Genetic analysis of cabbages and related cultivated plants using the bag-of-words model

Abstract

Abstract In this study, we aim to introduce the analytical method bag-of-words, which is mainly used as a tool for the analysis (document classification, authorship attribution and so on; e.g. [1, 2]) of natural languages. Quantitative linguistic methods similar to bag-of-words (e.g. Damerau–Levenshtein distance in the paper by Serva and Petroni [3]) have been used for the mapping of language evolution within the field of glottochronology. We attempt to apply this method in the field of biological taxonomy – on the Brassicaceae (Cruciferae) family. The subjects of our interest are well-known cultivated crops, which at first sight are morphologically very different and culturally perceived as objects of different interests (e.g. oil from oilseed rape, turnip as animal feed and cabbage as a side dish). Despite the phenotypic divergence of these crops, they are very closely related, which is not morphologically obvious at first sight. For this reason, we think that Brassicaceae crops are appropriate illustrative examples for introducing the method. For the analysis, we use genetic markers (internal transcribed spacer [ITS] and maturase K [matK]). Until now, the bag-of-words model has not been used for biological taxonomisation purposes; therefore, the results of the bagof-words analysis are compared with the existing very well-developed Brassica taxonomy. Our goal is to present a method that is suitable for language development reconstruction as well as possibly being usable for biological taxonomy purposes.