## 4 Omics of _X. dendrorho_: Genomics, Transcriptomics, Proteomics, and Metabolomics  
As was indicated above, the metabolic redirection is a suitable reality. It can be enhanced when it is supported by omics technologies, which have been tackled in this yeast from three points of view: genomics, transcriptomics, and proteomics. The first genomic analysis was done by using pulsed field gel electrophoresis, which defined a putative genome size of 25 Mb [85]. This genome size has been recently redefined by means of the Illumina sequencing methodology (see Table 2 for extraction protocols) [19; 86]. As a result, _X. dendrorho_ presents a 19.50 Mb genome with 6385 protein-coding genes [19]. These data were slightly lower (ca. 19 Mb and 6000 ORFs) when two different strains (CBS 7918T, CRUB 1149), in addition to the previously sequenced one (CBS 6938), were analysed. Thus, based on these three strains, which can be considered as different varieties in future, the existence of genetic heterogeneity within this red-pigmented yeast was demonstrated [87]. Genome-based pathway analysis presented sterols and carotenoids biosynthesis as the two prominent terpenoid pathways in _X. dendrorho_. These genes do not follow the typical cluster arrangement for other specific biosynthesis pathways of fungi, which is a peculiarity of this yeast. Besides, the key regulators that control the ethanol accumulation from glucose even under aerobic conditions prior to be re-used on the stationary phase, have been provided from the genome sequence. Those are capital to reach an optimal astaxanthin production increasing the precursors availability by means of pathway engineering [19; 87]. Also described was how _X. dendrorho_ is genetically fully equipped to cope with environmental oxidative stress that contributes to its genome shape [88]. The genome sequence also eased the phylogenetic analyses of this astaxanthin-producer basal agaricomycete with uncertain taxonomic placement, which presented _Wallemia_ as the most basal agaricomycetinous lineage followed by Tremellomycetes. Besides, the taxonomic analysis defined a sister-group relationship between the core Tremellomycetes and the Cystofibolasidiales [19]. Two sampling points (18 and 72 h) and two different carbon sources (glucose and succinate) were used by [PERSON] and co-workers [86] to obtain RNA after mechanical rupture by glass beads and Tri-Reagent (Ambion, Foster City, CA, USA) extraction (Table 2). The subsequent RNAseq analysis was the base to determine sequence lengths, expression levels, GC% content, as well as the codon usage and codon context biases of the open reading frames (ORFs) [86]. A total of 1695 ORFs were the basis of the analysis in contrast with one previously described by [PERSON] and [PERSON] [89] based on 10 ribosomal genes. Thus, a codon usage table of highly expressed ORFs of _X. dendrorhous_ was properly defined, which is highly relevant for the heterologous expression of recombinant genes in the biotechnology industry [90]. Proteome analysis has been the most used omics methodology applied to _X. dendrorhous_, which goes from a reference map and mutant analysis to the comparison in the use of different carbon sources [91; 92; 93; 94]. Besides, the sampling point and procedure help to discriminate those biomolecules directly involved in the process from those contaminants that include noise in the system. For example, this is the case of extracellular proteome (secretome) analysis, where proteins obtained by degradation (degradome) should be avoided [95]. To date, just the intra-cellular proteome has been analysed in _X. dendrorhous_. Those methodologies used for protein extraction, visualisation, and analysis are summarised in Table 2.  
Firstly, [PERSON] and co-workers [93] developed a heterologous protein identification approach due to the poor genome characterisation at that time. Three time points were selected (lag, late exponential, and stationary growth phases) in minimal media (MM-glucose), where pigment accumulation is evident during the stationary phase.