The theme_roots and theme_basis plugins have both been deprecated in Totara 13.
A custom theme can not only change the appearance of your Totara significantly, it can be branded and styled to look similar to your organisation's website or other systems you use internally. You can read more guidance on developing themes for Totara Learn in the developer documentation.
Totara also has a number of in-built themes which can be enabled and (depending on your selected theme) customised by a Site Administrator. You can select which theme to apply using the Theme selector.
We recommend using the Ventura theme, which is new to Totara 13.
(This video is taken from the Dashboards and basic theming course on the Totara Academy, where you can access more resources and learning materials - including other videos).
The Element library contains a set of sample elements that are used on your Totara site, this is useful to ensure that everything has been correctly themed. You can reach the element library from the quick-access menu via Appearance > Themes > Element Library.
There are options for a number of theme areas, including toolbars, flexible icons, and a pattern library. There is more information for flexible icons in the developer documentation.
Customising HTML email
You can read more about how to do this in the public developer documentation.
The Totara Academy has a whole course dedicated to usingDashboards and basic theming in Totara . Here you can learn more on how to customise your site's appearance, see best practice, and give it a go yourself.