VEGMQAZ/Sorghum

Sorghum is a widely grown cereal crop originating from Africa that possesses a wide degree of diversity and uses (e.g. consumption, biomass, etc...). The purpose of this repository is the maintenance of relevant code for TIPs analyses of S. bicolor species. ## Introduction Sorghum is a widely grown cereal crop originating from Africa. Five primary landraces: *durra*, *guinea*, *caudatum*, *kafir*, and *bicolor* (*BTx623*)Traits: *Heat tolerant, drought tolerant, and nitrogen efficient*. A very diverse species with various uses ranging from consumption by humans and livestock, to biomass. ## Motivation A holistic understanding of sorghum biodiversity through studying its genetic architecture and the various mechanisms contributing said biodiversity, namely TIPs (Transposon Insertion-site Polymorphisms). Cultivation around the world has declined over the last four decades at a rate of over 0.15 million hectares per year with production peaking during the 80s; Followed by a decline by ~13–15 % per year” - *(Hariprasanna, 2017)*. Countries including Brazil, Ethiopia, Sudan, Australia, Mexico, Nigeria, and Burkina Faso have expanded cultivation. With the advent of global warming and increasing temperatures and instances of drought, Sorghum becomes increasing important. Wild types in particular are of interest due to their potential contributions to sorghum biodiversity. ## Sorghum Reference Mobilome Sorghum (*Sorghum bicolor,* BTx623) contains 20,240 uniquely identified TE sequences identified using RepeatModeler2 and RepeatMasker (v4.10). ### Mobilome Composition General characterization of repeats shows a high portion of the genome consists of (1) Class I (LTR), (2) simple repeats and (3) Unknown elements. This is consistent with observations of repeats in other *Poaceae*. Repetitive elements by themselves are known to be mutagenic in the advent of insertion into exonic regions. ## TIPs: Transposon Insertion-site Polymorphisms TIPs are sequences derived from TSD (target-site duplications) created upon insertion of a transposable element into a given loci. Variants within TSDs and other insertion sites are known as TIPs, and these are believed to contribute to phenotypic variants, and potentially impact gene …