論文
Genome of wild mandarin and domestication history of mandarin
Molecular Plant
2018
Huazhong Agricultural University
當(dāng)前階段還是重點關(guān)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
野生柑橘基因組組裝與注釋
- 二代測序技術(shù)
短片段文庫（230bp和500bp）
長片段文庫（2kb，5kb,20kb） - 組裝軟件
Platanus
Gapcloser
BWA;Samtools(這一步的做法沒有看懂)
BUSCO
RepeatModeler;HMMsearch;blastn (the transposable element libraries)
AUGUSTUS GlimmerHMM (ab initio gene predictions)
trinity EVM
基因家族分析
7個柑橘屬基因組蛋白編碼基因——gene clustering analysis
- an all-versus-all comparison was performed using blastp
- clustering was conducted using OrthoMCL
dn/ds分析
7個柑橘屬單拷貝直系同源蛋白編碼基因
蛋白比對 ClustalW然后轉(zhuǎn)換成對應(yīng)的CDS比對
PAML估算選擇壓力，兩個模型the free-ration branch model; the one-ration branch model
LRT 比較兩個模型
變異檢測
原始數(shù)據(jù)比對到甜橙基因組 BWA
samtools去除重復(fù)序列
picards為每個庫分組
GATK indels重新比對
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
測序深度，non-singleton(?) and biallelic SNPs; non-missing individuals across all five groups
####### 系統(tǒng)發(fā)育分析 主成分分析
46 mandarins
單拷貝蛋白編碼基因的SNP(還不包括在the candidate introgression regions)
raxmlHPC 構(gòu)建進(jìn)化樹 GTRGAMMA模型
PCA eigenstrat
the genetic structure structure software
物種特異SNP鑒定
這部分沒看懂呀！
inference of demographic (這個單詞咋翻譯呢) History
historical population sizes 歷史種群大小 PSMC model
over 35 X genome coverage
introgressed region were excluded before the PSMC analyses
柑橘記憶組高度分化的區(qū)域
種群分化 population differentiation was evaluated using Fst
vcftools 10-kb window and 5-kb sliding window
高度分化的區(qū)域篩選標(biāo)準(zhǔn)沒有看懂呀！
vcftools Tajima D
野生和栽培柑橘比較尋找馴化區(qū)域
Fst--genetic differentiation
π -- nucleotide diversity values vcftools 10-kb window and a 5-kb sliding window
XP-CLR 篩選栽培番茄中受選擇的區(qū)域（具體過程還看不太懂）
野生柑橘的基因滲入
這部分得花時間仔細(xì)看呀
轉(zhuǎn)錄組
糖和有機(jī)酸測定
soluble solid content 可溶性固形物
acidity 酸堿滴定
Compositions and concentrations of sugar and organic acids were determined using gas chromatography
