「文獻(xiàn)」多倍體植物基因組測序組裝當(dāng)前策略
文獻(xiàn)地址: Current Strategies of Polyploid Plant Genome Sequence Assembly
基因組多倍化主要發(fā)生在被子植物中宙地。很多多倍體植物都在農(nóng)業(yè)生產(chǎn)上有重大的價(jià)值嗅战，例如小麥(Triticum aestivum)宝冕，花生(Arachis hypogaea)，十字花科偷厦，馬鈴薯(Solanum tuberosum)，燕麥(Avena sativa)饥瓷，香蕉(Musa sp.)氓奈，草莓(Fragaria ananassa)，咖啡( Coffea arabica)等蜓肆。
多倍體分為兩種類型颜凯，來自于全基因組加倍的同源多倍體(Autopolyploidy)和物種間/物種內(nèi)雜交后染色體加倍的異源多倍體(allopolyploidy). 同源多倍體通常會(huì)有育性上的問題，而異源多倍體則可能出現(xiàn)雜交優(yōu)勢(heterosis or hybrid vigor).多倍體在表型和基因型上的關(guān)系更加復(fù)雜仗扬，例如它們需要比較復(fù)雜的調(diào)控才能保證同源基因相互間的表達(dá)一致症概。
在基因組組裝上，同源多倍體相對異源多倍體更加困難早芭。這是因?yàn)槿蚪M加倍事件之后通常還會(huì)跟著基因組重拍(genome rearrangement), 非典型重組(atypical recombination), 可移動(dòng)因子啟動(dòng)(transposable element activation)彼城，減數(shù)分裂/有絲分裂缺陷(meiotic/mitotic defects)，以及內(nèi)含子擴(kuò)張(intron expansions)與DNA缺失退个。因此組裝基因組一大挑戰(zhàn)就是不能錯(cuò)誤組裝了兩個(gè)亞基因組中的相似片段募壕。
作者在NCBI查詢并總結(jié)了到2018年為止已發(fā)表的多倍體物種，我更新了草莓(Fragaria?×?ananassa)语盈，香蕉(Musa balbisiana)和甘蔗(Saccharum spontaneum L.)
| ID | Organism name | Genome size (Mb) | Current status | 1st Release date in NCBI | Ploidy level | References/center |
|---|---|---|---|---|---|---|
| 1 | Arabidopsis lyrata subsp lyrata | 206.823 | Scaffold | 2009/11/30 | Tetraploid | Hu et al., 2011 |
| 2 | Glycine max | 978.972 | Chromosome | 2010/1/5 | Allotetraploid | Schmutz et al., 2010 |
| 3 | Triticum aestivum | 15344.7 | Chromosome 3B | 2010/7/15 | Allohexaploid | Choulet et al., 2010 |
| 4 | Solanum tuberosum | 705.934 | Scaffold | 2011/5/24 | Autotetraploid | Potato Genome Sequencing Consortium, 2011 |
| 5 | Actinidia chinensis | 604.217 | Contig | 2013/9/16 | Tetraploid | Huang et al., 2013 |
| 6 | Fragaria orientalis | 214.356 | Scaffold | 2013/11/27 | Tetraploid | Hirakawa et al., 2014 |
| 7 | Fragaria x ananassa | 805.488 | Chromosome | 2019/2/25 | Allooctaploid | Edger et al., 2019 |
| 8 | Beta vulgaris | 566.55 | Chromosome | 2013/12/18 | 2n, 4n (Beyaz et al., 2013) | Dohm et al., 2014 |
| 9 | Oryza minuta | 45.1659 | Chromosome | 2014/4/16 | Tetraploid | Oryza Chr3 Short Arm Comparative Sequencing Project |
| 10 | Camelina sativa | 641.356 | Chromosome | 2014/4/17 | Hexaploid | Kagale et al., 2014 |
| 11 | Brassica napus | 976.191 | Chromosome | 2014/5/5 | Allotetraploid | Chalhoub et al., 2014 |
| 12 | Brassica oleracea var. oleracea | 488.954 | Chromosome | 2014/5/22 | Hexaploid | NCBI |
| 13 | Nicotiana tabacum | 3643.47 | Scaffold | 2014/5/29 | Allotetraploid | Sierro et al., 2014 |
| 14 | Eragrostis tef | 607.318 | Scaffold | 2015/4/8 | Allotetraploid | Cannarozzi et al., 2014 |
| 15 | Gossypium hirsutum | 2189.14 | Chromosome | 2015/4/29 | Allotetraploid | Li et al., 2015 |
| 16 | Zoysia japonica | 334.384 | Scaffold | 2016/3/15 | Tetraploid | Tanaka et al., 2016 |
| 17 | Zoysia matrella | 563.439 | Scaffold | 2016/3/15 | Allotetraploid | Tanaka et al., 2016 |
| 18 | Zoysia pacifica | 397.01 | Scaffold | 2016/3/15 | Allotetraploid | Tanaka et al., 2016 |
| 19 | Musa itinerans | 455.349 | Scaffold | 2016/5/21 | 2n, 3n hybrids (Wu et al.,2016) | South China Botanic Garden, CAS |
| 20 | Rosa x damascena | 711.72 | Scaffold | 2016/6/13 | Tetraploid | BIO-FD & C CO., LTD |
| 21 | Chenopodium quinoa | 1333.55 | Scaffold | 2016/7/11 | Tetraploid | Jarvis et al., 2017 |
| 22 | Brassica juncea var. tumida | 954.861 | Chromosome | 2016/7/19 | Allotetraploid | Zhejiang University |
| 23 | Hibiscus syriacus | 1748.25 | Scaffold | 2016/7/29 | 2n, 3n, 4n (Van Huylenbroeck et al., 2000) | Korea Research Institute of Science and Biotechnology (Kim et al., 2017) |
| 24 | Gossypium barbadense | 2566.74 | Scaffold | 2016/10/28 | Tetraploid | Huazhong Agricultural University |
| 25 | Momordica charantia | 285.614 | Scaffold | 2016/12/27 | 2n to 6n (Kausar et al., 2015) | Urasaki et al., 2016 |
| 26 | Drosera capensis | 263.788 | Scaffold | 2016/12/30 | Tetraploid (Rothfels and Heimburger, 1968) | Butts et al., 2016 |
| 27 | Capsella bursa-pastoris | 268.431 | Scaffold | 2017/1/29 | Tetraploid | Lomonosov Moscow State University |
| 28 | Saccharum hybrid cultivar | 1169.95 | Contig | 2017/3/3 | It varies (D’Hont, 2005) | Ria?o-Pachón and Mattiello, 2017 |
| 29 | Xerophyta viscosa | 295.462 | Scaffold | 2017/3/31 | Hexaploid | Costa et al., 2017 |
| 30 | Triticum dicoccoides | 10495 | Chromosome | 2017/5/18 | Tetraploid | WEWseq consortium |
| 31 | Utricularia gibba | 100.689 | Chromosome | 2017/5/31 | 16-ploid | Lan et al., 2017 |
| 32 | Eleusine coracana | 1195.99 | Scaffold | 2017/6/8 | Allotetraploid | Hittalmani et al., 2017 |
| 33 | Dioscorea rotundata | 456.675 | Chromosome | 2017/7/28 | Tetraploid | Iwate Biotechnology Research Center |
| 34 | Ipomoea batatas | 837.013 | Contig | 2017/8/26 | Autohexaploid | Yang et al., 2017 |
| 35 | Echinochloa crus-galli | 1486.61 | Scaffold | 2017/10/23 | Hexaploid | Zhejiang University |
| 36 | Pachycereus pringlei | 629.656 | Scaffold | 2017/10/31 | Autotetraploid | Zhou et al., 2017 |
| 37 | Olea europaea | 1141.15 | Chromosome | 2017/11/1 | 2n, 4n, 6n (Besnard et al., 2007) | Unver et al., 2017 |
| 38 | Monotropa hypopitys | 2197.49 | Contig | 2018/1/3 | Hexaploid | Institute of Bioengineering, RAS |
| 39 | Dactylis glomerata | 839.915 | Scaffold | 2018/1/19 | Autotetraploid | Sichuan Agricultural University |
| 40 | Panicum miliaceum | 848.309 | Scaffold | 2018/1/23 | Allotetraploid | China Agricultural University |
| 41 | Euphorbia esula | 1124.89 | Scaffold | 2018/2/6 | Hexaploid | USDA-ARS |
| 42 | Santalum album | 220.961 | Scaffold | 2018/2/12 | 2n, 4n etc (Xin-Hua et al., 2010) | Center for Cellular and Molecular Platforms |
| 43 | Avena sativa | 67.3266 | Contig | 2018/2/26 | Hexaploid | The Sainsbury Laboratory |
| 44 | Panicum miliaceum | 850.677 | Chromosome | 2018/4/9 | Tetraploid | Shanghai Center for Plant Stress Biology |
| 45 | Arachis monticola | 2618.65 | Chromosome | 2018/4/23 | Tetraploid | Henan Agricultural University |
| 46 | Arachis hypogaea | 2538.28 | Chromosome | 2018/5/2 | Allotetraploid | International Peanut Genome Initiative |
| 47 | Artemisia annua | 1792.86 | Scaffold | 2018/5/8 | Tetraploid | Shen et al., 2018 |
| 48 | Saccharum spontaneum L. | 2.9 G | Chromosome | 2018/09/10 | octoploid | Zhang et al., 2018 |
| 49 | Musa balbisiana | 430 | Chromosome | 2019/7/15 | Tetraploid | Wang et al., 2019 |
在倍性預(yù)測上舱馅，有兩種方法可以使用
- 使用流式細(xì)胞儀測量C-值, 參考網(wǎng)站Plant DNA C-values Database
- 基于NGS的生信策略: ploidyNG ConPADE
而在單倍型組裝上，作者列了如下工具黎烈，當(dāng)然最靠譜的肯定是最新的习柠，也就是HapCUT2
- HapCompass (Aguiar and Istrail, 2012)
- HaploSim (Bastiaansen et al., 2012)
- HapCut (Bansal and Bafna, 2008)
- HapCUT2 (Edge et al., 2017)
在解決多倍體問題上匀谣，作者給出了兩種策略
- 基因組上: 盡量挑選單倍型照棋，或者先測二倍體祖先
- 分析流程上: 三代測序, BioNano, HiC
最終资溃，作者總結(jié)了目前植物可用的資源網(wǎng)站
| DB name | Resources | Plants | URL |
|---|---|---|---|
| Genbank | Genomic | Various plant species | https://www.ncbi.nlm.nih.gov/genbank/ |
| EMBL | Genomic | Various plant species | https://www.ebi.ac.uk/ |
| DDBJ | Genomic | Various plant species | http://www.ddbj.nig.ac.jp/ |
| UniProt | Protein and functional | Various plant species | http://www.uniprot.org/ |
| NCBI | Genomic | Various plant species | https://www.ncbi.nlm.nih.gov/ |
| GOLD | Genomic, metagenomics, transcriptomic | Various plant species | https://gold.jgi.doe.gov/cgi-bin/GOLD/bin/gold.cgi |
| Phytozom | Genomic | 92 assembled and annotated plant species | https://phytozome.jgi.doe.gov/pz/portal.html |
| Plantgdb | Genomic, transcriptomic | 27 assembled and annotated plant species | http://www.plantgdb.org/ |
| Sol | Genomic | 11 Solanaceae species | https://solgenomics.net/ |
| Gramene | Genomic, genetic markers, QTLs | 53 plant species | http://www.gramene.org/ |
| MaizeGCB | Genomic, annotations, tool host | Zea mays | https://www.maizegdb.org/ |
| Tair | Genetic and molecular biology data | Arabidopsis thaliana | https://www.arabidopsis.org/ |
| CottonGE | Genomic, Genetic and breeding resources | 49 Gossypium species | https://www.arabidopsis.org/ |
| PLEXdb | Gene expression | 14 plant species | http://www.plexdb.org/ |
| RicePro | Gene expression | Oryza sativa | http://ricexpro.dna.affrc.go.jp/ |
| CerealsDB | Genetic markers | Triticum aestivum | http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/indexNEW.php |
| PeanutBa | Genome, MAS, QTLs, Germplasm | Arachis hypogaea | https://peanutbase.org/ |
| SoyKb | Genetic markers, genomic resources | Glycine max | http://soykb.org/ |
| SoyBase | Genetic markers, QTLs, genomic resources | G. max | https://soybase.org/ |
| PGDBj | Genetic markers, QTLs, genomic resources | 80 plant species | http://pgdbj.jp/ |
| SNP-Seek | Genotype, Phenotype and Variety information | O. sativa | http://snp-seek.irri.org/ |
| GrainGene | Genome, Genetic markers, QTLs, genomic resources | T. aestivum, Hordeum vulgare, Secale cereale, Avena sativa etc | https://wheat.pw.usda.gov/GG3/ |
| ASRP | small RNA | A. thaliana | http://asrp.danforthcenter.org/ |
| CSRDB | small RNA | Z. mays | http://sundarlab.ucdavis.edu/smrnas/ |
| BrassicaIn | Genomic | 7 Brassica species | http://brassica.info/ |
| BRAD | Genomics, Genetic Markers and Maps | Brassica | http://brassicadb.org/brad/ |
| Ensembl Plants | Genomic | 45 plant species | http://plants.ensembl.org/index.html |
| Ipomoea Genome Hub | Genomic, EST | Ipomoea batatas | https://ipomoea-genome.org/ |
| PGSC | Genomic, annotation | S. tuberosum, S.chacoense | http://solanaceae.plantbiology.msu.edu/pgsc_download.shtml |
| GDR | Genomics, Genetics, breeding | Rosaceae | https://www.rosaceae.org/analysis/266 |
| HWG | Genomics, Transcriptomics, Genetic Markers | Forest trees and woody plants | https://www.hardwoodgenomics.org/ |
