Consequently, when gene rearrangements occur, they may provide compelling phylogenetic markers that can corroborate or contradict hypotheses based on primary sequence data and provide resolution for deeper nodes that are often weakly supported in sequence-based phylogenies [ 2- 6].
NCU00403 and NCU00455 each exhibit unique frameshift inducing indels and both deletions are strongly supported in the sequence data.
The highly conserved rbcL protein sequences consistently failed to recover three clades that were otherwise highly supported in all DNA sequence data sets (Cryptomonas marssonii, C. ovata and C. pyrenoidifera), because phylogenetic information was predominantly based on synonymous substitutions.
The monophyly of Calochroi, Caroviolacei, Dibaphi, Elegantiores, Napi, Pseudoglaucopodes and Splendentes was supported in our maximum likelihood sequence analysis.
Monophyly of the suborder Spirurina was well supported in nuclear SSU rRNA gene sequence analyses [ 12, 14], but was rejected in mt genome sequence analyses in Kang et al. [ 23], Park et al. [ 24], Sultana et al. [ 25] and the present study.
However, this is not supported in our searches of the sequence databases.
Reciprocal monophyly of these two genes is supported in an analysis based on sequence evolution, but excluding secondary structure (supplementary fig. S3 a, Supplementary Material online).
The Protoperidinium/Diplopsalis clade and the Karenia clade were strongly supported in trees inferred from Hsp90 sequences (Figures 1, 2).
This research was supported in part by the Genome Sequencing Facility of the Greehey Children's Cancer Research Institute, UTHSCSA, which provided RNA-seq service.
However, update of activation sequence is not supported in an IC.
The fourth hairpin precursor was slightly divergent showing minor sequence changes in the mature and star sequences supported by sequence reads in our libraries.
