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Open AccessArticle

Global Evolutionary Analysis of 11 Gene Families Part of Reactive Oxygen Species (ROS) Gene Network in Four Eucalyptus Species

1
Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China
2
Laboratoire de Recherche en Sciences Végétales, CNRS, UPS, Université de Toulouse, 31326 Castanet-Tolosan, France
3
School of advanced agriculture and bioengineering, Yangtze Normal University, Chongqing 408100, China
*
Author to whom correspondence should be addressed.
Antioxidants 2020, 9(3), 257; https://doi.org/10.3390/antiox9030257
Received: 27 February 2020 / Revised: 17 March 2020 / Accepted: 18 March 2020 / Published: 21 March 2020
(This article belongs to the Special Issue Enzymatic and Non-Enzymatic Molecules with Antioxidant Function)
Eucalyptus is a worldwide hard-wood species which increasingly focused on. To adapt to various biotic and abiotic stresses, Eucalyptus have evolved complex mechanisms, increasing the cellular concentration of reactive oxygen species (ROS) by numerous ROS controlling enzymes. To better analyse the ROS gene network and discuss the differences between four Eucalyptus species, ROS gene network including 11 proteins families (1CysPrx, 2CysPrx, APx, APx-R, CIII Prx, Diox, GPx, Kat, PrxII, PrxQ and Rboh) were annotated and compared in an expert and exhaustive manner from the genomic data available from E. camaldulensis, E. globulus, E. grandis, and E. gunnii. In addition, a specific sequencing strategy was performed in order to determine if the missed sequences in at least one organism are the results of gain/loss events or only sequencing gaps. We observed that the automatic annotation applied to multigenic families is the source of miss-annotation. Base on the family size, the 11 families can be categorized into duplicated gene families (CIII Prx, Kat, 1CysPrx, and GPx), which contain a lot of gene duplication events and non-duplicated families (APx, APx-R, Rboh, DiOx, 2CysPrx, PrxII, and PrxQ). The gene family sizes are much larger in Eucalyptus than most of other angiosperms due to recent gene duplications, which could give higher adaptability to environmental changes and stresses. The cross-species comparative analysis shows gene gain and loss events during the evolutionary process. The 11 families possess different expression patterns, while in the Eucalyptus genus, the ROS families present similar expression patterns. Overall, the comparative analysis might be a good criterion to evaluate the adaptation of different species with different characters, but only if data mining is as exhaustive as possible. It is also a good indicator to explore the evolutionary process. View Full-Text
Keywords: reactive oxygen species; Eucalyptus; expert annotation; divergence time; peroxidases; evolutionary rate reactive oxygen species; Eucalyptus; expert annotation; divergence time; peroxidases; evolutionary rate
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MDPI and ACS Style

Li, Q.; San Clemente, H.; He, Y.; Fu, Y.; Dunand, C. Global Evolutionary Analysis of 11 Gene Families Part of Reactive Oxygen Species (ROS) Gene Network in Four Eucalyptus Species. Antioxidants 2020, 9, 257.

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