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Items: 22

1.

Draft Genome Sequence of the Ectomycorrhizal Ascomycete Sphaerosporella brunnea.

Benucci GMN, Haridas S, Labutti K, Marozzi G, Antonielli L, Sanchez S, Marco P, Wang X, Barry K, Lipzen A, Chovatia M, Hundley H, Baciarelli Falini L, Murat C, Martin F, Albertini E, Donnini D, Grigoriev IV, Bonito G.

Microbiol Resour Announc. 2019 Dec 12;8(50). pii: e00857-19. doi: 10.1128/MRA.00857-19.

2.

Engineered Root Bacteria Release Plant-Available Phosphate from Phytate.

Shulse CN, Chovatia M, Agosto C, Wang G, Hamilton M, Deutsch S, Yoshikuni Y, Blow MJ.

Appl Environ Microbiol. 2019 Aug 29;85(18). pii: e01210-19. doi: 10.1128/AEM.01210-19. Print 2019 Sep 15.

3.

Comparative genomics reveals unique wood-decay strategies and fruiting body development in the Schizophyllaceae.

Almási É, Sahu N, Krizsán K, Bálint B, Kovács GM, Kiss B, Cseklye J, Drula E, Henrissat B, Nagy I, Chovatia M, Adam C, LaButti K, Lipzen A, Riley R, Grigoriev IV, Nagy LG.

New Phytol. 2019 Oct;224(2):902-915. doi: 10.1111/nph.16032. Epub 2019 Aug 1.

PMID:
31257601
4.

Megaphylogeny resolves global patterns of mushroom evolution.

Varga T, Krizsán K, Földi C, Dima B, Sánchez-García M, Sánchez-Ramírez S, Szöllősi GJ, Szarkándi JG, Papp V, Albert L, Andreopoulos W, Angelini C, Antonín V, Barry KW, Bougher NL, Buchanan P, Buyck B, Bense V, Catcheside P, Chovatia M, Cooper J, Dämon W, Desjardin D, Finy P, Geml J, Haridas S, Hughes K, Justo A, Karasiński D, Kautmanova I, Kiss B, Kocsubé S, Kotiranta H, LaButti KM, Lechner BE, Liimatainen K, Lipzen A, Lukács Z, Mihaltcheva S, Morgado LN, Niskanen T, Noordeloos ME, Ohm RA, Ortiz-Santana B, Ovrebo C, Rácz N, Riley R, Savchenko A, Shiryaev A, Soop K, Spirin V, Szebenyi C, Tomšovský M, Tulloss RE, Uehling J, Grigoriev IV, Vágvölgyi C, Papp T, Martin FM, Miettinen O, Hibbett DS, Nagy LG.

Nat Ecol Evol. 2019 Apr;3(4):668-678. doi: 10.1038/s41559-019-0834-1. Epub 2019 Mar 18.

5.

Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome.

Bowman JL, Kohchi T, Yamato KT, Jenkins J, Shu S, Ishizaki K, Yamaoka S, Nishihama R, Nakamura Y, Berger F, Adam C, Aki SS, Althoff F, Araki T, Arteaga-Vazquez MA, Balasubrmanian S, Barry K, Bauer D, Boehm CR, Briginshaw L, Caballero-Perez J, Catarino B, Chen F, Chiyoda S, Chovatia M, Davies KM, Delmans M, Demura T, Dierschke T, Dolan L, Dorantes-Acosta AE, Eklund DM, Florent SN, Flores-Sandoval E, Fujiyama A, Fukuzawa H, Galik B, Grimanelli D, Grimwood J, Grossniklaus U, Hamada T, Haseloff J, Hetherington AJ, Higo A, Hirakawa Y, Hundley HN, Ikeda Y, Inoue K, Inoue SI, Ishida S, Jia Q, Kakita M, Kanazawa T, Kawai Y, Kawashima T, Kennedy M, Kinose K, Kinoshita T, Kohara Y, Koide E, Komatsu K, Kopischke S, Kubo M, Kyozuka J, Lagercrantz U, Lin SS, Lindquist E, Lipzen AM, Lu CW, De Luna E, Martienssen RA, Minamino N, Mizutani M, Mizutani M, Mochizuki N, Monte I, Mosher R, Nagasaki H, Nakagami H, Naramoto S, Nishitani K, Ohtani M, Okamoto T, Okumura M, Phillips J, Pollak B, Reinders A, Rövekamp M, Sano R, Sawa S, Schmid MW, Shirakawa M, Solano R, Spunde A, Suetsugu N, Sugano S, Sugiyama A, Sun R, Suzuki Y, Takenaka M, Takezawa D, Tomogane H, Tsuzuki M, Ueda T, Umeda M, Ward JM, Watanabe Y, Yazaki K, Yokoyama R, Yoshitake Y, Yotsui I, Zachgo S, Schmutz J.

Cell. 2017 Oct 5;171(2):287-304.e15. doi: 10.1016/j.cell.2017.09.030.

6.

Genome Sequence of Roseovarius sp. Strain MCTG156(2b) Isolated from a Phytoplankton Net Trawl on the Scottish West Coast.

Gutierrez T, Whitman WB, Huntemann M, Copeland A, Chen A, Vargese N, Kyrpides NC, Pillay M, Ivanova N, Mikhailova N, Mukherjee S, Stamatis D, Reddy TBK, Ngan CY, Chovatia M, Daum C, Shapiro N, Woyke T.

Genome Announc. 2017 Aug 31;5(35). pii: e00837-17. doi: 10.1128/genomeA.00837-17.

7.

Genome Sequence of Oceanicola sp. Strain MCTG156(1a), Isolated from a Scottish Coastal Phytoplankton Net Sample.

Gutierrez T, Whitman WB, Huntemann M, Copeland A, Chen A, Vargese N, Kyrpides NC, Pillay M, Ivanova N, Mikhailova N, Mukherjee S, Stamatis D, Reddy TBK, Ngan CY, Chovatia M, Daum C, Shapiro N, Woyke T.

Genome Announc. 2017 Aug 10;5(32). pii: e00796-17. doi: 10.1128/genomeA.00796-17.

8.

Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach.

Gontang EA, Aylward FO, Carlos C, Glavina Del Rio T, Chovatia M, Fern A, Lo CC, Malfatti SA, Tringe SG, Currie CR, Kolter R.

PLoS One. 2017 May 18;12(5):e0177189. doi: 10.1371/journal.pone.0177189. eCollection 2017.

9.

Characterization of four endophytic fungi as potential consolidated bioprocessing hosts for conversion of lignocellulose into advanced biofuels.

Wu W, Davis RW, Tran-Gyamfi MB, Kuo A, LaButti K, Mihaltcheva S, Hundley H, Chovatia M, Lindquist E, Barry K, Grigoriev IV, Henrissat B, Gladden JM.

Appl Microbiol Biotechnol. 2017 Mar;101(6):2603-2618. doi: 10.1007/s00253-017-8091-1. Epub 2017 Jan 12.

PMID:
28078400
10.

Genome Sequence of Marinobacter sp. Strain MCTG268 Isolated from the Cosmopolitan Marine Diatom Skeletonema costatum.

Gutierrez T, Whitman WB, Huntemann M, Copeland A, Chen A, Kyrpides N, Markowitz V, Pillay M, Ivanova N, Mikhailova N, Ovchinnikova G, Andersen E, Pati A, Stamatis D, Reddy TB, Ngan CY, Chovatia M, Daum C, Shapiro N, Cantor MN, Woyke T.

Genome Announc. 2016 Sep 8;4(5). pii: e00937-16. doi: 10.1128/genomeA.00937-16.

11.

Genome Sequence of Arenibacter algicola Strain TG409, a Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton.

Gutierrez T, Whitman WB, Huntemann M, Copeland A, Chen A, Kyrpides N, Markowitz V, Pillay M, Ivanova N, Mikhailova N, Ovchinnikova G, Andersen E, Pati A, Stamatis D, Reddy TB, Ngan CY, Chovatia M, Daum C, Shapiro N, Cantor MN, Woyke T.

Genome Announc. 2016 Aug 4;4(4). pii: e00765-16. doi: 10.1128/genomeA.00765-16.

12.

Genome Analysis of Planctomycetes Inhabiting Blades of the Red Alga Porphyra umbilicalis.

Kim JW, Brawley SH, Prochnik S, Chovatia M, Grimwood J, Jenkins J, LaButti K, Mavromatis K, Nolan M, Zane M, Schmutz J, Stiller JW, Grossman AR.

PLoS One. 2016 Mar 25;11(3):e0151883. doi: 10.1371/journal.pone.0151883. eCollection 2016.

13.

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea.

Olsen JL, Rouzé P, Verhelst B, Lin YC, Bayer T, Collen J, Dattolo E, De Paoli E, Dittami S, Maumus F, Michel G, Kersting A, Lauritano C, Lohaus R, Töpel M, Tonon T, Vanneste K, Amirebrahimi M, Brakel J, Boström C, Chovatia M, Grimwood J, Jenkins JW, Jueterbock A, Mraz A, Stam WT, Tice H, Bornberg-Bauer E, Green PJ, Pearson GA, Procaccini G, Duarte CM, Schmutz J, Reusch TB, Van de Peer Y.

Nature. 2016 Feb 18;530(7590):331-5. doi: 10.1038/nature16548. Epub 2016 Jan 27.

PMID:
26814964
14.

Genomics and Transcriptomics Analyses of the Oil-Accumulating Basidiomycete Yeast Trichosporon oleaginosus: Insights into Substrate Utilization and Alternative Evolutionary Trajectories of Fungal Mating Systems.

Kourist R, Bracharz F, Lorenzen J, Kracht ON, Chovatia M, Daum C, Deshpande S, Lipzen A, Nolan M, Ohm RA, Grigoriev IV, Sun S, Heitman J, Brück T, Nowrousian M.

mBio. 2015 Jul 21;6(4):e00918. doi: 10.1128/mBio.00918-15.

15.

Genome Sequence of Halomonas sp. Strain MCTG39a, a Hydrocarbon-Degrading and Exopolymeric Substance-Producing Bacterium.

Gutierrez T, Whitman WB, Huntemann M, Copeland A, Chen A, Kyrpides N, Markowitz V, Pillay M, Ivanova N, Mikhailova N, Ovchinnikova G, Andersen E, Pati A, Stamatis D, Reddy TB, Ngan CY, Chovatia M, Daum C, Shapiro N, Cantor MN, Woyke T.

Genome Announc. 2015 Jul 16;3(4). pii: e00793-15. doi: 10.1128/genomeA.00793-15.

16.

Genome Sequence of Porticoccus hydrocarbonoclasticus Strain MCTG13d, an Obligate Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton.

Gutierrez T, Whitman WB, Huntemann M, Copeland A, Chen A, Kyrpides N, Markowitz V, Pillay M, Ivanova N, Mikhailova N, Ovchinnikova G, Andersen E, Pati A, Stamatis D, Reddy TB, Ngan CY, Chovatia M, Daum C, Shapiro N, Cantor MN, Woyke T.

Genome Announc. 2015 Jun 18;3(3). pii: e00672-15. doi: 10.1128/genomeA.00672-15.

17.

Correction: Transgenic expression of the dicotyledonous pattern recognition receptor EFR in rice leads to ligand-dependent activation of defense responses.

Schwessinger B, Bahar O, Thomas N, Holton N, Nekrasov V, Ruan D, Canlas PE, Daudi A, Petzold CJ, Singan VR, Kuo R, Chovatia M, Daum C, Heazlewood JL, Zipfel C, Ronald PC.

PLoS Pathog. 2015 Apr 23;11(4):e1004872. doi: 10.1371/journal.ppat.1004872. eCollection 2015 Apr.

18.

Transgenic expression of the dicotyledonous pattern recognition receptor EFR in rice leads to ligand-dependent activation of defense responses.

Schwessinger B, Bahar O, Thomas N, Holton N, Nekrasov V, Ruan D, Canlas PE, Daudi A, Petzold CJ, Singan VR, Kuo R, Chovatia M, Daum C, Heazlewood JL, Zipfel C, Ronald PC.

PLoS Pathog. 2015 Mar 30;11(3):e1004809. doi: 10.1371/journal.ppat.1004809. eCollection 2015 Mar. Erratum in: PLoS Pathog. 2015 Apr;11(4):e1004872. Thomas, Nicolas [corrected to Thomas, Nicholas].

19.

Genome Sequence of Polycyclovorans algicola Strain TG408, an Obligate Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton.

Gutierrez T, Thompson HF, Angelova A, Whitman WB, Huntemann M, Copeland A, Chen A, Kyrpides N, Markowitz V, Palaniappan K, Ivanova N, Mikhailova N, Ovchinnikova G, Andersen E, Pati A, Stamatis D, Reddy TB, Ngan CY, Chovatia M, Daum C, Shapiro N, Cantor MN, Woyke T.

Genome Announc. 2015 Mar 26;3(2). pii: e00207-15. doi: 10.1128/genomeA.00207-15.

20.

A reference genome for common bean and genome-wide analysis of dual domestications.

Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C, Torres-Torres M, Geffroy V, Moghaddam SM, Gao D, Abernathy B, Barry K, Blair M, Brick MA, Chovatia M, Gepts P, Goodstein DM, Gonzales M, Hellsten U, Hyten DL, Jia G, Kelly JD, Kudrna D, Lee R, Richard MM, Miklas PN, Osorno JM, Rodrigues J, Thareau V, Urrea CA, Wang M, Yu Y, Zhang M, Wing RA, Cregan PB, Rokhsar DS, Jackson SA.

Nat Genet. 2014 Jul;46(7):707-13. doi: 10.1038/ng.3008. Epub 2014 Jun 8.

21.

Metagenomic profiling reveals lignocellulose degrading system in a microbial community associated with a wood-feeding beetle.

Scully ED, Geib SM, Hoover K, Tien M, Tringe SG, Barry KW, Glavina del Rio T, Chovatia M, Herr JR, Carlson JE.

PLoS One. 2013 Sep 4;8(9):e73827. doi: 10.1371/journal.pone.0073827. eCollection 2013.

22.

Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883).

Chovatia M, Sikorski J, Schröder M, Lapidus A, Nolan M, Tice H, Glavina Del Rio T, Copeland A, Cheng JF, Lucas S, Chen F, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Saunders E, Detter JC, Brettin T, Rohde M, Göker M, Spring S, Bristow J, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Eisen JA.

Stand Genomic Sci. 2009 Nov 22;1(3):254-61. doi: 10.4056/sigs.40645.

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