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「JCVI教程」使用JCVI进行基因组共线性分析(中)

在「JCVI教程」使用JCVI进行基因组共线性分析(上)还是有一个尴尬的事情，就是只用到两个物种，不能展示出JCVI画图的方便之处，因此这里参考https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)的分析，只不过画图部分拓展下思路。

首先要运行如下代码获取目的数据

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python -m jcvi.apps.fetch phytozome Vvinifera,Ppersica,Tcacao
python -m jcvi.formats.gff bed --type=mRNA --key=Name Vvinifera_145_gene.gff3.gz -o grape.bed
python -m jcvi.formats.gff bed --type=mRNA --key=Name Ppersica_139_gene.gff3.gz -o peach.bed
python -m jcvi.formats.gff bed --type=mRNA --key=Name Tcacao_233_gene.gff3.gz -o cacao.bed
python -m jcvi.formats.fasta format --sep="|" Vvinifera_145_cds.fa.gz grape.cds
python -m jcvi.formats.fasta format --sep="|" Ppersica_139_cds.fa.gz peach.cds
python -m jcvi.formats.fasta format --sep="|" Tcacao_233_cds.fa.gz cacao.cds
# find ortholog
python -m jcvi.compara.catalog ortholog grape peach --cscore=.99
python -m jcvi.compara.catalog ortholog peach cacao --cscore=.99
# build .simpe
python -m jcvi.compara.synteny screen --minspan=30 --simple grape.peach.anchors grape.peach.anchors.new 
python -m jcvi.compara.synteny screen --minspan=30 --simple peach.cacao.anchors peach.cacao.anchors.new

然后按照教程的配置文件进行画图

layout文件内容如下

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# y, xstart, xend, rotation, color, label, va,  bed
 .7,     .2,    .4,      45,      , Grape, top, grape.bed
 .5,     .2,    .8,       0,      , Peach, top, peach.bed
 .7,     .4,    .8,     -45,      , Cacao, bottom, cacao.bed
# edges
e, 0, 1, grape.peach.anchors.simple
e, 1, 2, peach.cacao.anchors.simple

seqids文件内容如下

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chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19
scaffold_1,scaffold_2,scaffold_3,scaffold_4,scaffold_5,scaffold_6,scaffold_7,scaffold_8
scaffold_1,scaffold_2,scaffold_3,scaffold_4,scaffold_5,scaffold_6,scaffold_7,scaffold_8,scaffold_9,scaffold_10r

运行python -m jcvi.graphics.karyotype seqids layout会得到如下结果

三个物种的共线性图

我就在思考一个问题如何让他形成一个三角形。经过一波三角运算和不断尝试，我定义了如下的layout

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# y, xstart, xend, rotation, color, label, va,  bed
 .5,      0.025,    0.625,      60,      , Grape, top, grape.bed
 .2,      0.2,    .8,       0,      , Peach, top, peach.bed
 .5,     0.375,    0.975,     -60,      , Cacao, top, cacao.bed
# edges
e, 0, 1, grape.peach.anchors.simple
e, 1, 2, peach.cacao.anchors.simple

那么效果怎么样呢？运行python -m jcvi.graphics.karyotype seqids layout吧

三角形

当然这里只展示了，grape和peach, peach和cacao之间的共线性，我又想着能不能加上grape和caocao呢？我尝试着运行下面的代码，

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python -m jcvi.compara.catalog ortholog grape cacao --cscore=.99
python -m jcvi.compara.synteny screen --minspan=30 --simple grape.cacao.anchors grape.cacao.anchors.new

并继续修改了layout

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# y, xstart, xend, rotation, color, label, va,  bed
 .5,      0.025,    0.625,      60,      , Grape, top, grape.bed
 .2,      0.2,    .8,       0,      , Peach, top, peach.bed
 .5,     0.375,    0.975,     -60,      , Cacao, top, cacao.bed
# edges
e, 0, 1, grape.peach.anchors.simple
e, 1, 2, peach.cacao.anchors.simple
e, 0, 2, grape.cacao.anchors.simple

运行python -m jcvi.graphics.karyotype seqids layout会得到如下结果

awesome

我觉得给我一点时间，我也能用JCVI画出下面的图了

amazing

图片来自于https://science.sciencemag.org/content/345/6199/950