Malus genome
Creators: name: Elejalde-Palmett, Carolina
name: Billet, Kévin
name: Lanoue, Arnaud
name: Craene, Johan-Owen De
name: Glévarec, Gaëlle
name: Pichon, Olivier
name: Clastre, Marc
name: Courdavault, Vincent
name: St-Pierre, Benoit
name: Giglioli-Guivarc'h, Nathalie
name: Bernonville, Thomas Dugé de
name: Besseau, Sébastien
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Rosales
Rosaceae
Malus
Malus genome

description: 2.1. Identification of the UGT88F subfamily in Malus genome   
 A previous study have reported the identification of seven UGT88F in apple tree genome (Zhou et al., 2017). This result was re-examined by an exhaustive identification of UGT88F subfamily members using the updated and improved Malus x domestica genome assembly (Daccord et al., 2017). Based on predicted protein sequence identity to UGT88F1 (Jugdé et al., 2008; threshold of 60% total protein identity), only five locus tags were obtained instead of seven: MD15D1407600, MD15G1407300, MD08G1219100, MD08G1219000 and MD08G1218900. Among them, the first two correspond respectively to the already reported UGT88F1 (Jugdé et al., 2008) and UGT88F4 (Gosch et al., 2010a), whereas the last three, which were previously identified by Zhou et al. (2017) as MDP0000461555, MDP0000288715 and MDP0000170162, are uncharacterized members that we have been named UGT88F6 (KC895981), UGT88F7 (KC895982) and UGT88F8 (KC895983) respectively. On the two additional sequences found by Zhou et al. (2017), MDP0000361449 is a partial sequence corresponding to UGT88F1 which probably arise from incomplete reconstruction of the first version of apple tree genome (Velasco et al., 2010), whereas MDP0000318101 have a protein identity lower than 60% with other UGT88Fs. Finally, the previously cloned UGT88F5 were not found in either old or new genome versions and seems to be an allelic sequence of UGT88F4 (Gosch et al., 2010a).   
 The new genome assembly prompt us to investigate the genomic context of the UGT8 8F members. Unlike most UGTs, these five gene models do not possess any introns. This unique gene structure, their similar lengths (1446 bp ± 3 to 6 bp) and their high sequence identity between 79,9 and 91,9% at the protein level (Fig. 2C), support a common origin. UGT8 8F genes are organized into two genomic clusters on chromosome 8 and 15 (Fig. 2A). UGT88F1 is located closer to UGT88F4 on chromosome 15 and both genes share the same orientation. An additional truncated sequence corresponding to an UGT pseudogene is found nearby UGT88F1. On chromosome 8, UGT88F6, UGT88F7 and UGT88F8 form a physical cluster sharing again the same orientation. Interestingly, UGT organization and genomic environment is conserved between these two clusters (Fig. 2A). In fact, it has been previously proposed that chromosome 8 originates from a truncated copy of chromosome 15 as a result of the global apple tree genome duplication event (Daccord et al., 2017). However, slight differences between the two clusters can be noticed, indicating modifications (insertion/deletion) after chromosomal duplication event including, among others, partial loss of one UGT sequence on chromosome 15 leading to a pseudogene. Finally, DNA phylogeny analysis revealed a higher identity of UGT within clusters than between clusters (Fig. 2B). Taking together, these results preclude us from determine whether gene duplication within clusters occurred prior or after the global genome duplication event.
description: Published as part of Elejalde-Palmett, Carolina, Billet, Kévin, Lanoue, Arnaud, Craene, Johan-Owen De, Glévarec, Gaëlle, Pichon, Olivier, Clastre, Marc, Courdavault, Vincent, St-Pierre, Benoit, Giglioli-Guivarc'h, Nathalie, Bernonville, Thomas Dugé de & Besseau, Sébastien, 2019, Genome-wide identification and biochemical characterization of the UGT 88 F subfamily in Malus x domestica Borkh, pp. 135-144 in Phytochemistry 157 on page 136, DOI: 10.1016/j.phytochem.2018.10.019, http://zenodo.org/record/10481366