生醫資訊學導論 _ 期末報告
Origin and Spread of de Novo Genes in Drosophila melanogaster Populations
第 7 組 課程老師 : 趙坤茂老師
報告學生 : 游偉寗、唐皇、黃雍文 報告日期 :103.5.26
大綱
1. 簡介 -- 游偉寗 2. 實驗 -- 游偉寗
3. 結果與討論 -- 唐皇 4. 總結 -- 黃雍文
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1. 簡介
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• Comparative genomic analyses have revealed that genes may arise from ancestrally nongeni c sequence.
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• We identified 142 segregating and 106 fixed te stis-expressed de novo genes in a population s ample of Drosophila melanogaster.
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• Evidence for these “de novo” genes has gener ally derived from a combination of phylogene tic and genomic/transcriptomic analyses that r eveal evidence of lineage- or species-specific t ranscripts associated with nongenic orthologo us sequences in sister species.
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• De novo genes, which were first identified in D rosophila, have also been identified in humans , rodents, rice, and yeast .
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• In Drosophila, de novo genes tend to be speci fically expressed in tissues associated with mal e reproduction.
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• we used population genomic and transcriptom ic data from Drosophila melanogaster and its clos e relatives to investigate the origin and spread of de novo genes within populations.
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2. 實驗
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• Illumina paired-end RNAsequencing (RNA-seq) and de novo and reference-guided assembly a nd alignment were used to characterize the te stis transcriptome of six previously sequenced inbred Raleigh (RAL) D. melanogaster strains.
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• The RNA-sequencing data from each strain we re used for de novo transcriptome assembly, a s well as a reference sequence guided transcri ptome assembly. These two approaches are co mplementary, and as expected, were highly co ncordant.
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•Illumina paired-endRNAsequencing (RNA-seq):
de novo transcriptome assembly
• De novo transcriptome assembly is the metho d of creating a transcriptome without the aid of a reference genome.
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reference-based assembly
• A set of assembled transcripts allows for initial gene expression studies. Prior to the develop ment of transcriptome assembly computer pr ograms, transcriptome data were analyzed pri marily by mapping on to a reference genome.
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De novo vs. reference-based assembly:
• Though genome alignment is a robust way of ch aracterizing transcript sequences, this method i s disadvantaged by its inability to account for in cidents of structural alterations of mRNA transc ripts, such as alternative splicing Since a genom e contains the sum of all introns and exons that may be present in a transcript, spliced variants that do not align continuously along the genom e may be discounted as actual protein isoforms.
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3. 結果與討論
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4. 總結
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Conculsion
• There are many polymorphic de novo male-specific gene s likely recruited by selection primarily from ancestral, u nexpressed ORFs.
• Existence of many more fixed de novo D.melanogaster g enes than previously inferred
• de novo genes have been influenced by directional selec tion
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