論文

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

https://www.nature.com/articles/ng.3886/

蘋果基因組ng.3886.pdf

今天的推文我們來試著復現(xiàn)一下論文中的Figure3c

image.png

論文中對應的圖注

Distribution of sequence identity values between genomic copies and consensus repeats in the GDDH13 assembly (based on 2,198,722 data points). The relative frequencies per percentage of identity of the Helitron, TIR, LTR, LINE, SINE and unclassified TEs (NoCat) are represented in different colors.

論文中的部分數(shù)據(jù)存儲在這個鏈接

https://iris.angers.inra.fr/gddh13/the-apple-genome-downloads.html

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這個TE注釋里有identity這個值（這里我不太確定是不是用到的這個值來畫圖）

文件的格式

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寫個腳本把SINE LINE 和Helitron的值提取出來

import sys
import re

input_txt = sys.argv[1]
output_txt = sys.argv[2]



pattern01 = sys.argv[3]

regexp01 = re.compile(pattern01)

pattern02 = "ID=\S+;"

regexp02 = re.compile(pattern02)

fr = open(input_txt,'r')

ID_list = []

for line in fr:
    if 'TargetDescription' in line and len(regexp01.findall(line)) >= 1:
        ID_list.append(regexp02.findall(line)[0].replace("ID=","").replace(";",""))
        
        
print(len(ID_list))

fr.close()

fr = open(input_txt,'r')

pattern03 = "Parent=\S+;"
regexp03 = re.compile(pattern03)

pattern04 = "Identity=\S+"
regexp04 = re.compile(pattern04)

fw = open(output_txt,'w')
for line in fr:
    if "Parent" in line and regexp03.findall(line)[0].replace("Parent=","").replace(";","") in ID_list:
        if len(regexp04.findall(line)) >= 1:
            fw.write("%s=%s\n"%(regexp04.findall(line)[0],pattern01))

fw.close()

運行腳本

python appleNG.py GDDH13_1-1_TE.gff3 line_identity.txt LINE
python appleNG.py GDDH13_1-1_TE.gff3 sine_identity.txt SINE
python appleNG.py GDDH13_1-1_TE.gff3 helitron_identity.txt Helitron

輸出文件格式

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接下來是畫圖代碼

library(tidyverse)

dfsine<-read_delim("sine_identity.txt",
               delim = "=",
               col_names = FALSE)
dfline<-read_delim("line_identity.txt",
                   delim = "=",
                   col_names = FALSE)
dfhelitron<-read_delim("helitron_identity.txt",
                   delim = "=",
                   col_names = FALSE)

df<-bind_rows(dfsine,dfline,dfhelitron)



ggplot(data=df,aes(x=X2,stat(density),color=X3))+
  geom_freqpoly(binwidth=1,linewidth=3)+
  theme_classic()+
  scale_x_continuous(expand = expansion(mult = c(0,0)),
                     limits = c(60,100))+
  scale_y_continuous(expand = expansion(mult = c(0,0)),
                     limits = c(0,0.1))+
  labs(y="Frequency",x="Identity")+
  scale_color_manual(values = c("#2d2884","#c2a20c","#6497d0"),
                     name="Element")

image.png

和論文中的圖并不能完全對應上，不太清楚論文中是怎么來統(tǒng)計這個值的

怎么根據(jù)這個identity的值算插入時間暫時還沒有搞明白

這個圖的峰和binwidth的值設置是有關系，binwidth如果改動，line的第二個峰也會有影響，不太明白這個參數(shù)應該怎么設置

論文中對這個圖的描述文字

To investigate the evolutionary history of TEs in the apple genome, we plotted the distribution of identity values between genomic copies and their consensus sequences (Fig. 3c). Distributions for all classes of repeats showed a peak at 77% identity. By considering the mutation rate that has been reported for LTR-RTs in plants (1.3 × 10?8 base substitutions per site per year40,41), we estimated the age of those insertions as described by the International Human Genome Sequencing Consortium42. We concluded that the peak at 77% identity corresponded to an insertion age of around 21 million years ago (Mya) (Fig. 3c).
We also noted a second peak, particularly for LINE elements, at 98% identity that corresponded to a TE burst at ~1.6 Mya

TEs also have an important role in structuring genomes. The in-depth TE annotation we performed showed a major TE burst in apple that we estimated to have happened around 21 Mya. This affected all types of TEs, suggesting that the precursor of the modern apple underwent environmental changes with resulting stresses that led to the activation of these TEs50. The observed TE burst corresponds to the Miocene epoch (23 Mya to 5 Mya) and may coincide with two events: the divergence between pear and apple48 and an uplift event occurring at the Tian Shan mountains51, which cover the region where the ancestor of the apple originates from52. We hypothesize that these TE bursts, which presumably must have been very different in the predecessor of pear and apple, have contributed to the diversification, and possibly even speciation, of these plants.

推文記錄的是自己的學習筆記，很可能存在錯誤，請大家批判著看