Although the "naked coral" scenario is supported by analyses of protein sequence data, phylogenetics based on mt nucleotide sequences instead strongly support scleractinian monophyly (Stolarski et al. 2011; Kayal et al. 2013; Kitahara et al. 2014).
This finding was supported by analyses of Expressed Sequence Tags (ESTs) [ 2, 3], which suggested an additional duplication event, with estimated times of approximately 14 and 44 mya.
This information is particularly useful for identifying proteins that are tethered to the membrane via protein-protein or protein-lipid interactions or for condition-specific changes in protein localization which cannot be revealed by analyses of protein sequence content alone.
However, rather than the deep split between these two groups implied by analyses of ribosomal sequences, our phylogeny places the "robust" coral clade within the "complex" radiation, following the precedent of Fukami et al. [11].
As a consequence, the old Polyzoa (=Bryozoa sensu lato) hypothesis was revived [ 27, 28, 30- 34], which has been supported by a few morphologists [ 47], and which has recently also been corroborated by analyses of rDNA sequences [ 12, 13], albeit with weak support.
Sequence signatures can be analyzed directly on the short reads, and the biological functions can be studied by downstream analyses of sequence signatures that are selected as discriminative for the classification.
This latter scenario, the "naked coral" hypothesis, is strongly supported by analyses based on mitochondrial (mt) protein sequences, whereas the former is equally strongly supported by analyses of mt nucleotide sequences.
By analyses of multiple transitional sequences, we clearly showed the origin and the growing procedure of the satellite repeat in tomato genome.
One batch of trypsin contained two distinct TTSuV1 plus one TTSuV2 genome, suggesting that this might have been the source of contamination, as supported by phylogenetic analyses of sequenced amplicons.
We analyzed the genetic diversity of HMPV by phylogenetic analyses of sequences obtained for part of the F (n = 84) and the complete G open reading frames (ORFs) (n = 35).
