Editing Cotton (section)

==Genome==
{{Update|section|talk="Genome" section needs revision and updating|date=April 2021}}
{{Technical|section=Cotton genome|date=January 2011}}
There is a public effort to sequence the genome of cotton. It was started in 2007 by a consortium of public researchers.<ref>{{cite journal |last1=Chen |first1=Z. Jeffrey |last2=Scheffler |first2=Brian E. |last3=Dennis |first3=Elizabeth |last4=Triplett |first4=Barbara A. |last5=Zhang |first5=Tianzhen |last6=Guo |first6=Wangzhen |last7=Chen |first7=Xiaoya |last8=Stelly |first8=David M. |last9=Rabinowicz |first9=Pablo D. |last10=Town |first10=Christopher D. |last11=Arioli |first11=Tony |last12=Brubaker |first12=Curt |last13=Cantrell |first13=Roy G. |last14=Lacape |first14=Jean-Marc |last15=Ulloa |first15=Mauricio |last16=Chee |first16=Peng |last17=Gingle |first17=Alan R. |last18=Haigler |first18=Candace H. |last19=Percy |first19=Richard |last20=Saha |first20=Sukumar |last21=Wilkins |first21=Thea |last22=Wright |first22=Robert J. |last23=Van Deynze |first23=Allen |last24=Zhu |first24=Yuxian |last25=Yu |first25=Shuxun |last26=Abdurakhmonov |first26=Ibrokhim |last27=Katageri |first27=Ishwarappa |last28=Kumar |first28=P. Ananda |last29=Zafar |first29=Yusuf |last30=Yu |first30=John Z. |last31=Kohel |first31=Russell J. |last32=Wendel |first32=Jonathan F. |last33=Paterson |first33=Andrew H. |last34=Paterson |first34=AH |title=Toward Sequencing Cotton (''Gossypium'') Genomes |journal=Plant Physiology |date=December 2007 |volume=145 |issue=4 |pages=1303–1310 |doi=10.1104/pp.107.107672 |pmid=18056866 |pmc=2151711 }}</ref> Their aim is to sequence the genome of cultivated, tetraploid cotton. "Tetraploid" means that its nucleus has two separate genomes, called A and D. The consortium agreed to first sequence the D-genome wild relative of cultivated cotton (''G. raimondii'', a Central American species) because it is small and has few repetitive elements. It has nearly one-third of the bases of tetraploid cotton, and each chromosome occurs only once.{{Clarify|date=January 2011}} Then, the A genome of ''G. arboreum'' would be sequenced. Its genome is roughly twice that of ''G. raimondii''. Part of the difference in size is due to the amplification of ''retrotransposons'' (GORGE). After both diploid genomes are assembled, they would be used as models for sequencing the genomes of tetraploid cultivated species. Without knowing the diploid genomes, the euchromatic DNA sequences of AD genomes would co-assemble, and their repetitive elements would assemble independently into A and D sequences respectively. There would be no way to untangle the mess of AD sequences without comparing them to their diploid counterparts.

The public sector effort continues with the goal to create a high-quality, draft genome sequence from reads generated by all sources. The effort has generated Sanger reads of BACs, fosmids, and plasmids, as well as 454 reads. These later types of reads will be instrumental in assembling an initial draft of the D genome. In 2010, the companies [[Monsanto]] and [[Illumina (company)|Illumina]] completed enough Illumina sequencing to cover the D genome of ''G. raimondii'' about 50x.<ref>{{Cite web|title = Monsanto and Illumina Reach Key Milestone in Cotton Genome Sequencing|url = http://www.monsanto.com/newsviews/pages/monsanto-illumina-key-milestone-cotton-genome-sequencing.aspx|website = www.monsanto.com|access-date = 2016-01-31|last = APPDMZ\gyoung|archive-url = https://web.archive.org/web/20160201042838/http://www.monsanto.com/newsviews/pages/monsanto-illumina-key-milestone-cotton-genome-sequencing.aspx|archive-date = 1 February 2016}}</ref> They announced that they would donate their raw reads to the public. This public relations effort gave them some recognition for sequencing the cotton genome. Once the D genome is assembled from all of this raw material, it will undoubtedly assist in the assembly of the AD genomes of cultivated varieties of cotton, but much work remains.

As of 2014, at least one assembled cotton genome had been reported.<ref>{{cite journal |last1=Li |first1=Fuguang |last2=Fan |first2=Guangyi |last3=Wang |first3=Kunbo |last4=Sun |first4=Fengming |last5=Yuan |first5=Youlu |last6=Song |first6=Guoli |last7=Li |first7=Qin |last8=Ma |first8=Zhiying |last9=Lu |first9=Cairui |last10=Zou |first10=Changsong |last11=Chen |first11=Wenbin |last12=Liang |first12=Xinming |last13=Shang |first13=Haihong |last14=Liu |first14=Weiqing |last15=Shi |first15=Chengcheng |last16=Xiao |first16=Guanghui |last17=Gou |first17=Caiyun |last18=Ye |first18=Wuwei |last19=Xu |first19=Xun |last20=Zhang |first20=Xueyan |last21=Wei |first21=Hengling |last22=Li |first22=Zhifang |last23=Zhang |first23=Guiyin |last24=Wang |first24=Junyi |last25=Liu |first25=Kun |last26=Kohel |first26=Russell J |last27=Percy |first27=Richard G |last28=Yu |first28=John Z |last29=Zhu |first29=Yu-Xian |last30=Wang |first30=Jun |last31=Yu |first31=Shuxun |title=Genome sequence of the cultivated cotton Gossypium arboreum |journal=Nature Genetics |date=June 2014 |volume=46 |issue=6 |pages=567–572 |doi=10.1038/ng.2987 |pmid=24836287 |s2cid=13477556 |doi-access=free }}</ref>