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

Qiang Li,Christophe Dunand,Yongrui He,Yongyao Fu,Hélène San Clemente

doi:10.3390/antiox9030257

Abstract

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.

Highlights

Due to their fast growth rate, valuable wood and fibre properties, and wide adaptabilities, Eucalyptus species with a haploid chromosome number of 11 have been rapidly introduced fromAustralia to other countries such as France, Brazil, Portugal, and China
Thanks to the semi-automatic and manual protocol used for the annotation, 884 genes from 11 families have been annotated from the four genomes of Eucalyptus species including complete, partial and pseudogenes sequences (Table 1)
92 proteins were correctly predicted by Phytozome using homology-based FgenesH

Summary

Introduction

Due to their fast growth rate, valuable wood and fibre properties, and wide adaptabilities, Eucalyptus species with a haploid chromosome number of 11 have been rapidly introduced fromAustralia to other countries such as France, Brazil, Portugal, and China. Due to their fast growth rate, valuable wood and fibre properties, and wide adaptabilities, Eucalyptus species with a haploid chromosome number of 11 have been rapidly introduced from. Along with the genomic sequencing projects [2] and the expansion of the expressed sequence tag (EST) libraries for some species such as E. camaldulensis, E. globulus, E. grandis, and E. gunnii, expert annotation and comparative analysis have become possible. These four species originated from different environments, with different morphologies and genotypes. E. camadulensis is a species widely represented throughout Australia, very tolerant to salt stress and drought, and a variable tolerance to cold depending on the origin. The trees are most often of medium size and they are highly cultivated

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