A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

被引:7
作者
Ayala-Usma, David A. [1 ,2 ,3 ]
Cardenas, Martha [3 ]
Guyot, Romain [4 ,5 ]
De Mares, Maryam Chaib [1 ,2 ]
Bernal, Adriana [6 ]
Munoz, Alejandro Reyes [1 ,2 ,7 ]
Restrepo, Silvia [3 ]
机构
[1] Univ Los Andes, Dept Biol Sci, Res Grp Computat Biol & Microbial Ecol, Bogota, Colombia
[2] Univ Los Andes, Max Planck Tandem Grp Computat Biol, Bogota, Colombia
[3] Univ Los Andes, Dept Chem & Food Engn, Lab Mycol & Plant Pathol LAMFU, Bogota, Colombia
[4] Univ Montpellier, CIRAD, Inst Rech Dev, F-34394 Montpellier, France
[5] Univ Autonoma Manizales, Dept Elect & Automat, Manizales, Colombia
[6] Univ Los Andes, Dept Biol Sci, Lab Mol Interact Agr Microbes LIMMA, Bogota, Colombia
[7] Washington Univ, Sch Med, Edison Family Ctr Genome Sci & Syst Biol, St Louis, MO 63108 USA
基金
英国生物技术与生命科学研究理事会;
关键词
PLANT; SEQUENCE; ALIGNMENT; FAMINE; TOOL;
D O I
10.1186/s12864-021-08079-y
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Background: Pathogens of the genus Phytophthora are the etiological agents of many devastating diseases in several high-value crops and forestry species such as potato, tomato, cocoa, and oak, among many others. Phytophthora betacei is a recently described species that causes late blight almost exclusively in tree tomatoes, and it is closely related to Phytophthora infestans that causes the disease in potato crops and other Solanaceae. This study reports the assembly and annotation of the genomes of P. betacei P8084, the first of its species, and P. infestans RC1-10, a Colombian strain from the EC-1 lineage, using long-read SMRT sequencing technology. Results: Our results show that P. betacei has the largest sequenced genome size of the Phytophthora genus so far with 270 Mb. A moderate transposable element invasion and a whole genome duplication likely explain its genome size expansion when compared to P. infestans, whereas P. infestans RC1-10 has expanded its genome under the activity of transposable elements. The high diversity and abundance (in terms of copy number) of classified and unclassified transposable elements in P. infestans RC1-10 relative to P. betacei bears testimony of the power of long-read technologies to discover novel repetitive elements in the genomes of organisms. Our data also provides support for the phylogenetic placement of P. betacei as a standalone species and as a sister group of P. infestans. Finally, we found no evidence to support the idea that the genome of P. betacei P8084 follows the same gene-dense/genre-sparse architecture proposed for P. infestans and other filamentous plant pathogens. Conclusions: This study provides the first genome-wide picture of P. betacei and expands the genomic resources available for P. infestans. This is a contribution towards the understanding of the genome biology and evolutionary history of Phytophthora species belonging to the subclade 1c.
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页数:21
相关论文
共 65 条
[1]   Genetic diversity of Phytophthora infestans sensu lato in Ecuador provides new insight into the origin of this important plant pathogen [J].
Adler, NE ;
Erselius, LJ ;
Chacón, MG ;
Flier, WG ;
Ordoñez, ME ;
Kroon, LPNM ;
Forbes, GA .
PHYTOPATHOLOGY, 2004, 94 (02) :154-162
[2]   Phytophthora megakarya and Phytophthora palmivora, Closely Related Causal Agents of Cacao Black Pod Rot, Underwent Increases in Genome Sizes and Gene Numbers by Different Mechanisms [J].
Ali, Shahin S. ;
Shao, Jonathan ;
Lary, David J. ;
Kronmiller, Brent A. ;
Shen, Danyu ;
Strem, Mary D. ;
Amoako-Attah, Ishmael ;
Akrofi, Andrew Yaw ;
Begoude, B. A. Didier ;
ten Hoopen, G. Martijn ;
Coulibaly, Klotioloma ;
Kebe, Boubacar Ismael ;
Melnick, Rachel L. ;
Guiltinan, Mark J. ;
Tyler, Brett M. ;
Meinhardt, Lyndel W. ;
Bailey, Bryan A. .
GENOME BIOLOGY AND EVOLUTION, 2017, 9 (03) :536-557
[3]   BASIC LOCAL ALIGNMENT SEARCH TOOL [J].
ALTSCHUL, SF ;
GISH, W ;
MILLER, W ;
MYERS, EW ;
LIPMAN, DJ .
JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410
[4]   Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum [J].
Armitage, Andrew D. ;
Lysoe, Erik ;
Nellist, Charlotte F. ;
Lewis, Laura A. ;
Cano, Liliana M. ;
Harrison, Richard J. ;
Brurberg, May B. .
PLOS ONE, 2018, 13 (10)
[5]   Extensive duplication and reshuffling in the arabidopsis genome [J].
Blanc, G ;
Barakat, A ;
Guyot, R ;
Cooke, R ;
Delseny, I .
PLANT CELL, 2000, 12 (07) :1093-1101
[6]  
Cline ET., 2008, Plant Health Progress, V9, P32, DOI [10.1094/PHP-2008-0318-01-RV, DOI 10.1094/PHP-2008-0318-01-RS, 10.1094/PHP-2008-0318-01-RS]
[7]   UpSetR: an R package for the visualization of intersecting sets and their properties [J].
Conway, Jake R. ;
Lex, Alexander ;
Gehlenborg, Nils .
BIOINFORMATICS, 2017, 33 (18) :2938-2940
[8]   The two-speed genomes of filamentous pathogens: waltz with plants [J].
Dong, Suomeng ;
Raffaele, Sylvain ;
Kamoun, Sophien .
CURRENT OPINION IN GENETICS & DEVELOPMENT, 2015, 35 :57-65
[9]   Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectors [J].
Evangelisti, Edouard ;
Gogleva, Anna ;
Hainaux, Thomas ;
Doumane, Mehdi ;
Tulin, Frej ;
Quan, Clement ;
Yunusov, Temur ;
Floch, Kevin ;
Schornack, Sebastian .
BMC BIOLOGY, 2017, 15
[10]  
Fry W, 2008, MOL PLANT PATHOL, V9, P385, DOI [10.1111/j.1364-3703.2007.00465.x, 10.1111/J.1364-3703.2007.00465.X]