跳到主要內容

臺灣博碩士論文加值系統

(18.204.48.69) 您好!臺灣時間:2021/07/29 14:34
字體大小: 字級放大   字級縮小   預設字形  
回查詢結果 :::

詳目顯示

: 
twitterline
研究生:吳紀德
研究生(外文):Wu, Gideon Chi-Teh
論文名稱:阿拉伯芥基因組的外顯子演化速率之決定因子分析探討
論文名稱(外文):Determinants of Exon-level Evolutionary Rates in Arabidopsis Species
指導教授:陳豐奇陳豐奇引用關係
指導教授(外文):Chen, Feng-Chi
口試委員:趙淑妙陳豐奇莊樹諄謝立青林勇欣
口試委員(外文):Chaw, Shu-MiawChen, Feng-ChiChuang, Trees-JuenHsieh, Li-ChingLin, Yeong-Shin
口試日期:2012-05-23
學位類別:博士
校院名稱:國防醫學院
系所名稱:生命科學研究所
學門:生命科學學門
學類:生物學類
論文種類:學術論文
論文出版年:2012
畢業學年度:100
語文別:中文
論文頁數:151
中文關鍵詞:外顯子演化速率非同義置換率同義置換率主成分迴歸阿拉伯芥
外文關鍵詞:exonic evolutionary ratesnonsynonymous substitution ratesynonymous substitution rateprincipal component regressionArabidopsis thaliana
相關次數:
  • 被引用被引用:0
  • 點閱點閱:205
  • 評分評分:
  • 下載下載:23
  • 收藏至我的研究室書目清單書目收藏:0
生物演化是一個變動的過程,而有哪些生物因子決定其演化速率的大小,是分子演化學上的基本課題。蛋白質編碼序列的演化速率在基因與物種間變動很大,演化速率決定因子的廣泛研究結果,普遍認為基因的表達量及其緊密程度特徵是兩類主要的參數。但在基因裡或基因間的外顯子層面,其相關決定因子是哪些,則尚未詳細研究。
本論文利用主成份迴歸的統計分析方法,探討阿拉伯芥基因組裡,與外顯子的非同義置換率(dN)、同義置換率(dS),以及非同義置換率對同義置換率之比值(dN/dS)變異有關的決定因子。選取分析的生物特徵計有:外顯子長度、結構-功能特徵參數、外顯子表達量、mRNA剪接特徵參數、緊密程度特徵參數、外顯子的鹼基G與C含量比、以及外顯子可複製性(ED, exon duplicability)。
主成份迴歸分析結果顯示,與基因層面的決定因子組成有相當的差異。基因內與基因間的外顯子演化速率dN/dS及dN變異之最重要決定因子是結構-功能特徵參數,第二重要的決定因子,在同一基因內的外顯子之間是mRNA剪接特徵參數,而不同基因之間的演化速率變異者為外顯子長度。對基因內與基因間的dS演化速率變異來說,外顯子表達量、長度、以及結構-功能特徵(或剪接特徵)參數的組合,可決定其百分之六十五以上的已解釋之速率變異。而外顯子表達量與另兩參數的結合,可能是基因或外顯子的轉譯效率需求,因此與編碼子偏誤使用之同義置換率有較密切相關。
本論文也與最近發表的哺乳動物相關研究結果比較,顯示兩類生物的外顯子演化速率之決定因子組成與比重,有相當的差異,而且mRNA剪接特徵參數對動物外顯子演化速率之影響,明顯大於對植物的影響。我們的分析結果認為:哺乳動物與植物之間,各演化速率之間的決定因子組成與比重的差異,主要是由於選取分析的外顯子類型不同所致。本論文是第一篇探討植物外顯子演化速率決定因子的報告,我們的分析結果已對植物外顯子演化的研究,提供了新的洞見與方向。

What causes the variations in evolutionary rates is fundamental to molecular evolution. Evolutionary rates of protein-coding sequences vary in different genes and lineages. Broad studies of genomic determinants of rate variance so far have suggested the general finding of expression level and compactness features as dominant factors at gene level. On the other hand, for exons as the element of gene structure, what are the major correlates of rate variations in exons from the same genes or from different genes has not been studied in plants and remains for further elucidations.
Here, we use principal component regression analysis to study the determinants of exonic variance in non-synonymous substitution rate (dN), synonymous substitution rate (dS), and the dN/dS ratio in Arabidopsis genome. The analyzed biological features here are exon length, structural-functional features, exonic expression level, splicing features, compactness features, G+C content of exon, and exon duplicability.
We demonstrate that, quite contrary to the result of rate determinants at gene-level, structural-functional features and splicing features are the two most important determinants accounting for dN/dS and dN rate variance in exons from the same gene. Meanwhile, for exons from different genes, structural-functional features and exon length are the two most important correlates in explaining such variances. As for dS variations, the combination of expression level, exon length, and structural-functional (or splicing) features can account for at least 65% of total variance explained, with expression level being a relatively important one in codon usage for synonymous site change.
When compared with another study on determinants of mammalian exonic evolutionary rates, both determinants profiles show different patterns for both within- and between- gene datasets. Furthermore, the influences of splicing features on exon evolution are less important in plants than in animals. We attribute this dissimilar priority of correlates, either in mammals and plants or for dS and dN/dS (and dN), to the significantly different exon types chosen for analysis between mammals and plants. Our analysis thus has provided new insights into plant exon evolution.

主目錄

正文目錄 ..................................................... II
表目錄 ....................................................... V
圖目錄 ..................................................... VII
附錄目錄 .................................................... IX
中文摘要 ..................................................... X
英文摘要 ................................................. XII

正文目錄
第一章 緒言 .................................................. 1
第一節 演化速率的分子生物層面 ........................... 3
壹、 影響基因間與基因內的分子演化速率之相關因子......... 5
貳、 剪接與複製-兩個微妙的決定因子 .................... 6
參、 動物與植物的差異 .................................. 9
第二節 植物外顯子演化速率決定因子的選取 ................. 10
第三節 實驗設計與分析結果概述 ............................12

第二章 材料與方法 ........................................... 15
第一節 資料來源與序列比對 ................................15
第二節 估算外顯子表達的特徵參數 ..........................17
第三節 外顯子演化速率的估算 ..............................19
第四節 計算mRNA剪接的特徵參數 ..........................20
第五節 估算結構-功能的特徵參數 ...........................21
第六節 量測緊密程度及其它的特徵參數 ......................22
第七節 統計分析 ..........................................23

第三章 結果 ................................................ 25
第一節 選取的外顯子特徵參數與演化速率間的相關程度 ........ 25
壹、 Pearson’s correlation coefficients ....................... 25
貳、 Partial correlation coefficients ..........................26
第二節 選取的特徵參數間可組合為有生物學意義的類群 ........ 28
第三節 阿拉伯芥基因內與基因間的PCR分析結果 ............. 30
第四節 結構-功能特徵類群是dN/dS及dN演化速率的決定因子 .... 35
第五節 演化速率dS的決定因子是不同特徵類群的組合 .......... 38

第四章 討論 ................................................. 41
第一節 特徵類群的演化生物學上意義........................ 41
第二節 內凜與外凜因子對遺傳序列演化速率的重要性 ......... 43
第三節 表達量與結構-功能特徵參數對基因間外顯子
△dN/dS和△dN的相對重要性之再確認 ................. 46
第四節 植物與動物外顯子演化速率的決定因子比較 ............ 50
第五節 阿拉伯芥可解釋的外顯子演化速率變異在
基因內與基因間不同的可能原因 ..................... 56
第六節 可解釋的演化速率dN/dS變異-不同物種間的異同點 ..... 58
第七節 阿拉伯芥可解釋的演化速率變異-基因層面
與外顯子層面的比較 ............................. 60
第八節 淨相關度分析結果與PCR分析結果之差異探討.......... 64
第九節 可能衍生的問題與未來研究方向 ...................... 67

第五章 結論 ................................................. 70

第六章 參考文獻 ............................................. 75


表目錄
表 1 參與主成份迴歸分析的十一個外顯子特徵參數與
dN/dS,dN及dS的Pearson相關係數 ......................... 83
表 2 參與主成份迴歸分析的十一個外顯子特徵參數與
dN/dS,dN及dS的淨相關係數 ............................... 84
表 3 基因內(within-gene)外顯子PCA分析的各主成份
特徵參數組成 .......................................... 85
表 4 基因間(between-gene)外顯子PCA分析的各主成份
特徵參數組成 .......................................... 86
表 5 由外顯子特徵參數組合的十一個主成份與dN/dS,dN
及dS的Pearson相關係數 ................................. 87
表 6 基因內(within-gene)外顯子演化速率dN/dS變異,
各主成份的11項特徵參數解釋的百分比值 (上半);
11項特徵參數組合成六個類群所解釋的百分比值(下半) ...... 88
表 7 基因內(within-gene)外顯子演化速率dN變異,
各主成份的11項特徵參數解釋的百分比值 (上半);
11項特徵參數組合成六個類群所解釋的百分比值(下半) ...... 89
表 8 基因內(within-gene)外顯子演化速率dS變異,
各主成份的11項特徵參數解釋的百分比值 (上半);
11項特徵參數組合成六個類群所解釋的百分比值(下半) ...... 90
表 9 基因間(between-gene)外顯子演化速率dN/dS變異,
各主成份的11項特徵參數解釋的百分比值 (上半);
11項特徵參數組合成六個類群所解釋的百分比值(下半) ...... 91
表 10 基因間(between-gene)外顯子演化速率dN變異,
各主成份的11項特徵參數解釋的百分比值 (上半);
11項特徵參數組合成六個類群所解釋的百分比值(下半) ...... 92
表 11 基因間(between-gene)外顯子演化速率dS變異,
各主成份的11項特徵參數解釋的百分比值 (上半);
11項特徵參數組合成六個類群所解釋的百分比值(下半) ....... 93
表 12 植物與動物外顯子演化速率的決定因子比較 ................ 94
表 13 外顯子PCA分析的各主成份特徵參數組成
(上半-基因內;下半-基因間) ........................... 95
表 14 基因內(within-gene)外顯子演化速率dN/dS變異,
各主成份的9項特徵參數解釋的百分比值 (上半);
9項特徵參數組合成六個類群所解釋的百分比值(下半) ....... 96
表 15 基因內(within-gene)外顯子演化速率dN變異,
各主成份的9項特徵參數解釋的百分比值 (上半);
9項特徵參數組合成六個類群所解釋的百分比值(下半) ....... 97
表 16 基因內(within-gene)外顯子演化速率dS變異,
各主成份的9項特徵參數解釋的百分比值 (上半);
9項特徵參數組合成六個類群所解釋的百分比值(下半) ....... 98
表 17 基因間(between-gene)外顯子演化速率dN/dS變異,
各主成份的9項特徵參數解釋的百分比值(上半);
9項特徵參數組合成六個類群所解釋的百分比值(下半) ……… 99
表 18 基因間(between-gene)外顯子演化速率dN變異,
各主成份的9項特徵參數解釋的百分比值(上半);
9項特徵參數組合成六個類群所解釋的百分比值(下半) ……… 100
表 19 基因間(between-gene)外顯子演化速率dS變異,
各主成份的9項特徵參數解釋的百分比值(上半);
9項特徵參數組合成六個類群所解釋的百分比值(下半) ……… 101


圖目錄

圖 1 外顯子類型與計算加權頻度釋例 ......................... 102
圖 2 各主成份組成參數的相關負荷所組合之投映類型 ........... 103
圖 3 由各主成份所解釋的(A)基因內(B)基因間之外顯子
dN/dS及dN變異百分比 ................................... 104
圖 4 由各主成份所解釋的(A)基因內(B)基因間之外顯子
dS變異百分比 ......................................... 105
圖 5 外顯子表達量差異(△Ln(expL))與演化速率差異之
線性相關趨勢(△Ln(dN/dS) -上列, △Ln(dN) -下列) ........... 106
圖 6 可接觸溶劑的胺基酸殘基比例差異(△PSA)與演化速率差異之
線性相關趨勢(△Ln(dN/dS) -上列, △Ln(dN) -下列) ........... 107
圖 7 內凜失序區域比例差異(△PIDR)與演化速率差異之
線性相關趨勢(△Ln(dN/dS) -上列, △Ln(dN) -下列) ........... 108
圖 8 蛋白質結構域比例差異(△PD)與演化速率差異之
線性相關趨勢(△Ln(dN/dS) -上列, △Ln(dN) -下列) ........... 109
圖 9 由九個主成份所解釋的(A)基因內(B)基因間之外顯子
演化速率變異百分比 ................................... 110
附錄目錄

附錄 一、中英文專有名詞及其縮寫對照表 ....................... 附錄一之1
附錄 二、博士學位候選人資格考試通過證明 .............. 附錄二之1
附錄 三、博士論文進度報告 ............................ 附錄三之1
附錄 四、已發表之論文................................. 附錄四之1
Wu GC-T, Chen F-C. Determinants of exon-level evolutionary rates in Arabidopsis species. Evolutionary Bioinformatics (Evol Bioinform Online). 2012; 8:389-415.

1.Wuketits FM, Ayala FJ, eds. The Evolution of Living Systems (Including Hominids). KGaA, Weinheim: Wiley-VCH Verlag GmbH & Co.; 2005. Handbook of Evolution. No. 2.
2.Gingerich PD. Rates of Evolution. Annual Review of Ecology, Evolution, and Systematics. 2009;40:657-675.
3.Erwin DH. Macroevolution is more than repeated rounds of microevolution. Evolution & Development. 2000;2:78-84.
4.Leroi AM. The scale independence of evolution. Evolution & Development. 2000;2:67-77.
5.Carroll SB. The big picture. Nature. 2001;409:669-669.
6.Reznick DN, Shaw FH, Rodd FH, Shaw RG. Evaluation of the rate of evolution in natural populations of guppies (Poecilia reticulata). Science. 1997;275:1934-1937.
7.Kane NC, Barker MS, Zhan SH, Rieseberg LH. Molecular evolution across the Asteraceae: micro- and macroevolutionary processes. Molecular Biology and Evolution. 2011;28:3225-3235.
8.Li W-H. Molecular Evolution. Sunderland, MA: Sinauer Associates, Inc.; 1997.
9.Templeton AR. Population genetics and microevolutionary theory. Hoboken, NJ: John Wiley & Sons, Inc.; 2006.
10.Pal C, Papp B, Lercher MJ. An integrated view of protein evolution. Nature Reviews Genetics. 2006;7:337-348.
11.Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH. Why highly expressed proteins evolve slowly. Proceedings of the National Academy of Sciences of the United States of America. 2005;102:14338 -14343.
12.Popescu CE, Borza T, Bielawski JP, Lee RW. Evolutionary rates and expression level in Chlamydomonas. Genetics. 2006;172:1567-1576.
13.Rocha EP. The quest for the universals of protein evolution. Trends in Genetics. 2006;22:412-416.
14.Park SG, Choi SS. Expression breadth and expression abundance behave differently in correlations with evolutionary rates. BMC Evolutionary Biology. 2010;10:241.
15.Yang L, Gaut BS. Factors that contribute to variation in evolutionary rate among Arabidopsis genes. Molecular Biology and Evolution. 2011;28: 2359-2369.
16.Liao B-Y, Scott NM, Zhang J. Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins. Molecular Biology and Evolution. 2006;23:2072-2080.
17.Liao B-Y, Weng M-P, Zhang J. Impact of extracellularity on the evolutionary rate of mammalian proteins. Genome Biology and Evolution. 2010;2:39-43.
18.Tang CSM, Epstein RJ. A structural split in the human genome. PLoS One. 2007;2:e603.
19.Zhang L, Lu HHS, Chung W-y, Yang J, Li W-H. Patterns of segmental duplication in the human genome. Molecular Biology and Evolution. 2005;22:135-141.
20.Duret L, Galtier N. Biased gene conversion and the evolution of mammalian genomic landscapes. Annual Review of Genomics and Human Genetics. 2009;10:285-311.
21.Galtier N, Duret L, Glemin S, Ranwez V. GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates. Trends in Genetics. 2009;25:1-5.
22.Lin YS, Hsu WL, Hwang JK, Li WH. Proportion of solvent-exposed amino acids in a protein and rate of protein evolution. Molecular Biology and Evolution. 2007;24:1005-1011.
23.Ramsey DC, Scherrer MP, Zhou T, Wilke CO. The relationship between relative solvent accessibility and evolutionary rate in protein evolution. Genetics. 2011;188:479-488.
24.Brown CJ, Johnson AK, Daughdrill GW. Comparing models of evolution for ordered and disordered proteins. Molecular Biology and Evolution. 2010;27:609-621.
25.Brown CJ, Takayama S, Campen AM, et al. Evolutionary rate heterogeneity in proteins with long disordered regions. Journal of Molecular Evolution. 2002;55:104-110.
26.Chen FC, Pan CL, Lin HY. Independent effects of alternative splicing and structural constraint on the evolution of mammalian coding exons. Molecular Biology and Evolution. 2011;29:187-193.
27.Hanks S, Quinn A, Hunter T. The protein kinase family: conserved features and deduced phylogeny of the catalytic domains. Science. 1988; 241:42-52.
28.Kazi JU, Kabir NN, Soh J-W. Bioinformatic prediction and analysis of eukaryotic protein kinases in the rat genome. Gene. 2008;410:147-153.
29.Wolf YI, Gopich IV, Lipman DJ, Koonin EV. Relative contributions of intrinsic structural-functional constraints and translation rate to the evolution of protein-coding genes. Genome Biology and Evolution. 2010;2:190-199.
30.Hallegger M, Llorian M, Smith CWJ. Alternative splicing: global insights. FEBS Journal. 2010;277:856-866.
31.Keren H, Lev-Maor G, Ast G. Alternative splicing and evolution: diversification, exon definition and function. Nature Reviews Genetics. 2010;11:345-355.
32.Kim E, Goren A, Ast G. Alternative splicing: current perspectives. BioEssays. 2008;30:38-47.
33.Chen FC, Chaw SM, Tzeng YH, Wang SS, Chuang TJ. Opposite evolutionary effects between different alternative splicing patterns. Molecular Biology and Evolution. 2007;24:1443-1446.
34.Chen FC, Wang SS, Chen CJ, Li WH, Chuang TJ. Alternatively and constitutively spliced exons are subject to different evolutionary forces. Molecular Biology and Evolution. 2006;23:675-682.
35.Dehal P, Boore JL. Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biology. 2006;3:e314.
36.Jiao Y, Wickett NJ, Ayyampalayam S, et al. Ancestral polyploidy in seed plants and angiosperms. Nature. 2011;473:97-100.
37.Xing Y, Lee C. Alternative splicing and RNA selection pressure -- evolutionary consequences for eukaryotic genomes. Nature Reviews Genetics. 2006;7:499-509.
38.Barbazuk WB, Fu Y, McGinnis KM. Genome-wide analyses of alternative splicing in plants: opportunities and challenges. Genome Research. 2008;18:1381-92.
39.Kim E, Magen A, Ast G. Different levels of alternative splicing among eukaryotes. Nucleic Acids Research. 2007;35:125-131.
40.Filichkin SA, Priest HD, Givan SA, et al. Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Research. 2010; 20:45-58.
41.Wang BB, Brendel V. Genomewide comparative analysis of alternative splicing in plants. Proceedings of the National Academy of Sciences of the United States of America. 2006;103:7175-80.
42.Mable BK. ‘Why polyploidy is rarer in animals than in plants’: myths and mechanisms. Biological Journal of the Linnean Society. 2004;82: 453-466.
43.Soltis PS, Soltis DE. The role of hybridization in plant speciation. Annual Review of Plant Biology. 2009;60:561-588.
44.Vision TJ, Brown DG, Tanksley SD. The origins of genomic duplications in Arabidopsis. Science. 2000;290:2114-2117.
45.Lockton S, Gaut BS. Plant conserved non-coding sequences and paralogue evolution. Trends in Genetics. 2005;21:60-65.
46.Chen F-C, Liao B-Y, Pan C-L, Lin H-Y, Chang AY-F. Assessing determinants of exonic evolutionary rates in mammals. Molecular Biology and Evolution. 2012;doi: 10.1093/molbev/mss116.
47.Dyson HJ, Wright PE. Intrinsically unstructured proteins and their functions. Nature Reviews Molecular Cell Biology. 2005;6:197-208.
48.Uversky VN. Intrinsically disordered proteins from A to Z. The International Journal of Biochemistry & Cell Biology. 2011;43:1090 -1103.
49.Uversky VN, Dunker AK. Understanding protein non-folding. Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics. 2010; 1804:1231-1264.
50.Carmel L, Koonin EV. A universal nonmonotonic relationship between gene compactness and expression levels in multicellular eukaryotes. Genome Biology and Evolution. 2009;1:382-390.
51.Ren X-Y, Vorst O, Fiers MWEJ, Stiekema WJ, Nap J-P. In plants, highly expressed genes are the least compact. Trends in Genetics. 2006;22:528 -532.
52.Chatterjee S, Hadi AS. Regression analysis by example. 4th ed. Hoboken, New Jersey: John Wiley & Sons, Inc.; 2006.
53.Drummond DA, Raval A, Wilke CO. A single determinant dominates the rate of yeast protein evolution. Molecular Biology and Evolution. 2006; 23:327-337.
54.Plotkin JB, Fraser HB. Assessing the determinants of evolutionary rates in the presence of noise. Molecular Biology and Evolution. 2007;24:1113 -1121.
55.Kersey PJ, Staines DM, Lawson D, et al. Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. Nucleic Acids Research. 2012;40:D91-D97.
56.Youens-Clark K, Buckler E, Casstevens T, et al. Gramene database in 2010: updates and extensions. Nucleic Acids Research. 2011;39:D1085 -D1094.
57.Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research. 2004;32:1792-1797.
58.Leinonen R, Sugawara H, Shumway M. The Sequence Read Archive. Nucleic Acids Research. 2011;39:D19-D21.
59.Langmead B, Trapnell C, Pop M, Salzberg S. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology. 2009;10:R25.
60.Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078-2079.
61.Roberts A, Pimentel H, Trapnell C, Pachter L. Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics. 2011; 27:2325-2329.
62.Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25:1105-1111.
63.Yang Z. PAML 4: a program package for phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution. 2007;24:1586 -1591.
64.Yang Z, Nielsen R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Molecular Biology and Evolution. 2000;17:32-43.
65.Nekrutenko A, Makova KD, Li W-H. The KA/KS ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study. Genome Research. 2002;12:198-202.
66.Cheng J, Randall AZ, Sweredoski MJ, Baldi P. SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Research. 2005;33:W72-W76.
67.Ward JJ, McGuffin LJ, Bryson K, Buxton BF, Jones DT. The DISOPRED server for the prediction of protein disorder. Bioinformatics. 2004;20:2138-2139.
68.Finn RD, Mistry J, Tate J, et al. The Pfam protein families database. Nucleic Acids Research. 2010;38:D211-D222.
69.Camacho C, Coulouris G, Avagyan V, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421.
70.StatSoft Inc. STATISTICA (data analysis software system), version 7. 2004. Available at: www.statsoft.com.
71.R Development Core Team. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing, 2011. Available at: http://www.R-project.org.
72.Wolf MY, Wolf YI, Koonin EV. Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution. Biology Direct. 2008;3:40.
73.Camiolo S, Rau D, Porceddu A. Mutational biases and selective forces shaping the structure of Arabidopsis genes. PLoS One. 2009;4:e6356.
74.Yang H. In plants, expression breadth and expression level distinctly and non-linearly correlate with gene structure. Biology Direct. 2009;4:45; discussion 45.
75.Woody JL, Severin AJ, Bolon Y-T, et al. Gene expression patterns are correlated with genomic and genic structure in soybean. Genome. 2011; 54:10-18.
76.Duret L, Mouchiroud D. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 1999;96:4482-4487.
77.Hiraoka Y, Kawamata K, Haraguchi T, Chikashige Y. Codon usage bias is correlated with gene expression levels in the fission yeast Schizosaccharomyces pombe. Genes to Cells. 2009;14:499-509.
78.Lavner Y, Kotlar D. Codon bias as a factor in regulating expression via translation rate in the human genome. Gene. 2005;345:127-138.
79.Drummond DA, Wilke CO. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell. 2008;134:341 -352.
80.Slotte T, Bataillon T, Hansen TT, St. Onge K, Wright SI, Schierup MH. Genomic determinants of protein evolution and polymorphism in Arabidopsis. Genome Biology and Evolution. 2011;3:1210-1219.
81.Tilgner H, Nikolaou C, Althammer S, et al. Nucleosome positioning as a determinant of exon recognition. Nature Structural & Molecular Biology. 2009;16:996-1001.
82.Schwartz S, Meshorer E, Ast G. Chromatin organization marks exon-intron structure. Nature Structural & Molecular Biology. 2009;16: 990-995.
83.Luco RF, Pan Q, Tominaga K, Blencowe BJ, Pereira-Smith OM, Misteli T. Regulation of alternative splicing by histone modifications. Science. 2010;327:996-1000.
84.Charlesworth B. Fundamental concepts in genetics: Effective population size and patterns of molecular evolution and variation. Nature Reviews Genetics. 2009;10:195-205.
85.Tsai IJ, Bensasson D, Burt A, Koufopanou V. Population genomics of the wild yeast Saccharomyces paradoxus: Quantifying the life cycle. Proceedings of the National Academy of Sciences of the United States of America. 2008;105:4957-4962.
86.Lundemo S, Falahati-Anbaran M, StenØIen HK. Seed banks cause elevated generation times and effective population sizes of Arabidopsis thaliana in northern Europe. Molecular Ecology. 2009;18:2798-2811.



QRCODE
 
 
 
 
 
                                                                                                                                                                                                                                                                                                                                                                                                               
第一頁 上一頁 下一頁 最後一頁 top
無相關論文