Plant pan-genomes are the new reference.

Nature Plants
Philipp E BayerDavid Edwards

Abstract

Recent years have seen a surge in plant genome sequencing projects and the comparison of multiple related individuals. The high degree of genomic variation observed led to the realization that single reference genomes do not represent the diversity within a species, and led to the expansion of the pan-genome concept. Pan-genomes represent the genomic diversity of a species and includes core genes, found in all individuals, as well as variable genes, which are absent in some individuals. Variable gene annotations often show similarities across plant species, with genes for biotic and abiotic stress commonly enriched within variable gene groups. Here we review the growth of pan-genomics in plants, explore the origins of gene presence and absence variation, and show how pan-genomes can support plant breeding and evolution studies.

References

Feb 21, 1998·Proceedings of the National Academy of Sciences of the United States of America·D LeisterP Schulze-Lefert
Sep 21, 2005·Proceedings of the National Academy of Sciences of the United States of America·Hervé TettelinClaire M Fraser
Dec 28, 2006·Cell·John F DoebleyBruce D Smith
Nov 1, 1953·Genetics·B McClintock
Feb 16, 2007·Current Opinion in Plant Biology·Michele MorganteSlobodanka Radovic
Oct 10, 2009·Proceedings of the National Academy of Sciences of the United States of America·Jennifer S HawkinsJonathan F Wendel
May 21, 2010·PLoS Genetics·Margaret R WoodhouseMichael Freeling
Aug 4, 2012·Journal of Experimental Botany·Moshe FeldmanAbraham Korol
Feb 4, 2014·The Plant Cell·Candice N HirschC Robin Buell
Sep 19, 2014·ELife·Jorge Ruiz-OreraM Mar Alba
Jan 1, 2014·Horticulture Research·Feng ChengXiaowu Wang
Nov 26, 2015·Plant Biotechnology Journal·Agnieszka A GoliczDavid Edwards
May 18, 2016·Proceedings of the National Academy of Sciences of the United States of America·Eli Rodgers-MelnickEdward S Buckler
Jun 12, 2016·Plant Physiology·Nicholas PanchyShin-Han Shiu
Aug 9, 2016·Molecular Biology and Evolution·Sara PinosioMichele Morgante
Nov 12, 2016·Nature Communications·Agnieszka A GoliczDavid Edwards
Dec 27, 2016·Applied & Translational Genomics·Keywan Hassani-PakChristopher Rawlings
Feb 24, 2017·The Plant Journal : for Cell and Molecular Biology·Juan D MontenegroDavid Edwards
Mar 3, 2017·Nature Genetics·Birte KehrKari Stefansson
Feb 6, 2018·Trends in Plant Science·Agnieszka A GoliczMohan B Singh
Jun 9, 2018·The New Phytologist·Kevin A BirdPatrick P Edger
Jul 7, 2018·The Plant Journal : for Cell and Molecular Biology·Agnieszka A GoliczMohan B Singh
Aug 18, 2018·Science·R H Ramírez-GonzálezC Uauy
Aug 18, 2018·Science·UNKNOWN International Wheat Genome Sequencing Consortium (IWGSC)Cristobal Uauy
Sep 20, 2018·Plant Biotechnology Journal·Philipp E BayerJacqueline Batley

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Citations

Nov 27, 2020·Nature·Murukarthick JayakodiNils Stein
Dec 29, 2020·Journal of Plant Physiology·Federico ScossaAlisdair R Fernie
Dec 8, 2020·The New Phytologist·Bhavna HurgobinMathew G Lewsey
Dec 2, 2020·The Plant Journal : for Cell and Molecular Biology·Zhixi TianBin Han
Dec 17, 2020·Molecular Ecology Resources·Annabel WhibleyShawn R Narum
Jan 15, 2021·Current Opinion in Plant Biology·Showkat Ahmad GanieGoetz Hensel
Nov 17, 2020·Frontiers in Plant Science·Andrés J CortésLarry E Bedoya-Canas
Jan 6, 2021·International Journal of Molecular Sciences·Aldrin Y CantilaJacqueline Batley
Jan 18, 2021·Current Opinion in Plant Biology·Jong Hum KimSheng Yang He
Oct 16, 2020·International Journal of Molecular Sciences·Utpal BoseMichelle L Colgrave
Mar 9, 2021·Frontiers in Plant Science·Mary-Ann BlätkeSebastian Beier
Feb 4, 2021·Molecular Ecology Resources·Lior Glick, Itay Mayrose
Apr 7, 2021·Nature Plants·Péter SzövényiFay-Wei Li
Mar 16, 2021·G3 : Genes - Genomes - Genetics·Kenta ShirasawaSachiko Isobe
Apr 15, 2021·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Jacob I MarshDavid Edwards
Apr 20, 2021·Journal of Plant Physiology·Alisdair R Fernie, Uwe Sonnewald
May 1, 2021·International Journal of Molecular Sciences·Fabrizio Grassi, Gabriella De Lorenzis
Mar 30, 2021·The New Phytologist·Kathleen K Markham, Kathleen Greenham
May 8, 2021·Nature Genetics·Michael D Purugganan, Scott A Jackson
May 30, 2021·Nature Reviews. Genetics·Wouter De CosterFritz J Sedlazeck
Jun 3, 2021·Genes·Andrés J Cortés, Felipe López-Hernández
Jun 10, 2021·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Junrey AmasJacqueline Batley
May 5, 2021·Plant Biotechnology Journal·Davoud TorkamanehFrançois Belzile
Jun 30, 2021·Trends in Genetics : TIG·Pushpendra K Gupta
Jun 16, 2021·Current Opinion in Biotechnology·Yezhang DingEric A Schmelz
Jun 12, 2021·Journal of Experimental Botany·Ali RazzaqSergey Shabala
Jul 22, 2021·The Plant Genome·Philipp E BayerDavid Edwards
Jun 9, 2021·Plant Biotechnology Journal·Yuxuan YuanDavid Edwards
Apr 11, 2021·The Plant Journal : for Cell and Molecular Biology·Hassan GhazalEzekiel Adebiyi
Aug 12, 2021·Breeding Science·Kenta ShirasawaChittaranjan Kole
Aug 21, 2021·Genome Biology·Prashant PandeyCarl Kingsford
Aug 20, 2021·Proceedings of the National Academy of Sciences of the United States of America·Tuomas HämäläPeter Tiffin
Aug 22, 2021·BMC Plant Biology·Margaret R WoodhouseCarson M Andorf

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