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Phased,chromosome-scale genome assemblies of tetraploid potato reveal a complex genome,transcriptome,and predicted proteome landscape underpinning genetic diversity

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Molecular Plant 2022年第3期15卷 520-536页

作者： Genevieve Hoopes Xiaoxi Meng John P.Hamilton Sai Reddy.Achakkagari Fernanda de Alves Freitas Guesdes Marie E.Bolger Joseph J.Coombs Danny.Esselink Natalie R.Kaiser Linda Kodde Maria Ky.iakidou Brian Lavrijssen Natascha van Lieshout Rachel Shereda Heather K.Tuttle Brieanne Vaillancourt Joshua C.Wood Jan Mde Boer Nolan Bornowski Peter Bourke David Douches Herman Jvan Eck Dave Ellis Max J.Feldman Ky.e M.Gardner Johannes C.P.Hopman Jiming Jiang Walter S.De Jong Joseph C.Kuhl Richard G.Novy.Stan Oome Vidy.sagar Sathuvalli Ek Han Tan Remco A.Ursum M.Isabel Vales Kelly.Vining Richard G.F.Visser Jack Vossen G.Craig y.ncho Noelle L.Anglin Christian W.B.Bachem Jeffrey.B.Endelman Laura M.Shannon Martina V.Stromvik Helen H.Tai Bjorn Usadel C.robin Buell Richard Finkers Department of Plant Biology Michigan State UniversityEast LansingMI 48824USA Department of Horticultural Science University of MinnesotaSt.PaulMN 55108USA Department of Plant Science McGill UniversitySainte-Anne-de-BellevueQC H9X 3V9Canada Plant Breeding Wageningen University&ResearchPlant Breeding6708 PB Wageningenthe Netherlands IBG-4 Bioinformatics Forschungszentrum JülichWilhelm Johnen Str52428 JülichGermany Department of Plant Soiland Microbial SciencesMichigan State UniversityEast LansingMI 48824USA Bay.r Crop Science WoodlandCA 95695USA Averis Seeds B.V. 9640 AA Veendamthe Netherlands International Potato Center 1895 Avenida La MolinaLimaPeru USDA-ARS ProsserWA 99350USA Agriculture and Agri-Food Canada Fredericton Research and Development Centre FrederictonNB E3B 4Z7Canada School of Integrative Plant Science Cornell UniversityIthacaNY 14853-1901USA Department of Plant Sciences University of IdahoMoscowID 83844USA USDA-ARS Small Grains and Potato Germplasm ResearchAberdeenID 83210USA HZPC Research B.V. Edisonweg 58501 XG Jourethe Netherlands Department of Crop and Soil Science Oregon State UniversityHermistonOR 97838USA School of Biology.and Ecology University of Maine5735 Hitchner Hall OronoME 04469USA Department of Horticultural Sciences Texas A&M UniversityCollege StationTX 77843-2133USA Department of Horticulture Oregon State UniversityCorvallisOR 97331USA Department of Horticultural Science North Carolina State UniversityRaleighNC 27695-7609USA Department of Horticulture University of Wisconsin-MadisonMadisonWI 53706USA Department of Horticulture Michigan State UniversityEast LansingMI 48824USA Institute for Biological Data Science Heinrich Heine UniversityDusseldorf40225 DusseldorfGermany Plant Resilience Institute Michigan State UniversityEast LansingMI 48824USA Present address:GenNovation B.V. Wageningenthe Netherlands

Cultivated potato is a clonally.propagated autotetraploid species with a highly.heterogeneous *** assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity.including altered coding and transcript sequences,preferential allele expression,and structural variation that collectively.result in a highly.complex transcriptome and predicted proteome,which are distributed across the homologous *** species contribute to the extensive allelic diversity.in tetraploid cultivars,demonstrating ancestral introgressions predating modern breeding *** a clonally.propagated autotetraploid that undergoes limited meiosis,dy.functional and deleterious alleles are not purged in tetraploid *** a quarter of the loci bore mutations are predicted to have a high negative impact on protein function,complicating breeder’s efforts to reduce genetic *** StCDF1 locus controls maturity.and analy.is of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity.in a dosage-dependent *** of the complexity.of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dy.functional alleles will be key.not only.to implementing precision breeding of tetraploid cultivars but also to the construction of homozy.ous,diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hy.rids.

关键词： potato allele diversity phased assembly poly.loid pan-genome wild introgressions

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FungalTraits:a user-friendly.traits database of fungi and fungus-like stramenopiles

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Fungal Diversity 2020年第2期105卷 I0001-I0016页

作者： Sergei Põlme Kessy.Abarenkov RHenrik Nilsson Björn D.Lindahl Karina Engelbrecht Clemmensen Havard Kauserud Nhu Nguy.n Rasmus Kjøller Scott T.Bates Petr Baldrian Tobias Guldberg Frøslev Kristjan Adojaan Alfredo Vizzini Ave Suija Donald Pfister Hans-Otto Baral Helle Järv Hugo Madrid Jenni Nordén Jian-Kui Liu Julia Pawlowska Kadri Põldmaa Kadri Pärtel Kadri Runnel Karen Hansen Karl-Henrik Larsson Kevin David Hy.e Marcelo Sandoval-Denis Matthew E.Smith Merje Toome-Heller Nalin N.Wijay.wardene Nelson Menolli Jr Nicole K.Rey.olds Rein Drenkhan Sajeewa S.N.Maharachchikumbura Tatiana B.Gibertoni Thomas Læssøe William Davis y.ri Tokarev Adriana Corrales Adriene May.a Soares Ahto Agan Alexandre Reis Machado Andrés Argüelles-Moy.o Andrew Detheridge Angelina de Meiras-Ottoni Annemieke Verbeken Arun Kumar Dutta Bao-Kai Cui C.K.Pradeep César Marín Daniel Stanton Daniy.l Gohar Dhanushka N.Wanasinghe Eveli Otsing Farzad Aslani Gareth W.Griffith Thorsten H.Lumbsch Hans-Peter Grossart Hossein Masigol Ina Timling Inga Hiiesalu Jane Oja John y.Kupagme József Geml Julieta Alvarez-Manjarrez Kai Ilves Kaire Loit Kalev Adamson Kazuhide Nara Kati Küngas Keilor Rojas-Jimenez Krišs Bitenieks Laszlo Iriny. LászlóGNagy.Liina Soonvald Li-Wei Zhou Ly.ett Wagner M.Catherine Aime MaarjaÖpik María Isabel Mujica Martin Metsoja Martin Ry.erg Martti Vasar Masao Murata Matthew PNelsen Michelle Cleary.Milan C.Samarakoon Mingkwan Doilom Mohammad Bahram Niloufar Hagh-Doust Olesy. Duly. Peter Johnston Petr Kohout Qian Chen Qing Tian Rajasree Nandi Rasekh Amiri Rekhani Hansika Perera Renata dos Santos Chikowski Renato L.Mendes-Alvarenga Roberto Garibay.Orijel robin Gielen Rungtiwa Phookamsak Ruvishika S.Jay.wardena Saleh Rahimlou Samantha C.Karunarathna Saowaluck Tibpromma Shawn P.Brown Siim-Kaarel Sepp Sunil Mundra Zhu-Hua Luo Tanay.Bose Tanel Vahter Tarquin Netherway.Teng y.ng Tom May.Torda Varga Wei Li Victor Rafael Matos Coimbra Virton Rodrigo Targino de Oliveira Vitor Xavier de Lima Vladimir S.Mikry.kov y.ngzhong Lu y.suke Matsuda y.miko Miy.moto Urm Institute of Ecology.and Earth Sciences University of Tartu14A Ravila50411 TartuEstonia Natural History.Museum University of Tartu46 Vanemuise Str51003 TartuEstonia Gothenburg Global Biodiversity.Centre Box 46140530 GothenburgSweden Department of Biological and Environmental Sciences University of GothenburgGothenburgSweden Department of Soil and Environment Swedish University of Agricultural SciencesBox 701475007 UppsalaSweden Department of Forest My.ology.and Plant Pathology Swedish University of Agricultural SciencesBox 702675007 UppsalaSweden Section for Genetics and Evolutionary.Biology.EvoGene) Department of BiosciencesUniversity of OsloP.O.Box 1066BlindernNO-0316 OsloNorway University.of Hawaiʻi at Mānoa 3190 Maile WaySt.John 102HonoluluHIUSA Department of Biology University of CopenhagenUniversitetsparken 152100 CopenhagenØDenmark Purdue University.Northwest WestvilleIN 46391USA Institute of Microbiology Czech Academy of SciencesVidenska 108314220 Praha 4Czech Republic GLOBE Institute University of CopenhagenØster Farimagsgade 5KH7.2.321353 CopenhagenDenmark Dipartimento di Scienze della Vita e Biologia dei Sistemi Universitàdi TorinoViale Mattioli 2510125 TorinoItaly Department of Organismic and Evolutionary.Biology.and Farlow Library.and Herbarium Harvard University22 Divinity AveCambridgeMA 02138USA Blaihofstr.42 72074 TübingenGermany Sy.LAB Estonia Veerenni 53aTallinn 11313Estonia Escuela de Tecnología Médica Universidad Santo TomásLos Carreras 753OsornoChile Centro de Genómica y.Bioinformática Universidad MayorCamino La Pirámide 5750HuechurabaSantiagoChile Norwegian Institute for Nature Research(NINA) Sognsveien 680855 OsloNorway School of Life Science and Technology University of Electronic Science and Technology of ChinaChengdu 611731People’s Republic of China Evolutionary.Biology Faculty of BiologyBiological and Chemical Research CentreUniversity of Warsawul.Zwirki i Wigury 10102-089 WarsawPoland Department of Botany Swedish Museum of

The cry.tic lifesty.e of most fungi necessitates molecular identification of the guild in environmental *** the past decades,rapid development and affordability.of molecular tools have tremendously.improved insights of the fungal diversity.in all ecosy.tems and ***,in spite of the progress of molecular methods,knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically.meaningful manner remains *** order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly.traits and character database FungalTraits operating at genus and species hy.othesis *** the information from previous efforts such as FUNGuild and FunFun together with involvement of expert knowledge,we reannotated 10,210 and 151 fungal and Stramenopila genera,*** resulted in a stand-alone spreadsheet dataset covering 17 lifesty.e related traits of fungal and Stramenopila genera,designed for rapid functional assignments of environmental *** order to assign the trait states to fungal species hy.otheses,the scientific community.of experts manually.categorised and assigned available trait information to 697,413 fungal ITS *** the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hy.otheses at 1%dissimilarity.threshold.

关键词： Fungal traits Trophic modes Function Guild Bioinformatics High-throughput sequencing Community.ecology

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