Ancestral Resurrection and Directed Evolution of Fungal Mesozoic Laccases

2019445 citationsJournal Articlegreen Open Access

Authors

Gomez Fernandez, Bernardo J · University of California, Berkeley

Adam C. Rechtless · University of California, Berkeley

Rueda, Andrés · University of California, Berkeley

Adrien Rieux · Centre de Coopération Internationale en Recherche Agronomique pour le Développement

Abstract

&lt;p&gt;&lt;em&gt;Xylella fastidiosa &lt;/em&gt;is an economically important bacterial plant pathogen. With insights gained from 72 genomes, this study investigated differences among the three main subspecies, which have allopatric origins: &lt;em&gt;X. fastidiosa&lt;/em&gt; subsp. &lt;em&gt;fastidiosa&lt;/em&gt;, &lt;em&gt;multiplex&lt;/em&gt;, and &lt;em&gt;pauca&lt;/em&gt;. The origin of recombinogenic&lt;em&gt; X. fastidiosa&lt;/em&gt; subsp. &lt;em&gt;morus &lt;/em&gt;and &lt;em&gt;sandyi &lt;/em&gt;was also assessed. The evolutionary rate of the 622 genes of the species core genome was estimated at the scale of an &lt;em&gt;X. fastidiosa &lt;/em&gt;subsp. &lt;em&gt;pauca &lt;/em&gt;subclade (7.62 107 substitutions per site per year), which was subsequently used to estimate divergence time for the subspecies and introduction events. The study characterized genes present in the accessory genome of each of the three subspecies and investigated the core genome to detect genes potentially under positive selection. Recombination is recognized to be the major driver of diversity in &lt;em&gt;X. fastidiosa,&lt;/em&gt; potentially facilitating shifts to novel plant hosts. The relative effect of recombination in comparison to point mutation was calculated (r/m 2.259). Evidence of recombination was uncovered in the core genome alignment;&lt;em&gt; X. fastidiosa&lt;/em&gt; subsp. &lt;em&gt;fastidiosa &lt;/em&gt;in the United States was less prone to recombination, with an average of 3.22 of the 622 core genes identified as recombining regions, whereas a specific clade of &lt;em&gt;X. fastidiosa&lt;/em&gt; subsp. &lt;em&gt;multiplex &lt;/em&gt;was found to have on average 9.60 recombining genes, 93.2% of which originated from &lt;em&gt;X. fastidiosa&lt;/em&gt; subsp. &lt;em&gt;fastidiosa&lt;/em&gt;. Interestingly, for &lt;em&gt;X. fastidiosa&lt;/em&gt; subsp. &lt;em&gt;morus,&lt;/em&gt; which was initially thought to be the outcome of genome-wide recombination between &lt;em&gt;X. fastidiosa &lt;/em&gt;subsp.&lt;em&gt; fastidiosa &lt;/em&gt;and &lt;em&gt;X. fastidiosa &lt;/em&gt;subsp. &lt;em&gt;multiplex&lt;/em&gt;, intersubspecies homologous recombination levels reached 15.30% in the core genome. Finally, there is evidence of &lt;em&gt;X. fastidiosa &lt;/em&gt;subsp. &lt;em&gt;pauca&lt;/em&gt; strains from citrus containing genetic elements acquired from strains infecting coffee plants as well as genetic elements from both&lt;em&gt; X. fastidiosa &lt;/em&gt;subsp. &lt;em&gt;fastidiosa&lt;/em&gt; and &lt;em&gt;X. fastidiosa&lt;/em&gt; subsp. &lt;em&gt;multiplex&lt;/em&gt;. In summary, our data provide new insights into the evolution and epidemiology of this plant pathogen.&lt;/p&gt;

Topics & Keywords

Phytoplasmas and Hemiptera pathogens

Publication Details

Published in: Institutional Repository of the University of Granada (University of Granada)

DOI: 10.1128/aem

Field-Weighted Citation Impact: 43.33

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Ancestral Resurrection and Directed Evolution of Fungal Mesozoic Laccases

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Abstract

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Publication Details