HTT-DB: new features and updates

Abstract

Horizontal Transfer (HT) of genetic material between species is a common phenomenon among Bacteria and Archaea species and several databases are available for information retrieval and data mining. However, little attention has been given to this phenomenon among eukaryotic species mainly due to the lower proportion of these events. In the last years, a vertiginous amount of new HT events involving eukaryotic species was reported in the literature, highlighting the need of a common repository to keep the scientific community up to date and describe overall trends. Recently, we published the first HT database focused on HT of transposable elements among eukaryotes: the Horizontal Transposon Transfer DataBase (http://lpa.saogabriel.unipampa.edu.br: 8080/httdatabase/). Here, we present new features and updates of this unique database: (i) its expansion to include virus-host exchange of genetic material, which we called Horizontal Virus Transfer (HVT) and (ii) the availability of a web server for HT detection, where we implemented the online version of vertical and horizontal inheritance consistence analysis (VHICA), an R package developed for HT detection. These improvements will help researchers to navigate through known HVT cases, take data-informed decision and export figures based on keywords searches. Moreover, the availability of the VHICA as an online tool will make this software easily reachable even for researchers with no or little computation knowledge as well as foster our capability to detect new HT events in a wide variety of taxa. (Database URL: http://lpa.saogabriel.unipampa.edu.br:8080/httdatabase/).

Figure 1.

(A) Distribution of HVT events (endogenization) across different Phylum, outermost bars represent the number of HVT cases in the taxa shown. (B) HVT chart result from database search including all cases reported in the database, ssDNAs >50% of all known HVT events.

Figure 2.

(A) First panel of VHICA interface available for HTT detection through the HTT-DB database. Two optional (Gene Files and TE Files) and one optional box (Phylotree File) for files upload are available as well as an example of all those files used in the original VHICA paper (Wallau et al. 2016). (B) Second panel of VHICA interface. Here, the user can select one, a set of or all TEs for run VHICA. Since VHICA performs multiple comparisons there are two correction methods available for the user choice: Bonferroni and False Discovery Rate. TE divergence rate can be added, and then VHICA will estimate the HT time in Mya. User can also choose if they want to plot the results only for hosts’ species which presented a given TE or maintain all the other species in the plotting step.

Figure 3.

Three possible VHICA outputs. (A) Summary of all statistically supported HTT cases and associated data. (B) Resulting output when no significant HTT signal is detected. (C) Graphical output showing all host species and the significant pairwise comparison following P-value the legend colour.