Revamped pattern search simulation
Based on blockinfo file from Brassica rapa genome, in order to build a KS dotplot containing four models by WGDI (Fig. 2), we synthesized Bra-1 and Bra-2. The target species is Bra-1 and the reference species is Bra-2, forming a total of 10 * 10 comparison units. Based on the comparison units, the search simulation of the rearrangement pattern is performed. The feasibility of the EntroCR model was evaluated by simulation to determine whether the model could accurately detect chromosomal rearrangement patterns, i.e. the four patterns mentioned above.
KS dot plot between Bra-1 and Bra-2. The red boxes represent the chromosomes involved in the four basic rearrangement patterns.
Using the EntroCR model, the number of combinations formed by two comparison units is 450 and the number of combinations formed by four comparison units is 1620. The EntroCR model was used to find the rearrangement pattern of four units of comparison and two comparison units respectively. And the three combinations with the greatest similarity are obtained (Fig. 3), the similarity values are as follows (Table 2).
Chromosomal rearrangement pattern search results in Brassica rapa reconstruction genome. Note: The name of the combination is formed according to the clockwise direction of the comparison units, the name of the comparison unit consists of horizontal and vertical chromosome numbers.
In the CIIJ model, the range of similarity obtained by different combinations is [1.331, 2.661]. The combination of 0102-0302-0106-0306 detected by the model is our constructed CIIJ model, and the similarity is 2.578. The crossing between two chromosomes results in the translocation of the chromosomal arms towards each other. Chromosomes 1 and 3 of Bra-1 crossover, causing the first arm of chromosome 1 to combine with the second arm of chromosome 3 to form chromosome 2 of Bra-2, while the other two parts combine to form chromosome number 6 of Bra-2. combination of 0102-0302-0106-0306 is upside down from the standard model. 0508-0908-0510-0910 had the highest similarity of 2.661, but the number of collinear fragments did not fit the standard CIIJ pattern; the combination 0503-0703-0510-0710 did not match the number and positions of collinear segments in the standard CIIJ model.
In CIEJ, the range of similarity obtained by different combinations is [1.351, 2.195]. The combination of 0508-0908-0510-0910 detected by the model is our constructed CIEJ model, and the similarity is 2.195. It is when one chromosome crosses with another near the telomere to form a short chromosome and a long chromosome. Part of chromosome 5 of Bra-1 species forms chromosome 8 of Bra-2 species, while another part forms chromosome 10 of Bra-2 species together with chromosome 9. The combination of 0508 -0908-0510-0910 is upside down from the standard model. There is a big gap between the similarity of the combination of 0404-0804-0409-0809, 0106-0306-0110-0310 and the combination of 0508-0908-0510-0910.
In the CEEJ, the range of similarity obtained by different combinations is [0.512, 1.501]. The combination of 0203-0703 detected by the model is our constructed CEEJ model and the similarity is 1.397. That is, the end-to-end junction of the chromosomes. Chromosomes 2 and 7 of Bra-1 join to form chromosome 3 of Bra-2. The combination 0508-0908 has the highest similarity, which is 1.501, but the position of the collinear segment is quite different from the standard model; the direction of the collinear segment of the 0703-1003 combination is obviously different from the standard model.
In NCF, the range of similarity obtained by different combinations is [1.320, 2.488]. The combination of 0409-0809 detected by the model is our constructed NCF model and the similarity is 2.488. That is, nested chromosome fusions. Chromosome 4 of Bra-1 is inserted into chromosome 8 to form chromosome 9 of Bra-2. The combination of 0409-0809 is upside down from the standard model. The number of collinear fragments for the 0703-1003 combination and the 0203-0503 combination is significantly different from the standard motif.
Of the built Brassica rapa genome data, EntroCR found the combination of four models respectively, among which 0102-0302-0106-0306 is CIIJ model, 0508-0908-0510-0910 is CIEJ model, 0203-0703 is CEEJ model, 0409- 0809 is the NCF model. Moreover, other combinations are quite different from the standard model, which checks the validity of the model and shows that EntroCR has a certain search performance.
Look for rearrangement patterns of Gossypium raimondii and Arboreum Gossypium
The KS dotplot between the genomes of Gossypium raimondii and Arboreum Gossypium is chosen as the research object. The numbers on the x-axis represent the number of chromosomes from Gossypium raimondiithe numbers on the y-axis represent the number of chromosomes of Arboreum Gossypium, and the genes on the chromosomes are arranged in order. A total of 13 * 13 comparison units are formed. Using the EntroCR model, the number of combinations formed by two comparison units is 199, and the combination formed by four comparison units is 147. The EntroCR model was run on combinations formed by four comparison units to obtain the three combinations with the greatest similarity (Figure 4).
Search results for chromosome rearrangement patterns in the Gossypium raimondii and Arboreum Gossypium genomes.
The range of similarity achieved by different combinations is [1.426, 3.258]. The model detected the combination of 0201-0301-0202-0302 as a cross between the chromosomes of Gossypium raimondii and Arboreum Gossypium resulting in the mutual translocation of chromosomal arms, i.e. the CIIJ pattern, with a similarity of 3.258. The crossing of chromosomes 2 and 3 of Gossypium raimondii results in the combination of the first half of chromosome 2 and the second half of chromosome 3 to form chromosome 1 of Arboreum Gossypiumwhile the other two parts combined to form chromosome 2 of Arboreum Gossypium. The combinations 0202-1102-0210-1110 and 0810-1110-0812-1112 are significantly different from the standard CIIJ model, and their similarity is 3.151 and 3.143, respectively. This result is consistent with previous research.27.
Look for rearrangement patterns of Oryza sativa and Organic sorghum
The KS dotplot between the genomes of Oryza sativa and Organic sorghum is chosen as the research object. The numbers on the x-axis represent the number of chromosomes from Oryza sativathe numbers on the y-axis represent the number of chromosomes of Organic sorghum, and the genes on the chromosomes are arranged in order. A total of 12 * 10 comparison units are formed. Using the EntroCR model, the number of combinations formed by two comparison units is 421, and the combination formed by four comparison units is 945. The EntroCR model was run on combinations formed by two comparison units to obtain the three combinations with the greatest similarity (Fig. . 5).
Search results for chromosome rearrangement patterns in the Oryza sativa and Organic sorghum genomes.
The range of similarity achieved by different combinations is [1.153, 2.593]. The model detected the case where the combination of 0702-0902 was a nested chromosome fusion, i.e. the NCF motif, with a similarity of 2.593. Chromosome 7 of Oryza sativa is inserted into chromosome 9 to form Organic sorghum chromosome 2. The 0109-0509 combination is significantly different from the position of the collinear segment of the standard NCF model, with a similarity of 2.567. The combination 0702-0802 has the smallest similarity of 2.451, and the KS the value between collinear segments has a big difference. This result is consistent with previous research.37.
