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

Ali Shahin, Shao Jonathan, Lary David J., Kronmiller Brent A., Shen Danyu, Strem Mary, Amoako-Attah Ishmael, Yaw Akrofi Andrew, Begoude Dider, Ten Hoopen Gerben Martijn, Coulibaly Klotioloma, Kébé Boubacar Ismaël, Melnick Rachel L., Guiltinan Mark J., Tyler Brett, Meinhardt Lyndel W., Bailey Bryan. 2017. 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. Genome Biology and Evolution, 9 (3) : 536-557.

Quartile : Q1, Sujet : GENETICS & HEREDITY / Quartile : Q2, Sujet : EVOLUTIONARY BIOLOGY

Résumé : Phytophthora megakarya (Pmeg) and Phytophthora palmivora (Ppal) are closely related species causing cacao black pod rot. Although Ppal is a cosmopolitan pathogen, cacao is the only known host of economic importance for Pmeg. Pmeg is more virulent on cacao than Ppal. We sequenced and compared the Pmeg and Ppal genomes and identified virulence-related putative gene models (PGeneM) that may be responsible for their differences in host specificities and virulence. Pmeg and Ppal have estimated genome sizes of 126.88 and 151.23 Mb and PGeneM numbers of 42,036 and 44,327, respectively. The evolutionary histories of Pmeg and Ppal appear quite different. Postspeciation, Ppal underwent whole-genome duplication whereas Pmeg has undergone selective increases in PGeneM numbers, likely through accelerated transposable element-driven duplications. Many PGeneMs in both species failed to match transcripts and may represent pseudogenes or cryptic genetic reservoirs. Pmeg appears to have amplified specific gene families, some of which are virulence-related. Analysis of mycelium, zoospore, and in planta transcriptome expression profiles using neural network self-organizing map analysis generated 24 multivariate and nonlinear self-organizing map classes. Many members of the RxLR, necrosis-inducing phytophthora protein, and pectinase genes families were specifically induced in planta. Pmeg displays a diverse virulence-related gene complement similar in size to and potentially of greater diversity than Ppal but it remains likely that the specific functions of the genes determine each species' unique characteristics as pathogens.

Mots-clés Agrovoc : Phytophthora, Phytophthora palmivora, Theobroma cacao, Transcription génique, génome, gène, phylogénie, séquence nucléotidique, virulence, évolution

Mots-clés géographiques Agrovoc : Cameroun, Côte d'Ivoire

Mots-clés complémentaires : Phytophthora megakarya, Séquencage

Mots-clés libres : Cacao, Black pod rot, Phytophthora, Genome, Transcriptome

Classification Agris : H20 - Maladies des plantes
F30 - Génétique et amélioration des plantes

Champ stratégique Cirad : Axe 4 (2014-2018) - Santé des animaux et des plantes

Auteurs et affiliations

• Ali Shahin, USDA (USA)
• Shao Jonathan, USDA (USA)
• Lary David J., University of Texas (USA)
• Kronmiller Brent A., Oregon State University (USA)
• Shen Danyu, Nanjing Agricultural University (CHN)
• Strem Mary, USDA (USA)
• Amoako-Attah Ishmael, CRIG (GHA)
• Yaw Akrofi Andrew, CRIG (GHA)
• Begoude Dider, IRAD (CMR)
• Ten Hoopen Gerben Martijn, CIRAD-BIOS-UPR Bioagresseurs (TTO) ORCID: 0000-0003-2133-3130
• Coulibaly Klotioloma, CNRA (CIV)
• Kébé Boubacar Ismaël, CNRA (CIV)
• Melnick Rachel L., USDA (USA)
• Guiltinan Mark J., Pennsylvania State University (USA)
• Tyler Brett, Oregon State University (USA)
• Meinhardt Lyndel W., USDA (USA)
• Bailey Bryan, USDA (USA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/584305/)

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