Editing Arabidopsis thaliana (section)

====Nuclear genome====

Due to the small size of its [[genome]], and because it is [[diploid]], ''Arabidopsis thaliana'' is useful for genetic mapping and [[sequencing]] — with about 157 megabase pairs<ref>{{cite journal |vauthors=Bennett MD, Leitch IJ, Price HJ, Johnston JS |title=Comparisons with ''Caenorhabditis'' (approximately 100 Mb) and ''Drosophila'' (approximately 175 Mb) using flow cytometry show genome size in ''Arabidopsis'' to be approximately 157 Mb, thus approximately 25% larger than the ''Arabidopsis'' genome initiative estimate of approximately 125 Mb |journal=Annals of Botany |volume=91 |issue=5 |pages=547–57 |date=April 2003 |pmid=12646499 |pmc=4242247 |doi=10.1093/aob/mcg057}}</ref> and five [[chromosome]]s, ''A. thaliana'' has one of the smallest genomes among plants.<ref name="Genome Assembly"/> It was long thought to have the smallest genome of all flowering plants,<ref>(Leutwileret al., 1984). In our survey Arabidopsis ...</ref> but that title is now considered to belong to plants in the genus ''[[Genlisea]]'', order [[Lamiales]], with ''[[Genlisea tuberosa]]'', a carnivorous plant, showing a genome size of approximately 61&nbsp;Mbp.<ref name="Fleischmann 2014">{{cite journal |vauthors=Fleischmann A, Michael TP, Rivadavia F, Sousa A, Wang W, Temsch EM, Greilhuber J, Müller KF, Heubl G |title=Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms |journal=Annals of Botany |volume=114 |issue=8 |pages=1651–63 |date=December 2014 |pmid=25274549 |pmc=4649684 |doi=10.1093/aob/mcu189}}</ref> It was the first plant genome to be sequenced, completed in 2000 by the ''Arabidopsis'' Genome Initiative.<ref>{{cite journal |author=The Arabidopsis Genome Initiative |title=Analysis of the genome sequence of the flowering plant ''Arabidopsis thaliana'' |journal=Nature |volume=408 |issue=6814 |pages=796–815 |date=December 2000 |pmid=11130711 |doi=10.1038/35048692 |bibcode=2000Natur.408..796T |doi-access=free}}</ref> The most up-to-date version of the ''A. thaliana'' genome is maintained by the Arabidopsis Information Resource.<ref>{{Cite web |title=TAIR - Genome Annotation |url=http://www.arabidopsis.org/portals/genAnnotation/gene_structural_annotation/annotation_data.jsp |access-date=29 December 2008 |archive-date=14 October 2008 |archive-url=https://web.archive.org/web/20081014183552/http://www.arabidopsis.org/portals/genAnnotation/gene_structural_annotation/annotation_data.jsp |url-status=live}}</ref>

The genome encodes ~27,600 [[protein]]-coding [[gene]]s and about 6,500 non-coding genes.<ref>{{Cite web |title=Details - Arabidopsis_thaliana - Ensembl Genomes 63 |url=http://ensembl.gramene.org/Arabidopsis_thaliana/Info/Annotation/#assembly |access-date=2021-06-15 |website=ensembl.gramene.org |language=en-gb |archive-date=24 June 2021 |archive-url=https://web.archive.org/web/20210624195651/http://ensembl.gramene.org/Arabidopsis_thaliana/Info/Annotation/#assembly |url-status=live}}</ref> However, the Uniprot database lists 39,342 proteins in their ''Arabidopsis'' reference proteome.<ref>{{Cite web |title=''Arabidopsis thaliana'' (Mouse-ear cress) |url=https://www.uniprot.org/proteomes/UP000006548 |access-date=2021-06-15 |website=www.uniprot.org |language=en |archive-date=21 May 2021 |archive-url=https://web.archive.org/web/20210521205551/https://www.uniprot.org/proteomes/UP000006548 |url-status=live}}</ref> Among the 27,600 protein-coding genes 25,402 (91.8%) are now annotated with "meaningful" product names,<ref>{{Cite journal |last1=Cheng |first1=Chia-Yi |last2=Krishnakumar |first2=Vivek |last3=Chan |first3=Agnes P. |last4=Thibaud-Nissen |first4=Françoise |last5=Schobel |first5=Seth |last6=Town |first6=Christopher D. |date=2017 |title=Araport11: a complete reannotation of the ''Arabidopsis thaliana'' reference genome |journal=The Plant Journal |language=en |volume=89 |issue=4 |pages=789–804 |doi=10.1111/tpj.13415 |pmid=27862469 |s2cid=12155857 |issn=1365-313X |doi-access=free }}</ref> although a large fraction of these proteins is likely only poorly understood and only known in general terms (e.g. as "DNA-binding protein without known specificity"). Uniprot lists more than 3,000 proteins as "uncharacterized" as part of the reference proteome.