十三. 基因组核型演化分析-WGDI

一. 准备文件

首先，下载基因组注释文件abc.gff3和蛋白序列文件abc.aa；然后，进行格式转换和重命名，得到abc.gff，abc.lens，abc.pep；接着做blast，得到abc_abc.blast 文件

python 01.getgff.py abc.gff3 old.gff
python 02.gff_lens.py old.gff Ela abc.gff abc.lens
python 03.seq_newname.py abc.gff abc.aa abc.pep
diamond makedb --in abc.pep -d abc
diamond blastp -d abc -q abc.pep -o abc_abc.blast -e 1e-5 -k 5

二. 找原始染色体

根据点阵图Dotplot，找出原始染色体，整理成ancestor.txt格式，然后利用-ak命令生成染色体gff，lens，pep文件,参照基于WGDI的祖先核型成分推断

wgdi -d total.conf
wgdi -ak total.conf

三. 绘制核型图

依次执行以下命令：

1. wgdi -icl total.conf
2. wgdi -bi total.conf
3. wgdi -c total.conf
4. wgdi -km total.conf
5. wgdi -k total.conf

附total.conf文件实例：

[collinearity]
gff1 = abc.gff
gff2 = AEK.gff
lens1 = abc.lens
lens2 = AEK.lens
blast = abc_AEK.blast
blast_reverse = false
multiple  = 1
process = 8
evalue = 1e-5
score = 100
grading = 50,40,25
mg = 25,25
pvalue = 1
repeat_number = 10
positon = order
savefile = abc_AEK.collinearity
#wgdi -icl total.conf

[blockinfo]
blast = abc_AEK.blast
gff1 =  abc.gff
gff2 =  AEK.gff
lens1 = abc.lens
lens2 = AEK.lens
collinearity = abc_AEK.collinearity
score = 100
evalue = 1e-5
repeat_number = 20
position = order
ks = none
ks_col = ks_NG86
savefile = abc_AEK.blockinfo.csv
#wgdi -bi total.conf

[correspondence]
blockinfo =  abc_AEK.blockinfo.csv
lens1 = abc.lens
lens2 = AEK.lens
tandem = true
tandem_length = 200
pvalue = 0.2
block_length = 50
tandem_ratio = 0.5
multiple  = 1
homo = -1,1
savefile = abc_AEK.blockinfo.new.csv
#wgdi -c total.conf

[karyotype_mapping]
blast = abc_AEK.blast
blast_reverse = false
gff1 = abc.gff
gff2 = AEK.gff
score = 100
evalue = 1e-5
repeat_number = 5
#ancestor_left = ancestor location file (Only one of ('left', 'top') can be reserved)
ancestor_top = AEK.ancestor.txt
the_other_lens = abc.lens
blockinfo = abc_AEK.blockinfo.new.csv
blockinfo_reverse = false
limit_length = 5
the_other_ancestor_file =  abc.ancestor.txt
#wgdi -km total.conf

[karyotype]
ancestor = abc.ancestor.txt
width = 0.5
figsize = 10,6.18
savefig = abc.ancestor.pdf
#wgdi -k total.conf

[blockks]
lens1 = abc.lens
lens2 = AEK.lens
genome1_name =  abc
genome2_name =  AEK
blockinfo = abc_AEK.blockinfo.csv
pvalue = 0.05
tandem = true
tandem_length = 200
markersize = 1
area = -1,2
block_length =  5
figsize = 8,8
savefig = abc_bk_ks.dotplot.pdf
#wgdi -bk total.conf

[dotplot]
blast = abc_AEK.blast
gff1 =  abc.gff
gff2 =  AEK.gff
lens1 = abc.lens
lens2 = AEK.lens
genome1_name =  abc
genome2_name =  AEK
multiple  = 1
score = 100
evalue = 1e-5
repeat_number = 10
position = order
blast_reverse = false
ancestor_left = abc.ancestor.txt
ancestor_top = AEK.ancestor.txt
markersize = 0.5
figsize = 10,10
savefig = abc_AEK.dotplot.pdf
#wgdi -d total.conf

[ancestral_karyotype]
gff = abc.gff
pep_file = abc.pep
ancestor = abc_AEK.ancestor.txt1
mark = Jaeuk
ancestor_gff =  AEK.gff
ancestor_lens =  AEK.lens
ancestor_pep =  AEK.pep
ancestor_file =  AEK.ancestor.txt
#wgdi -ak total.conf