2016-6-15-de novo文献阅读

准备读四篇denovo的文献：

1. Nature Biotechnology(2015) - Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement
2. Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history
3. Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars
4. Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau

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1. 四倍体陆地棉基因组

allotetraploid：异源四倍体；Upland cotton：陆地棉
Structural rearrangements：结构重组；gene loss：基因缺失；disrupted genes：扰乱基因；sequence divergence：序列分歧；asymmetric evolution：不对称进化
方法：

1. whole-genome shotgun reads：全基因组鸟枪法
2. bacterial artificial chromosome (BAC)-end sequences：
3. genotype-by-sequencing genetic maps：

背景：虽然已有测序，但是exact donor species that led to the formation of the tetraploid cotton species 1–2 million years ago (MYA) no longer exists。
测序难点：discriminating between homoeologous sequences（识别同源序列）
传统做法：祖先的二倍体基因组序列，来指导异源多倍体的同源染色体的装配。
问题：关于同源关系的许多contigs 和 scaffolds 保持模棱两可。
本研究的核心优势：scaffolds (N50 = 1,600 kb)长，相比与Brassica napus (N50 = 764 kb)，Nicotiana tabacum(N50 = 345~386 kb)，wheat (contig N50 = 515~4,297 bp)，G. arboreum(N50 = 666 kb)

方法：
Genome sequencing data generation
sheared with a Bioruptor sonication device for short-insert paired-end (PE) library construction
with a Hydroshear DNA Shearing Device (Genomic Solutions Inc., Ann Arbor, MI, USA) for mate-pair library construction
Short-insert paired-end (180, 300, and 500 bp) and large-insert mate-pair libraries (2, 5, 10 kb) were prepared
All libraries were sequenced at 2 × 100 bp on an Illumina HiSeq 2000 platform. In total, 843 Gb of DNA sequencing read data were generated for the genome assembly, representing approximately 337-fold coverage of the raw genome.

BAC library construction and BAC end sequencing
read短，无法确定在基因组的位置，获得的只是contig。
BAC文库可以帮助我们拼接更长的序列。另外由于文库构建存在一定的偏好性，或者有一些序列GC含量太高或太低，当然还有一些repeat序列，所以BAC文库也可以帮助我们对这些序列更好的获得。现在主流的方法是：构建mate-pair文库+多插入片段PE文库+多测序平台结合+fish或者binano光学图谱。

Genome size estimation

Genome assembly, scaffolding and gap-closing

Linkage map construction using the TM-1 × Hai7124 mapping population

Correction of the TM-1 assembly using the SNP map and pseudomolecule chromosome construction

Assessment of genome assembly quality by PE reads

TM-1 assembly validation using mRNA sequences from the G. raimondii and G. hirsutum genomes

TM-1 assembly validation using 36 completely sequenced BACs

Gene prediction and annotation

Transcription factors annotation

Noncoding RNAs annotation

TE annotation

Identification of homoeologous gene sets and orthologous gene sets

Estimation of divergence time

Phylogenetic tree construction and evolution rate estimation

Syntenic analysis and whole-genome alignment

PSGs

Gene loss

Genes involved in the ongoing process of gene loss

2. 金丝猴基因组

3. 藏猪基因组

4. 地山雀基因组