Genome structure and content of the rice root-knot nematode (Meloidogyne graminicola)

被引:27
作者
Phan, Ngan Thi [1 ]
Orjuela, Julie [1 ]
Danchin, Etienne G. J. [2 ]
Klopp, Christophe [3 ]
Perfus-Barbeoch, Laetitia [2 ]
Kozlowski, Djampa K. [2 ]
Koutsovoulos, Georgios D. [2 ]
Lopez-Roques, Celine [4 ]
Bouchez, Olivier [4 ]
Zahm, Margot [3 ]
Besnard, Guillaume [5 ]
Bellafiore, Stephane [1 ]
机构
[1] Univ Montpellier II, IRD, Cirad, Interact Plantes Microorganismes Environm IPME, F-34394 Montpellier, France
[2] Univ Cote Azur, CNRS, Inst Sophia Agrobiotech, INRAE, Sophia Antipolis, France
[3] INRAE, Plateforme BioInfo Genotoul, UR875, Castanet Tolosan, France
[4] INRAE, US 1426, GeT PlaGe, Genotoul, Castanet Tolosan, France
[5] Univ Paul Sabatier, CNRS UPS IRD, EDB, UMR5174, 118 Route Narbonne, F-31062 Toulouse, France
来源
ECOLOGY AND EVOLUTION | 2020年 / 10卷 / 20期
关键词
cereals; horizontal gene transfer; pest; reference genome; root-knot nematode; transposable element; HORIZONTAL GENE-TRANSFER; TRANSCRIPTOME; SEQUENCE; PARASITISM; ALIGNMENT; INSIGHTS; HOST;
D O I
10.1002/ece3.6680
中图分类号
Q14 [生态学(生物生态学)];
学科分类号
071012 ; 0713 ;
摘要
Discovered in the 1960s,Meloidogyne graminicolais a root-knot nematode species considered as a major threat to rice production. Yet, its origin, genomic structure, and intraspecific diversity are poorly understood. So far, such studies have been limited by the unavailability of a sufficiently complete and well-assembled genome. In this study, using a combination of Oxford Nanopore Technologies and Illumina sequencing data, we generated a highly contiguous reference genome (283 scaffolds with an N50 length of 294 kb, totaling 41.5 Mb). The completeness scores of our assembly are among the highest currently published forMeloidogynegenomes. We predicted 10,284 protein-coding genes spanning 75.5% of the genome. Among them, 67 are identified as possibly originating from horizontal gene transfers (mostly from bacteria), which supposedly contribute to nematode infection, nutrient processing, and plant defense manipulation. Besides, we detected 575 canonical transposable elements (TEs) belonging to seven orders and spanning 2.61% of the genome. These TEs might promote genomic plasticity putatively related to the evolution ofM. graminicolaparasitism. This high-quality genome assembly constitutes a major improvement regarding previously available versions and represents a valuable molecular resource for future phylogenomic studies ofMeloidogynespecies. In particular, this will foster comparative genomic studies to trace back the evolutionary history ofM. graminicolaand its closest relatives.
引用
收藏
页码:11006 / 11021
页数:16
相关论文
共 99 条
  • [1] Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita
    Abad, Pierre
    Gouzy, Jerome
    Aury, Jean-Marc
    Castagnone-Sereno, Philippe
    Danchin, Etienne G. J.
    Deleury, Emeline
    Perfus-Barbeoch, Laetitia
    Anthouard, Veronique
    Artiguenave, Francois
    Blok, Vivian C.
    Caillaud, Marie-Cecile
    Coutinho, Pedro M.
    Dasilva, Corinne
    De Luca, Francesca
    Deau, Florence
    Esquibet, Magali
    Flutre, Timothe
    Goldstone, Jared V.
    Hamamouch, Noureddine
    Hewezi, Tarek
    Jaillon, Olivier
    Jubin, Claire
    Leonetti, Paola
    Magliano, Marc
    Maier, Tom R.
    Markov, Gabriel V.
    McVeigh, Paul
    Pesole, Graziano
    Poulain, Julie
    Robinson-Rechavi, Marc
    Sallet, Erika
    Segurens, Beatrice
    Steinbach, Delphine
    Tytgat, Tom
    Ugarte, Edgardo
    van Ghelder, Cyril
    Veronico, Pasqua
    Baum, Thomas J.
    Blaxter, Mark
    Bleve-Zacheo, Teresa
    Davis, Eric L.
    Ewbank, Jonathan J.
    Favery, Bruno
    Grenier, Eric
    Henrissat, Bernard
    Jones, John T.
    Laudet, Vincent
    Maule, Aaron G.
    Quesneville, Hadi
    Rosso, Marie-Noelle
    [J]. NATURE BIOTECHNOLOGY, 2008, 26 (08) : 909 - 915
  • [2] BASIC LOCAL ALIGNMENT SEARCH TOOL
    ALTSCHUL, SF
    GISH, W
    MILLER, W
    MYERS, EW
    LIPMAN, DJ
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) : 403 - 410
  • [3] SPLICING IN CAENORHABDITIS-ELEGANS DOES NOT REQUIRE AN AG AT THE 3' SPLICE ACCEPTOR SITE
    AROIAN, RV
    LEVY, AD
    KOGA, M
    OHSHIMA, Y
    KRAMER, JM
    STERNBERG, PW
    [J]. MOLECULAR AND CELLULAR BIOLOGY, 1993, 13 (01) : 626 - 637
  • [4] Aulino F, 2013, RADICAL EGALITARIANISM: LOCAL REALITIES, GLOBAL RELATIONS, P1
  • [5] Heterodera glycines utilizes promiscuous spliced leaders and demonstrates a unique preference for a species-specific spliced leader over C-elegans SL1
    Barnes, Stacey N.
    Masonbrink, Rick E.
    Maier, Thomas R.
    Seetharam, Arun
    Sindhu, Anoop S.
    Severin, Andrew J.
    Baum, Thomas J.
    [J]. SCIENTIFIC REPORTS, 2019, 9 (1)
  • [6] Intraspecific variability of the facultative meiotic parthenogenetic root-knot nematode (Meloidogyne graminicola) from rice fields in Vietnam
    Bellafiore, Stephane
    Jougla, Claire
    Chapuis, Elodie
    Besnard, Guillaume
    Suong, Malyna
    Phong Nguyen Vu
    De Waele, Dirk
    Gantet, Pascal
    Xuyen Ngo Thi
    [J]. COMPTES RENDUS BIOLOGIES, 2015, 338 (07) : 471 - 483
  • [7] On the Close Relatedness of Two Rice-Parasitic Root-Knot Nematode Species and the Recent Expansion of Meloidogyne graminicola in Southeast Asia
    Besnard, Guillaume
    Ngan Thi-Phan
    Ho-Bich, Hai
    Dereeper, Alexis
    Hieu Trang Nguyen
    Queneherve, Patrick
    Aribi, Jamel
    Bellafiore, Stephane
    [J]. GENES, 2019, 10 (02):
  • [8] The Genomes of Root-Knot Nematodes
    Bird, David McK.
    Williamson, Valerie M.
    Abad, Pierre
    McCarter, James
    Danchin, Etienne G. J.
    Castagnone-Sereno, Philippe
    Opperman, Charles H.
    [J]. ANNUAL REVIEW OF PHYTOPATHOLOGY, 2009, 47 : 333 - 351
  • [9] Transposable elements and microevolutionary changes in natural populations
    Bonchev, Georgi
    Parisod, Christian
    [J]. MOLECULAR ECOLOGY RESOURCES, 2013, 13 (05) : 765 - 775
  • [10] Analysis of drosophila species genome size and satellite DNA content reveals significant differences among strains as well as between species
    Bosco, Giovanni
    Campbell, Paula
    Leiva-Neto, Joao T.
    Markow, Therese A.
    [J]. GENETICS, 2007, 177 (03) : 1277 - 1290