Whole-genome sequencing and comparative genomic analysis of potential biotechnological strains of Trichoderma harzianum, Trichoderma atroviride, and Trichoderma reesei

被引：9

作者：

Rosolen, Rafaela Rossi ^{[1
,2
]}

Horta, Maria Augusta Crivelente ^{[1
,3
]}

de Azevedo, Paulo Henrique Campiteli ^{[1
,2
]}

da Silva, Carla Cristina ^{[1
]}

Sforca, Danilo Augusto ^{[1
]}

Goldman, Gustavo Henrique ^{[3
]}

de Souza, Anete Pereira ^{[1
,4
]}

机构：

[1] Univ Campinas UNICAMP, Ctr Mol Biol & Genet Engn CBMEG, Cidade Universitaria Zeferino Vaz, Campinas, SP, Brazil

[2] Univ Estadual Campinas, Inst Biol, Grad Program Genet & Mol Biol, Campinas, SP, Brazil

[3] Univ Sao Paulo, Fac Pharmaceut Sci Ribeirao Preto, Ribeirao Preto, SP, Brazil

[4] Univ Estadual Campinas, Inst Biol, Dept Plant Biol, Cidade Universitaria Zeferino Vaz, Rua Monteiro Lobato, Campinas, SP, Brazil

来源：

MOLECULAR GENETICS AND GENOMICS | 2023年 / 298卷 / 03期

基金：

巴西圣保罗研究基金会;

关键词：

Trichoderma; Genomes; Comparative analysis; Orthology analysis; Structural variant analysis; TOOL; ALIGNMENT; DATABASE; MODEL; TREE;

D O I：

10.1007/s00438-023-02013-5

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Trichoderma atroviride and Trichoderma harzianum are widely used as commercial biocontrol agents against plant diseases. Recently, T. harzianum IOC-3844 (Th3844) and T. harzianum CBMAI-0179 (Th0179) demonstrated great potential in the enzymatic conversion of lignocellulose into fermentable sugars. Herein, we performed whole-genome sequencing and assembly of the Th3844 and Th0179 strains. To assess the genetic diversity within the genus Trichoderma, the results of both strains were compared with strains of T. atroviride CBMAI-00020 (Ta0020) and T. reesei CBMAI-0711 (Tr0711). The sequencing coverage value of all genomes evaluated in this study was higher than that of previously reported genomes for the same species of Trichoderma. The resulting assembly revealed total lengths of 40 Mb (Th3844), 39 Mb (Th0179), 36 Mb (Ta0020), and 32 Mb (Tr0711). A genome-wide phylogenetic analysis provided details on the relationships of the newly sequenced species with other Trichoderma species. Structural variants revealed genomic rearrangements among Th3844, Th0179, Ta0020, and Tr0711 relative to the T. reesei QM6a reference genome and showed the functional effects of such variants. In conclusion, the findings presented herein allow the visualization of genetic diversity in the evaluated strains and offer opportunities to explore such fungal genomes in future biotechnological and industrial applications.

引用

页码：735 / 754

页数：20

共 99 条

[1] The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update [J].

Afgan, Enis ;

Baker, Dannon ;

Batut, Berenice ;

van den Beek, Marius ;

Bouvier, Dave ;

Cech, Martin ;

Chilton, John ;

Clements, Dave ;

Coraor, Nate ;

Gruening, Bjoern A. ;

Guerler, Aysam ;

Hillman-Jackson, Jennifer ;

Hiltemann, Saskia ;

Jalili, Vahid ;

Rasche, Helena ;

Soranzo, Nicola ;

Goecks, Jeremy ;

Taylor, James ;

Nekrutenko, Anton ;

Blankenberg, Daniel .

NUCLEIC ACIDS RESEARCH, 2018, 46 (W1) :W537-W544

[2] Tomato progeny inherit resistance to the nematode Meloidogyne java']javanica linked to plant growth induced by the biocontrol fungus Trichoderma atroviride [J].

Agripino de Medeiros, Hugo ;

de Araujo Filho, Jeronimo Vieira ;

de Freitas, Leandro Grassi ;

Castillo, Pablo ;

Belen Rubio, Maria ;

Hermosa, Rosa ;

Monte, Enrique .

SCIENTIFIC REPORTS, 2017, 7

[3] The synergistic actions of hydrolytic genes reveal the mechanism of Trichoderma harzianum for cellulose degradation [J].

Almeida, Deborah Aires ;

Crivelente Horta, Maria Augusta ;

Ferreira Filho, Jaire Alves ;

Murad, Natalia Faraj ;

de Souza, Anete Pereira .

JOURNAL OF BIOTECHNOLOGY, 2021, 334 :1-10

[4] Distinct roles of N- and O-glycans in cellulase activity and stability [J].

Amore, Antonella ;

Knott, Brandon C. ;

Supekar, Nitin T. ;

Shajahan, Asif ;

Azadi, Parastoo ;

Zhao, Peng ;

Wells, Lance ;

Linger, Jeffrey G. ;

Hobdey, Sarah E. ;

Vander Wall, Todd A. ;

Shollenberger, Todd ;

Yarbrough, John M. ;

Tan, Zhongping ;

Crowley, Michael F. ;

Himmel, Michael E. ;

Decker, Stephen R. ;

Beckham, Gregg T. ;

Taylor, Larry E., II .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2017, 114 (52) :13667-13672

[5] Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88 [J].

Andersen, Mikael R. ;

Salazar, Margarita P. ;

Schaap, Peter J. ;

van de Vondervoort, Peter J. I. ;

Culley, David ;

Thykaer, Jette ;

Frisvad, Jens C. ;

Nielsen, Kristian F. ;

Albang, Richard ;

Albermann, Kaj ;

Berka, Randy M. ;

Braus, Gerhard H. ;

Braus-Stromeyer, Susanna A. ;

Corrochano, Luis M. ;

Dai, Ziyu ;

van Dijck, Piet W. M. ;

Hofmann, Gerald ;

Lasure, Linda L. ;

Magnuson, Jon K. ;

Menke, Hildegard ;

Meijer, Martin ;

Meijer, Susan L. ;

Nielsen, Jakob B. ;

Samson, Rob A. ;

Stam, Hein ;

Tsang, Adrian ;

van den Brink, Johannes M. ;

Atkins, Alex ;

Aerts, Andrea ;

Shapiro, Harris ;

Pangilinan, Jasmyn ;

Salamov, Asaf ;

Lou, Yigong ;

Lindquist, Erika ;

Lucas, Susan ;

Grimwood, Jane ;

Grigoriev, Igor V. ;

Kubicek, Christian P. ;

Martinez, Diego ;

van Peij, Noel N. M. E. ;

Roubos, Johannes A. ;

Nielsen, Jens ;

Baker, Scott E. .

GENOME RESEARCH, 2011, 21 (06) :885-897

[6] Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics [J].

Ardui, Simon ;

Ameur, Adam ;

Vermeesch, Joris R. ;

Hestand, Matthew S. .

NUCLEIC ACIDS RESEARCH, 2018, 46 (05) :2159-2168

[7] Quantitative comparison of the biomass-degrading enzyme repertoires of five filamentous fungi [J].

Arntzen, Magnus O. ;

Bengtsson, Oskar ;

Varnai, Aniko ;

Delogu, Francesco ;

Mathiesen, Geir ;

Eijsink, Vincent G. H. .

SCIENTIFIC REPORTS, 2020, 10 (01)

[8] Draft Whole-Genome Sequence of the Biocontrol Agent Trichoderma harzianum T6776 [J].

Baroncelli, Riccardo ;

Piaggeschi, Giulia ;

Fiorini, Lisa ;

Bertolini, Edoardo ;

Zapparata, Antonio ;

Pe, Mario Enrico ;

Sarrocco, Sabrina ;

Vannacci, Giovanni .

GENOME ANNOUNCEMENTS, 2015, 3 (03)

[9] UniProt: the universal protein knowledgebase in 2021 [J].

Bateman, Alex ;

Martin, Maria-Jesus ;

Orchard, Sandra ;

Magrane, Michele ;

Agivetova, Rahat ;

Ahmad, Shadab ;

Alpi, Emanuele ;

Bowler-Barnett, Emily H. ;

Britto, Ramona ;

Bursteinas, Borisas ;

Bye-A-Jee, Hema ;

Coetzee, Ray ;

Cukura, Austra ;

Da Silva, Alan ;

Denny, Paul ;

Dogan, Tunca ;

Ebenezer, ThankGod ;

Fan, Jun ;

Castro, Leyla Garcia ;

Garmiri, Penelope ;

Georghiou, George ;

Gonzales, Leonardo ;

Hatton-Ellis, Emma ;

Hussein, Abdulrahman ;

Ignatchenko, Alexandr ;

Insana, Giuseppe ;

Ishtiaq, Rizwan ;

Jokinen, Petteri ;

Joshi, Vishal ;

Jyothi, Dushyanth ;

Lock, Antonia ;

Lopez, Rodrigo ;

Luciani, Aurelien ;

Luo, Jie ;

Lussi, Yvonne ;

Mac-Dougall, Alistair ;

Madeira, Fabio ;

Mahmoudy, Mahdi ;

Menchi, Manuela ;

Mishra, Alok ;

Moulang, Katie ;

Nightingale, Andrew ;

Oliveira, Carla Susana ;

Pundir, Sangya ;

Qi, Guoying ;

Raj, Shriya ;

Rice, Daniel ;

Lopez, Milagros Rodriguez ;

Saidi, Rabie ;

Sampson, Joseph .

NUCLEIC ACIDS RESEARCH, 2021, 49 (D1) :D480-D489

[10] Harnessing glycosylation to improve cellulase activity [J].

Beckham, Gregg T. ;

Dai, Ziyu ;

Matthews, James F. ;

Momany, Michelle ;

Payne, Christina M. ;

Adney, William S. ;

Baker, Scott E. ;

Himmel, Michael E. .

CURRENT OPINION IN BIOTECHNOLOGY, 2012, 23 (03) :338-345

← 1 2 3 4 5 6 7 8 9 10 →