ITS2 secondary structure for species circumscription: case study in southern African Strychnos L. (Loganiaceae)

Abstract

Recently developed computational tools in ITS2 sequence-structure phylogenetics are improving tree robustness by exploitation of the added information content of the secondary structure. Despite this strength, however, their adoption for species-level clarifications in angiosperms has been slow. We investigate the utility of combining ITS2 sequence and secondary structure to separate species of southern African Strychnos, and assess correlation between compensatory base changes (CBCs) and currently recognised species boundaries. Combined phylogenetic analysis of sequence and secondary structure datasets performed better, in terms of robustness and species resolution, than analysis involving primary sequences only, achieving 100 and 88.2 % taxa discriminations respectively. Further, the Strychnos madagascariensis complex is well-resolved by sequence-structure phylogenetic analysis. The 17 Strychnos species corresponded to 14 ITS2 CBC clades. Four of the five taxa in section Densiflorae belong to a single CBC clade, whose members tend to form natural hybrids. Our finding supports the application of ITS2 as a complementary barcoding marker for species identification. It also highlights the potential of comparative studies of ITS2 CBC features among prospective parental pairs in breeding experiments as a rapid proxy for cross compatibility assessment. This could save valuable time in crop improvement. Patterns of CBC evolution and species boundaries in Strychnos suggests a positive correlation. We conclude that the CBC pattern coupled with observed ITS2 sequence paraphyly in section Densiflorae points to a speciation work-in-progress.

Characterizing nrDNA ITS1, 5.8S and ITS2 secondary structures and their phylogenetic utility in the legume tribe Hedysareae with special reference to Hedysarum

“…The Hedysareae ITS2 secondary structure is comparable to those of other eukaryotes [ 17 , 49 , 61 ]. The four helices radiating from a large central loop proceed through the tribe by force homology modeling of ITS2DB and RNAfold tool.…”

“…Nevertheless, comparing the nuclear divergence time of H. sects. Hedysarum, Multicaulia and Stracheya originated at 15.88, 7.92, and 4.3 Ma ago [49], and Strychnos (12.72 Ma) [78], lead us to the conclusion of the probability of gene-exchanging capability among members. Instead, the observed rDNA ITS1 and ITS2 secondary structural features characterized the four clades of the genus Hedysarum and each partly delimited the species groups and inter-specific cases.…”

“…In addition, the presence of any compensatory base change (CBC) in the conserved regions of helices 2 and 3 of ITS2 revealed a correlation with incompatibility/ ability to sexually cross [32,33]. Detections about the effectiveness of ITS2 in distinguishing cryptic/pseudo-cryptic species via CBCs [34][35][36], resulting in its frequent use to resolve lower taxonomic affinities of copious primitive eukaryotes, such as diatoms and alveolates [2,[37][38][39][40][41][42][43], fungi [7,44,45], algae [34,[46][47][48]] some cases of terrestrial plants [22,[49][50][51] and zoophytes [52][53][54]. Furthermore, following Torres-Sua ´rez [55], utilizing hemi-CBCs (hCBCs) to assess relationships at the population and species levels and Karpenko et al, [51], using nonstructural substitutions (Nsts) and hCBCs at the species level, Ozgişi [27] applied both for species delimitation.…”