1:关于真菌基因组次级代谢分析

可以使用SMURF和AntiSMASH，基因组注释使用MAKER，基因与测使用AUGUSTUS并基于Aspergillus oryzae物种的训练结果。拼接使用的是VelvetOptimizer，基因功能注释使用的是interproscan.测序深度27x,N50 为48,518。1,231 contigs。基因组大小为：31,415,732bp。GC含量：48.24% 使用tRNAscan-SE与测tRNA.

2014-Draft Genome Sequence of Penicilliumexpansum Strain R19, Which Causes Postharvest Decay of Apple Fruit

2:关于真菌基因组的分析

在已知近源物种的基础上，可以分析结构变异

（例如染色体重排等）

2014-Complete Sequencing andChromosome-Scale Genome Assembly of the Industrial Progenitor Strain P2niaD18from the Penicillin Producer Penicillium chrysogenum

3:在真菌基因预测

本文分别使用了Fgenesh（Penicilliumfuniculosum 训练）与GeneMark- ES（基于自身训练），基于预测是在大于1Kb的且经过masker重复序列的基础上进行的将两者结果整合。关于功能注释内容包括：nr\interproscan\Swiss-Prot/UniProtKB\GO\kegg(KAAS )

2014-Genome sequencing of high-penicillin producingindustrial strain of Penicillium chrysogenum

4:这篇文章里关注了水平基因转移

组装完基因预测先是使用GeneMark and TWINSCAN分别与测然后再合并，再合并genewise的结果（Genomic sequences with 90% identity that spanned more than 80% of aprotein were ex- tended 500 bp up and downstream and passed to Gene-Wise topredict gene models. ）假定基因的功能注释使用blast2go.假定蛋白的功能域和GO分析可以使用 Agbase

2014-Genome sequencing and analysis of thepaclitaxel-producing endophytic fungus Penicillium aurantiogriseum NRRL 62431

5:细胞色素P450

（cytochromeP450或CYP450,简称CYP450）为一类亚铁血红素—硫醇盐蛋白的超家族，它参与内源性物质和包括药物、环境化合物在内的外源性物质的代谢.网址：http://drnelson.uthsc.edu/P450seqs.dbs.html。使用blastp(e<10-5).(A physical CYP gene cluster was de ned as threeor more CYPs present within a 100-kb sliding window of the genomic sequence orfewer than 10 genes between CYPs a er they had been sorted into groups alongthe chromosomes. If two adjacent clusters overlapped, they were merged to formone larger cluster)

2012-Genome sequence of the model medicinalmushroom Ganoderma lucid

http://drnelson.uthsc.edu/cytochromeP450.html

6:真菌基因组的大小范围

In fungi, the diversity of genomes varies from 8.97 Mb to 177.57 Mb.

Mohanta T K, Bae H. The diversity of fungalgenome[J]. Biological procedures online, 2015, 17(1)

原文地址：http://blog.sina.com.cn/s/blog_83f77c940102vx0h.html

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