br Conclusions br Conflict of

Conclusions
Conflict of interest
Introduction Plants often encounter a series of abiotic stresses during the growth process, including high salinity, extreme temperatures and drought (Knight and Knight, 2001). Plants can adapt through ionic and osmotic homeostasis or osmotic adjustment, control and repair of stress-related damage, or detoxification in response to abiotic stress (Zhu, 2002). Many genes associated with these processes have been identified, such as heat stress proteins or chaperones, late embryogenesis-abundant proteins, antifreeze proteins, detoxification enzymes (catalase, superoxide dismutase and ascorbate peroxidase) and free-radical scavengers (Bray et al., 2000, Wang et al., 2003), mitogen-activated protein kinases, calcium-dependent protein kinases (Ludwig et al., 2004), salt overly sensitive kinases (Zhu, 2001), phospholipases (Frank et al., 2000), transcription factors (Choi et al., 2000, Shinozaki and Yamaguchi-Shinozaki, 2000), and aquaporins and ion transporters (Blumwald, 2000). Furthermore, there is cross-communication among abiotic stresses, which causes rapid and excessive accumulation of reactive oxygen species (ROS). ROS induce lipid peroxidation or protein and DNA denaturation, and produce many highly active, harmful substances, such as alkanes, ketones and aldehydes (Bartels, 2001, Gill and Tuteja, 2010). These toxic products lead to cellular injury. Many plant genes enhance resistance to abiotic stress by indirectly detoxifying cellular ROS or aldehydes. In plants, little is known about aldehydes and their detoxification. Therefore, it is important to understand the mechanisms underlying the detoxification of aldehydes during environmental stresses and to mine endogenous resistance genes. Aldehyde dehydrogenases (ALDHs) are part of a conserved gene superfamily encoding NAD(P)+-dependent enzymes that catalyse the irreversible oxidation of endogenous and exogenous aromatic and aliphatic aldehydes into non-toxic carboxylic acids (Yoshida et al., 1998). The ALDHs identified to date have been classified into 24 families based on sequence identity. Plants contain 14 ALDH families: ALDH2, 3, 5, 6, 7, 10, 11, 12, 18, 19, 21, 22, 23 and 24. Among these 14 families, seven are exclusive to plants: ALDH11, 12, 19, 21, 22, 23 and 24. However, ALDH23 and ALDH24 only exist in Physcomitrella patens and Chlamydomonas reinhardtii, respectively (Wood and Duff, 2009). Significantly more research has been performed on animal ALDHs than on plant ALDHs (Jackson et al., 2011, Kirch et al., 2004). Studies have shown that some ALDHs protect plant NMS-873 against various abiotic stressors by indirectly detoxifying cellular ROS and/or reducing lipid peroxidation (Shin et al., 2009, Missihoun et al., 2011, Singh et al., 2013). ALDH10 (BADH) enzymes are known as betaine aldehyde dehydrogenases and are responsible for catalysing the oxidation of betaine aldehyde into glycine betaine (GB). GB is a major cellular osmolyte that plays crucial roles in protection against environmental stress (Le Rudulier et al., 1984). For instance, BADH improves resistance to salt stress in transgenic tobacco (Yang et al., 2008, Zhou et al., 2008). Kotchoni et al. (2006) found that ectopic expression of ALDH3I1 and ALDH7B4 significantly reduced lipid peroxidation and malondialdehyde (MDA) levels and increased tolerance to drought and salt stress in transgenic Arabidopsis thaliana. Moreover, over-expression of VvALDH2B4 in A. thaliana enhanced protection against high salt and pathogenic bacteria, and resulted in lower MDA levels (Wen et al., 2012). Furthermore, compared with control plants, the transgenic plants displayed higher germination ratios, root lengths, proline accumulation and antioxidant enzyme activities as well as lower MDA contents when ScALDH21 was introduced into tobacco (Yang et al., 2015). Completion of genome sequencing for increasing numbers of species has allowed more ALDHs to be identified and studied. Many ALDHs have been identified in higher plants, such as A. thaliana (Kirch et al., 2004), Vitis vinifera (Zhang et al., 2012), Zea mays (Jimenez-Lopez et al., 2010), Setaria italica (Chen et al., 2014), Glycine max (Kotchoni et al., 2012) and Oryza sativa (Gao and Han, 2009). However, ALDHs have not been studied in depth in Gossypium spp. (cotton). The cotton genus (Gossypium) contains 45 diploid (2n=26) and six tetraploid (2n=52) species (Hawkins et al., 2006, Grover et al., 2015). Diploid cottons are grouped into eight cytogenetic genome types, A-G and K (Lin et al., 2010). The most widely cultivated cotton species today, Gossypium hirsutum (AADD, AD1 genome) and G. barbadense (AADD, AD2 genome), are tetraploid, and are thought being originated from inter-genomic hybridization between an A-genome specie, G. herbaceum (A1) or G. arboreum (A2), and a native D-genome specie, G. raimondii (D5) or G. gossypioides (D6) (Senchina et al., 2003, Wendel and Cronn, 2003). Thus far, 30 ALDHs have been identified in G. raimondii (He et al., 2014), but there have been no reported analyses of the ALDH superfamily in other Gossypium species. Complete sequencing of the main Gossypium genome (Wang et al., 2012a, Paterson et al., 2012, Li et al., 2014, Liu et al., 2015b, Zhang et al., 2015) has made systematic identification and analysis of the Gossypium ALDH superfamily possible. In this study, we identified 30, 59 and 59 ALDHs from G. arboreum, G. hirsutum and G. barbadense, respectively, and classified them into 10 gene families. The structures of the genes and proteins as well as the chromosomal distribution and gene duplication of ALDHs were then analysed. Finally, we analysed the expression of GaALDHs and GhALDHs at the seedling stage under high salinity and drought. This study provides a foundation for further functional characterization of the ALDH gene superfamily in cotton and other angiosperms.