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. 2022 Nov 16;12(1):19707.
doi: 10.1038/s41598-022-22046-x.

An intelligent recognition method of chromosome rearrangement patterns based on information entropy

Fushun Wang #  1   2 , Ruolan Zhang #  1 , Xiaohua Sun  3 , Junhao Wang  1 , Hongquan Liu  4 , Kang Zhang  5   6   7 , Chunyang Wang  8   9
Affiliations

An intelligent recognition method of chromosome rearrangement patterns based on information entropy

Fushun Wang et al. Sci Rep. .

Abstract

Chromosome rearrangements play an important role in the speciation of plants and animals, and the recognition of chromosome rearrangement patterns is helpful to elucidate the mechanism of species differentiation at the chromosome level. However, the existing chromosome rearrangement recognition methods have some major limitations, such as low quality, barriers to parental selection, and inability to identify specific rearrangement patterns. Based on the whole genome protein sequences, we constructed the combined figure according to the slope of the collinear fragment, the number of homologous genes, the coordinates in the top left and bottom right of the collinear fragment. The standardized combination figure is compared with the four standard pattern figures, and then combined with the information entropy analysis strategy to automatically classify the chromosome images and identify the chromosome rearrangement pattern. This paper proposes an automatic karyotype analysis method EntroCR (intelligent recognition method of chromosome rearrangement based on information entropy), which integrates rearrangement pattern recognition, result recommendation and related chromosome determination, so as to infer the evolution process of ancestral chromosomes to the existing chromosomes. Validation experiments were conducted using whole-genome data of Gossypium raimondii and Gossypium arboreum, Oryza sativa and Sorghum bicolor. The conclusions were consistent with previous results. EntroCR provides a reference for researchers in species evolution and molecular marker assisted breeding as well as new methods for analyzing karyotype evolution in other species.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
The basic forms of chromosome rearrangement, modified from Meng. (a) CIIJ (chromosome inner-inner joining). (b) CIEJ (chromosome inner-end joining). (c) CEEJ (chromosome end-end joining). (d) NCF (nested chromosome fusions).
Figure 2
Figure 2
KS dotplot between Bra-1 and Bra-2. The red boxes represent the chromosomes involved in the four basic rearrangement patterns.
Figure 3
Figure 3
Search results of chromosome rearrangement pattern in Brassica rapa reconstruction genome. Note: The combination name is formed according to the clockwise direction of the comparison units, the comparison unit name consists of horizontal and vertical chromosome numbers.
Figure 4
Figure 4
Search results for chromosome rearrangement patterns in the Gossypium raimondii and Gossypium arboreum genomes.
Figure 5
Figure 5
Search results for chromosome rearrangement patterns in the Oryza sativa and Sorghum bicolo genomes.
See this image and copyright information in PMC

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