢測到類胡蘿卜素特征峰,而白腹錦雞紅、黃色羽毛顯示為褐黑素特征峰,兩種錦雞綠色羽毛為真黑素特征峰。然后對各羽毛進(jìn)行脂溶性色素的抽提,觀察到只有紅腹錦雞的紅、橙、黃色羽毛中可以提取到脂溶性色素,將這些物質(zhì)進(jìn)行質(zhì)譜分析并將分子量與數(shù)據(jù)庫比對,發(fā)現(xiàn)其中包含分子式為C40H540和C40H5602的類胡蘿卜素,其中C40H5602可能是葉黃素和玉米黃素這兩種互為同分異構(gòu)體的化合物。最后進(jìn)行高效液相色譜的外標(biāo)法分析,一方面利用葉黃素和玉米黃素標(biāo)準(zhǔn)品分析提取到的類胡蘿卜素,另一方面利用PTCA和TTCA分析真黑素和褐黑素,色譜結(jié)果與光譜一致,即紅腹錦雞羽毛色素成分包括類胡蘿卜素和黑色素,白腹錦雞羽毛中只有黑色素。3.轉(zhuǎn)錄組水平研究錦雞羽毛色素調(diào)控基因分別測定了紅腹錦雞和白腹錦雞胸腹、頸項(xiàng)、上背、下背、尾羽的羽毛毛囊組織轉(zhuǎn)錄組。進(jìn)行了兩個(gè)物種同等部位羽毛和不同顏色羽毛的差異表達(dá)基因的篩選和聚類分析。對于黑色素相關(guān)基因,TYR、 TYRP1、KIT、WNT7在真黑素為主要色素的上背羽毛中表達(dá),ASIP以及溶質(zhì)載體家族(solute carrier family)的一些成員在褐黑素為主的羽毛中表達(dá)。另外,ASIP和MITF由可變剪接產(chǎn)生的轉(zhuǎn)錄本中,ASIP-1A和MITF-1M在褐黑素富集的羽毛高表達(dá),推測與褐黑素合成有關(guān)。對于類胡蘿卜素相關(guān)基因,BC02在不含類胡蘿卜素的羽毛中表達(dá),參與脂類代謝的基因APOA1和CYP2J主要在含有類胡蘿卜素的羽毛中表達(dá),推測可能與類胡蘿卜素色素有關(guān)。另外,實(shí)時(shí)定量PCR分析發(fā)現(xiàn),GSTA2和APOD與類胡蘿卜素的沉積有關(guān)。
[Abstract]:Since the start of the human genome project, genomics has gradually become the focus of researchers. With the birth of the second generation sequencing technology, high throughput, high depth genome sequencing has been used for more and more non pattern organisms. For birds, the completion of the chicken genome sequencing in 2004 marks the advent of the poultry genome era. The study on the evolutionary relationship of the bird genome is also carried out. The color of the bird feathers is rich and colorful and gives birds unique and important advantages. It is an ideal model to study the color formation of vertebrates. Therefore, it is of great significance to study the regulation mechanism of the feather chroma from the bird genome level. Chrysolophus pictus is a famous ornamental pheasant native to Western China. In this study, the synthesis and deposition mechanism of melanin and carotenoid in feathers were explored in combination with the analysis of the genome of Caragana, transcriptional sequence and the composition of feather pigments. The whole genome sequence of the Caragana Caragana was measured by two generation sequencing technology. The sequence of the Caragana feather follicle tissue transcriptional group and the assembly were assembled, in which the size of the genome was 1.029 Gb, annotated to 16088 protein encoding genes, and the transcriptional assembly sequence of 10 samples was 57.66 Gb, and 15118 genes were annotated. After further analysis of the total genome ratio and the transcriptional expression between different colors of different colors. Analysis, and the identification of pigment components in different color feathers, a series of factors involved in the regulation of melanin and carotenoid in Caragana feathers were found, which laid the foundation for the study of the function of the pigments related genes. The whole group of.1. red belly Caragana and other birds first utilized the genome of Caragana Caragana. The sequence annotated single copy homologous genes construct the phylogenetic tree, indicating that the phylogenetic relationship of Caragana in phylogenetic relationship is closest to the chicken in the chicken form, and the original chicken is the next. Then the whole genome of chicken, Turkey and pheasant is compared with the outer group of pectoralis finch. In the number of copies of the gene, there are 44 pheasants in the red belly. The species specific gene family and 200 extended family of genes, the POU family, the family of lipid metabolism and the P keratin family are considered to be related to the synthesis and accumulation of melanin and lipochrome. In the genetic collinearity, the sequence of 58 scaffold genes in the false chromosome of the Caragana pheasant has been changed in sequence, including 3 large Genome rearrangement areas, genes affected by genome rearrangement include 15 and melanin related genes and 24 Hox genes. These genes directly or indirectly participate in the regulation of Caragana coloring in red abdomen,.2. red belly Caragana and white belly Caragana feather pigment composition, using spectrum and chromatography techniques to add pigment composition to different color feathers of Caragana First, the Raman spectrum was measured. The results showed that the Caragana, orange, yellow feather plume and the dry part of the green feather detected the carotenoid characteristic peak, while the white abdomen pheasant red, the Yellow Feather showed the characteristic peak of the brown melanin, and the two kinds of brocade chicken green feathers were the characteristic peak of the melanin. The liposoluble pigments were extracted. Only the red, orange and yellow feathers of Caragana were found to be liposoluble pigments. These substances were analyzed by mass spectrometry and compared with the database. It was found that there were carotenoids with molecular formula of C40H540 and C40H5602, of which C40H5602 may be lutein and zeaxanthin. On the one hand, the carotenoids extracted from the standard products of lutein and zeaxanthin were analyzed by high performance liquid chromatography. On the other hand, the PTCA and TTCA were used to analyze the true melanin and the brown melanin. The chromatographic results and the spectrum are the same, that is, the composition of the red belly Caragana feather pigment includes Hu like Hu. Caragana and melanin, only the melanin.3. transcript level in the Caragana feathers of the Caragana Caragana feathers were studied in the feather follicle tissue of Caragana Caragana and pheasant, neck, upper back, lower back and tail feathers, respectively. The differential expressions of two species of feather and different color feathers were carried out. For melanin related genes, TYR, TYRP1, KIT, WNT7 are expressed in the upper back feathers of the main pigment, and some members of the ASIP and the solute carrier family (solute carrier family) are expressed in the browning main feathers. In addition, ASIP and MITF are produced in the transcriptional transcript of variable splicing, ASIP-1A and MITF. -1M is highly expressed in the feathers enriched with brownish melanin, presumably related to the synthesis of brownish melanin. For carotenoid related genes, BC02 is expressed in the carotenoid free feathers, and the genes involved in lipid metabolism, APOA1 and CYP2J, are mainly expressed in the carotenoid feathers, presumably related to carotenoid pigments. In addition, real time Quantitative PCR analysis revealed that GSTA2 and APOD were related to the deposition of carotenoids.
【學(xué)位授予單位】：內(nèi)蒙古大學(xué)
【學(xué)位級別】：博士
【學(xué)位授予年份】：2016
【分類號】：Q953

【參考文獻(xiàn)】

相關(guān)期刊論文 前10條

1 高廣琦;王天元;白春玲;;紅腹錦雞大規(guī)模人工繁育技術(shù)[J];中國家禽;2015年13期

2 張靜;劉毅;劉安芳;;畜禽羽色候選基因ASIP和TYRP1的研究進(jìn)展[J];中國家禽;2015年01期

3 靳青;畢宇霖;劉曉牧;萬發(fā)春;;類胡蘿卜素代謝及功能研究進(jìn)展[J];動(dòng)物營養(yǎng)學(xué)報(bào);2014年12期

4 楊燦朝;梁偉;;通過光譜與視覺模型研究動(dòng)物體色[J];動(dòng)物學(xué)研究;2013年06期

5 Rose THOROGOOD;Nicholas B.DAVIES;;杜鵑模擬鷹及杜鵑外形多態(tài)性的進(jìn)化(英文)[J];Chinese Birds;2013年01期

6 薛茗元;;紅腹錦雞的人工養(yǎng)殖技術(shù)[J];中國家禽;2013年04期

7 李宏群;韓宗先;吳少斌;曹長雷;冉景盛;陳春;岳碧松;;重慶大木山自然保護(hù)區(qū)紅腹錦雞夏季沙浴地分析[J];西南大學(xué)學(xué)報(bào)(自然科學(xué)版);2012年12期

8 郭新亮;楊燦朝;李筑眉;梁偉;;貴州寬闊水自然保護(hù)區(qū)3種雉科鳥類的種群繁殖密度[J];海南師范大學(xué)學(xué)報(bào)(自然科學(xué)版);2012年03期

9 俞詩源;安晶晶;劉婷婷;王小勇;陳琛;;白腹錦雞和草原雕肝臟結(jié)構(gòu)的光鏡觀察及Bax蛋白、c-Fos、TGF-β_1的表達(dá)[J];西北師范大學(xué)學(xué)報(bào)(自然科學(xué)版);2012年04期

10 李宏群;韓宗先;吳少斌;曹長雷;岳碧松;;大木山自然保護(hù)區(qū)紅腹錦雞對冬季生境的選擇性[J];東北林業(yè)大學(xué)學(xué)報(bào);2011年11期

相關(guān)會(huì)議論文 前2條

1 丁長青;鞏會(huì)生;趙雷剛;向定乾;袁朝暉;鄭松峰;;秦嶺南麓不同地區(qū)紅腹錦雞繁殖密度的比較研究[A];中國鳥類學(xué)研究——第四屆海峽兩岸鳥類學(xué)術(shù)研討會(huì)文集[C];2000年

2 李筑眉;余志剛;蔣鴻;;寬闊水原生林紅腹錦雞棲息地與密度調(diào)查[A];中國鳥類學(xué)研究——第四屆海峽兩岸鳥類學(xué)術(shù)研討會(huì)文集[C];2000年

相關(guān)博士學(xué)位論文 前1條

1 何珂;紅腹錦雞SSR和Ⅱ類MHC位點(diǎn)的分離及種群遺傳結(jié)構(gòu)分析[D];浙江大學(xué);2012年

，

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