论文

Genome of wild mandarin and domestication history of mandarin
Molecular Plant
2018
Huazhong Agricultural University

当前阶段还是重点关注方法

植物材料（plant materials）

• 66 citrus accessions around the Nanling region and the neighboring area
• an additional 12 citrus accessions that are known cultivars maintained by the National Center of Ctrus Breeding
• 38 newly sequenced
• 66 were from previous studies

野生柑橘基因组组装与注释

• 二代测序技术
  短片段文库（230bp和500bp）
  长片段文库（2kb，5kb,20kb）
• 组装软件
  Platanus
  Gapcloser
  BWA;Samtools(这一步的做法没有看懂)
  BUSCO
  RepeatModeler;HMMsearch;blastn (the transposable element libraries)
  AUGUSTUS GlimmerHMM (ab initio gene predictions)
  trinity EVM

基因家族分析

7个柑橘属基因组蛋白编码基因——gene clustering analysis

• an all-versus-all comparison was performed using blastp
• clustering was conducted using OrthoMCL

dn/ds分析

7个柑橘属单拷贝直系同源蛋白编码基因
蛋白比对 ClustalW然后转换成对应的CDS比对
PAML估算选择压力，两个模型the free-ration branch model; the one-ration branch model
LRT 比较两个模型

变异检测

原始数据比对到甜橙基因组 BWA
samtools去除重复序列
picards为每个库分组
GATK indels重新比对

all genotype information for the polymorphic sites was retrieved using the GATK population method(?)
104 individuals
46 mandarins
21 pummelos
11 lchang papeda
8 citron
15 atalantias
1 C. mangshanensis 1 Yuanju 1 Clausena lansium
测序深度，non-singleton(?) and biallelic SNPs; non-missing individuals across all five groups
####### 系统发育分析 主成分分析
46 mandarins
单拷贝蛋白编码基因的SNP(还不包括在the candidate introgression regions)
raxmlHPC 构建进化树 GTRGAMMA模型
PCA eigenstrat
the genetic structure structure software

物种特异SNP鉴定

这部分没看懂呀！

inference of demographic (这个单词咋翻译呢) History

historical population sizes 历史种群大小 PSMC model
over 35 X genome coverage
introgressed region were excluded before the PSMC analyses

柑橘记忆组高度分化的区域

种群分化 population differentiation was evaluated using Fst
vcftools 10-kb window and 5-kb sliding window
高度分化的区域筛选标准没有看懂呀！
vcftools Tajima D

野生和栽培柑橘比较寻找驯化区域

Fst--genetic differentiation
π -- nucleotide diversity values vcftools 10-kb window and a 5-kb sliding window
XP-CLR 筛选栽培番茄中受选择的区域（具体过程还看不太懂）

野生柑橘的基因渗入

这部分得花时间仔细看呀

转录组

糖和有机酸测定

soluble solid content 可溶性固形物
acidity 酸碱滴定
Compositions and concentrations of sugar and organic acids were determined using gas chromatography

未完待续