Method, system and equipment for splitting allopolyploidy based on perl language and storage medium

Abstract

The invention discloses a method, a system and equipment for splitting an allopolyploid based on a perl language and a storage medium, and particularly relates to the technical field of bioinformatics analys.The method comprises the steps that a diploid species close to a to-be-split allopolyploid species is selected as a diploid reference species; calculating a distance SD value between chromosomes to form a matrix; a homologous chromosome group HG1. HGN is formed; according to the homologous chromosome group HG1... HGN, an allopolyploid to be split is split into AN subgenomes. The subgenome is split based on the mutation accumulation difference of the sexual maturity cycle, and the method has high flexibility; the method disclosed by the invention has wide applicability; the splitting method disclosed by the invention has the advantages of high accuracy, good visualization effect, simplicity and convenience in operation, reliable data support, capability of promoting genome research and the like; according to the invention, how different mutations are accumulated by different species under the difference of sexual maturity cycles can be well revealed, so that deep understanding of the evolutionary mechanism of the species is promoted.

Description

TECHNICAL FIELD

[0001] The present application relates to the technical field of bioinformatics analysis, and particularly relates to a method, system and device for splitting allopolyploidy based on a perl language and a storage medium. BACKGROUND

[0002] The splitting of allopolyploidy is of great significance in plant breeding and genomic research. Allopolyploidy generally has greater genetic diversity, which enables them to have stronger advantages in adapting to environmental changes, resisting pests and diseases, etc. By splitting allopolyploidy, researchers can better understand its genetic background and phenotypic characteristics, thereby providing important breeding materials.

[0003] Secondly, allopolyploidy plays a key role in crop improvement. They often can introduce new traits through gene recombination, such as increasing yield, improving quality or enhancing stress resistance. Correctly splitting allopolyploidy helps scientists choose appropriate parents for crossing, thereby accelerating the breeding process and meeting the needs of agricultural production.

[0004] The study of allopolyploidy also provides important clues for understanding the evolution and function of genomes. Through the analysis of its genomic characteristics, researchers can reveal evolutionary mechanisms, species origins, and interactions between genes. In summary, the splitting of allopolyploidy not only helps plant breeding, but also provides rich resources and important theoretical support for basic research.

[0005] In the study of allopolyploidy genomes, how to accurately split subgenomes is an important problem. Currently, there are mainly two methods for splitting allopolyploidy. Method 1 is to use the different copy frequencies of transposon sequences in different species genomes, thereby causing different species genomes to have species specificity, for example, the species AB formed by hybridization of (A, B) (in the AB genome after hybridization, the A and B genomes are referred to as subgenome A and subgenome B, respectively), due to the different copy numbers of transposon TA in the A and B genomes, and the random occurrence of this copy in different chromosomes throughout the genome, the subgenome A and subgenome B can be separated by comparing the content and enrichment level of transposons in homologous chromosomes (referring to the same chromosome between A and B); Method 2 is to split subgenomes based on phylogenetic relationships, for example, there are three species of phylogenetic species with the structure of ((A, C), B), and the allopolyploid species is an AB type allopolyploid genome formed by hybridization of A and B, since the genetic distance between C and A species is closer, the subgenome A and subgenome B can be separated by studying the phylogenetic distance of homologous chromosomes (referring to the same chromosome between A, B and C).

[0006] The two methods are the current methods for splitting allopolyploids, but both have certain constraints. For example, method 1 is based on the obvious difference in transposon content between the two species, which can split the A and B subgenomes. However, if the two species are closely related and there is no obvious difference in transposon content, the method will fail. Method 2 relies on the C species, which is more closely related to the A species. In practical applications, it is difficult to split the C species into a species that is more closely related to the A species. Therefore, the current methods have certain constraints. SUMMARY

[0007] Therefore, the present application provides a method, system, device and storage medium for splitting allopolyploids based on perl language, aiming to improve the problem of constraints in the prior art method for splitting allopolyploids.

[0008] The present application is implemented as follows: the method for splitting allopolyploids based on perl language includes the following steps: selecting a diploid species closely related to the allopolyploid species to be split as a diploid reference species; calculating the length of each chromosome of the diploid reference species and the allopolyploid species to be split, respectively, to obtain sets rchr1S…rchrNS and chr1S…chrNS; starting from the set rchr1S…rchrNS, traversing each set, taking the intersection and union of the traversed set and chr1S…chrNS, respectively, pairing the intersection and union results one by one, and calculating the distance SD value between chromosomes to form a matrix; In the matrix, sort the SD values of each row from small to large, select the corresponding number of columns according to the AN value, and select the chromosomes in chr1S…chrNS corresponding to the columns, which are the homologous chromosomes corresponding to rchr1S…rchrNS, construct the homologous chromosomes corresponding to each chromosome in rchr1S…rchrNS, and form a homologous chromosome group HG1..HGN; According to the homologous chromosome group HG1..HGN, the allopolyploid to be split is split into AN subgenomes.

[0009] Optionally, in some embodiments of the present application, the diploid reference species is numbered as rchr1…rchrN, and the heterologous polyploid species to be split is numbered as chr1…chrN; the length of each chromosome of the diploid reference species is rchr1L…rchrNL, and the length of each chromosome of the heterologous polyploid species to be split is chr1L…chrNL; K fragments of length L are taken from the first site of each chromosome of the diploid reference species and the heterologous polyploid species to be split, rchrNL-L+1 fragments K are taken from each chromosome of the diploid reference species, and chrNL-L+1 fragments K are taken from each chromosome of the heterologous polyploid species to be split, the fragments K from the same chromosome of the diploid reference species are defined as a set rchr1S…rchrNS, and the fragments K from the same chromosome of the heterologous polyploid species to be split are defined as a set chr1S…chrNS, 17≤L≤63, and L is an odd number.

[0010] Optionally, in some embodiments of the present application, the intersection and union of the set are obtained by intersecting and unioning the set with chr1S…chrNS, respectively, to obtain rchr1S_chr1S…rchr1S_chrNS…rchrNS_chrNS intersection results and rchr1S_chr1S…rchr1S_chrNS…rchrNS_chrNS union results, and the intersection and union results are paired one by one, and the distance SD between chromosomes is calculated by the number IN of elements in each intersection and the number CN of elements in the corresponding union.

[0011] Optionally, in some embodiments of the present application, SD=1-IN / CN.

[0012] Optionally, in some embodiments of the present application, the SD is calculated by using the multi-process of Perl language.

[0013] Optionally, in some embodiments of the present application, a matrix SD matrix is formed, the rows of the matrix SD matrix represent rchr1S…rchrNS, the columns of the matrix SD matrix represent chr1S…chrNS, and the values in the matrix SD matrix represent the SD values corresponding to the rows and columns.

[0014] Optionally, in some embodiments of the present application, the diploid reference species chromosomes rchr1…rchrN in HG1…HGN are taken as the abscissa, and the homologous chromosomes in each homologous chromosome group are sorted in ascending order of SD value to obtain a queue, and the chromosome with the highest SD value in each queue is selected to form subgenome 1, the chromosome with the second highest SD value is selected to form subgenome 2, and so on, and the chromosome with the nth highest SD value is selected to form subgenome n, until n equals AN, and finally the allopolyploid species to be split is split into AN subgenomes, and AN is the number of different sources of allopolyploid ancestors.

[0015] Correspondingly, the embodiments of the present application also provide an allopolyploid splitting system based on perl language, comprising: A diploid reference species obtaining module is configured to select a diploid species close to the allopolyploid species to be split as a diploid reference species. A set rchr1S…rchrNS and a set chr1S…chrNS obtaining module is configured to calculate the length of each chromosome of the diploid reference species and the allopolyploid species to be split respectively to obtain the set rchr1S…rchrNS and the set chr1S…chrNS. A matrix obtaining module is configured to traverse each set from the set rchr1S…rchrNS, take the intersection and union of the set and chr1S…chrNS respectively, pair the intersection and union results one by one, calculate the distance SD value between the chromosomes, and form a matrix. A homologous chromosome group HG1..HGN obtaining module is configured to sort the SD values in each row in the matrix in ascending order, select the corresponding number of columns according to the AN value, and select the chromosomes in chr1S…chrNS corresponding to the columns, which are the homologous chromosomes corresponding to rchr1S…rchrNS, to construct the homologous chromosomes corresponding to each chromosome in rchr1S…rchrNS, and form the homologous chromosome group HG1..HGN. A subgenome obtaining module is configured to split the allopolyploid to be split into AN subgenomes according to the homologous chromosome group HG1..HGN.

[0016] Correspondingly, the embodiments of the present application also provide a computer device comprising a storage and a processor, wherein the storage stores a computer program, and the computer program is executed by the processor to make the processor execute the steps of the above method.

[0017] Correspondingly, the embodiments of the present application also provide a computer readable storage medium storing a computer program, and the computer program is executed by a processor to make the processor execute the steps of the above method.

[0018] The application splits subgenomes based on the accumulated difference of mutation in the sexual maturation cycle, is not limited by traditional restrictions such as specific evolutionary history of species or chromosome number, and does not depend on specific species or genome structure, and has high flexibility; in addition, the method of the application only needs sequence data between genomes, and can be realized by genome comparison, and therefore is not limited by expensive experimental techniques or complex species resources, and has wide applicability; furthermore, the splitting method of the application has high accuracy, good visualization effect, simple operation, reliable data support, and the like, and provides an effective method for subgenome splitting and related research; in addition, the application can better reveal how different species accumulate different mutations under the difference in the sexual maturation cycle, and further promote in-depth understanding of the evolution mechanism of species. BRIEF DESCRIPTION OF DRAWINGS

[0019] In order to more clearly illustrate the technical solutions in the embodiments of the application, the drawings needed to be used in the embodiment description will be briefly introduced. Obviously, the drawings in the following description are only some embodiments of the application, and for those skilled in the art, other drawings can be obtained without creative labor on the basis of these drawings.

[0020] Figure 1 is a flowchart of the method for splitting allopolyploids based on perl language of the application; Figure 2 is the SD value change of each chromosome of L. rohita and the corresponding chromosome of C. carpio. DETAILED DESCRIPTION

[0021] The technical solutions in the embodiments of the application will be described clearly and completely in the following with reference to the drawings in the embodiments of the application. Obviously, the described embodiments are only some of the embodiments of the application, but not all the embodiments. Based on the embodiments in the application, all other embodiments obtained by those skilled in the art without creative labor are within the scope of protection of the application. In addition, it should be understood that the specific embodiments described herein are only used to illustrate and explain the application, and are not used to limit the application.

[0022] In the application, "and / or" describes the association relationship of the associated objects, and means that there can be three kinds of relationships, for example, A and / or B can mean: A exists alone, A and B exist together, and B exists alone. Wherein A and B can be singular or plural.

[0023] In the present application, "at least one" means one or more, and "multiple" means two or more. "One or more", "at least one of the following (one)", or similar expressions, refer to any combination of these items, including any combination of single or multiple items. For example, "at least one of a, b, or c", or "at least one of a, b, and c", can mean: a, b, c, a-b (i.e. a and b), a-c, b-c, or a-b-c, where a, b, and c can be single or multiple.

[0024] Various embodiments of the present application can exist in the form of a range; it should be understood that the description in the form of a range is only for the convenience and brevity, and should not be understood as a hard limit on the scope of the present application; therefore, it should be considered that the described range has specifically disclosed all possible sub-ranges and single values within the range. For example, it should be considered that the range description from 1 to 6 has specifically disclosed sub-ranges, such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6, etc., as well as single numbers within the described range, such as 1, 2, 3, 4, 5, and 6, regardless of the range. In addition, whenever a numerical range is indicated in this document, it refers to any cited number (fraction or integer) within the indicated range.

[0025] The technical solutions of the present application are as follows: Please refer to Figure 1 The method for splitting allopolyploidy based on perl language provided by the embodiments of the present application includes the following steps: S01, selecting a diploid species close to the allopolyploid species to be split as a diploid reference species; S02, calculating the length of each chromosome of the diploid reference species and the allopolyploid species to be split respectively, obtaining set rchr1S…rchrNS and set chr1S…chrNS; S03, starting from set rchr1S…rchrNS, traversing each set, taking the intersection and union of the traversed set and chr1S…chrNS respectively, pairing the intersection and union results one by one, and calculating the distance SD value between the chromosomes to form a matrix; S04, in the matrix, sorting the SD values of each row from small to large, selecting the corresponding number of columns according to the AN value, and selecting the chromosomes in chr1S…chrNS corresponding to the columns, which are the homologous chromosomes corresponding to rchr1S…rchrNS, constructing the homologous chromosomes corresponding to each chromosome in rchr1S…rchrNS, and forming a homologous chromosome group HG1..HGN; S05、According to the homologous chromosome group HG1..HGN, split the allopolyploid to be split into AN subgenomes.

[0026] The present application considers the different species maturation cycles before the formation of different subgenomes, and creates a new method for splitting subgenomes by Perl language. The principle on which the present application is based is that different species (A, B, for example, the sexual maturation age of A is 3 years, and the sexual maturation age of B is 5 years) are crossed to form AB. Between the formation of AB, the A species and the B species are different in the number of genetic generations experienced in the same evolution time (T), which are T / 3, T / 5, respectively, and the number of meiosis processes experienced is also different (T / 3, T / 5). In the first meiosis process, homologous recombination will cause mutations at certain sites. Due to this biological mechanism, before the A and B species are crossed to form the AB species, the cumulative mutations of their genomes are also different. Assuming that the mutation rate of each generation is V, the mutation accumulation of A and B species before crossing to form AB species is (T*V / 3, T*V / 5). Taking a sequence as an example, assuming that a sequence of A and B species before differentiation is ATCG. Now, due to the different mutation accumulation of A and B species, A species may be ATCC, and B species may be ATCG. At this time, any close relative species C is selected, and its sequence is ACGG. A and B have 1 mutation site compared with each other, A and C have 3 mutation sites compared with each other, and B and C have 2 mutation sites compared with each other. In the whole genome, by comparing the close genetic relationship of the species, a set of subgenomes with different cumulative mutations can be screened to split the subgenomes.

[0027] The present application splits subgenomes based on the mutation accumulation difference of the maturation cycle, which is not limited by the traditional restrictions such as the specific evolution history of the species or the number of chromosomes, and does not depend on specific species or genome structure, and has high flexibility. In addition, the method of the present application only needs sequence data between genomes, and can be realized by genome comparison, so it is not limited by expensive experimental techniques or complex species resources, and has wide applicability. Furthermore, the splitting method of the present application has high accuracy, good visualization effect, simple operation, reliable data support, and promotes genome research, and provides an effective method for subgenome splitting and related research. In addition, the present application can better reveal how different species accumulate different mutations under the difference of maturation cycle, and further promote the in-depth understanding of the evolution mechanism of species.

[0028] The split subgenomes help to clearly distinguish the genetic contributions between different species, making the understanding of whole genome recombination, mutation and evolutionary process more accurate. By splitting the subgenomes, the functional characteristics of different subgenomes can be more clearly identified and analyzed, providing support for subsequent functional gene research, especially the study of gene interactions and species-specific genes. When comparing genomes between species, by splitting the subgenomes, the bias caused by the difference in mutation accumulation between species can be excluded, and more reliable comparison results can be obtained.

[0029] In the S01, the following applies: In some embodiments, the allopolyploid is a combination of 2N chromosomes derived from N different diploid ancestors, and the gametic cell chromosome number of the reproductive cells in the sexually reproducing polyploid population is N.

[0030] For example, an allo-tetraploid species contains a total of A, A, B, B sets of chromosomes, wherein the same letter represents one chromosome from the father and the other from the mother, which is called the homologous chromosome of the reproductive source.

[0031] Because the sequences of the homologous chromosomes of the reproductive source are highly similar, only one chimeric chromosome can be assembled.

[0032] For example, an allo-tetraploid species 1 has 100 chromosomes in somatic cells, and its zygote is developed from the combination of 50 gametes from the paternal line and 50 gametes from the maternal line. Its genome assembly can assemble 50 chromosomes, which can be divided into 25 A1-A25 and 25 B1-B25 subgenomes according to their derivation from 2 ancestors (A and B). A1 and B1 are called the homologous chromosomes of the genome doubling source.

[0033] For example, allo-tetraploid species 1 selects a closely related diploid as species 2, assembles the chromosome sequences of species 2, and the chromosome sequences of species 2 contain 25 (1-25).

[0034] In the S02, the following applies: In some embodiments, the diploid reference species has chromosome numbers rchr1…rchrN, and the allopolyploid species to be split has chromosome numbers chr1…chrN; each chromosome of the diploid reference species has a length of rchr1L…rchrNL, and each chromosome of the allopolyploid species to be split has a length of chr1L…chrNL.

[0035] Further, K fragments of length L are taken from the first site of each chromosome of the diploid reference species and the allopolyploid species to be split, rchrNL-L+1 fragments of K are taken from each chromosome of the diploid reference species, and chrNL-L+1 fragments of K are taken from each chromosome of the allopolyploid species to be split, the fragments K from the same chromosome of the diploid reference species are defined as a set rchr1S…rchrNS, and the fragments K from the same chromosome of the allopolyploid species to be split are defined as a set chr1S…chrNS.

[0036] Further, 17≤L≤63, and L is an odd number.

[0037] In the S03, the set of the fragments K obtained by the intersection and the union of the sets rchr1S…rchrNS and chr1S…chrNS is obtained, and the intersection result of rchr1S_chr1S…rchr1S_chrNS…rchrNS_chrNS and the union result of rchr1S_chr1S…rchr1S_chrNS…rchrNS_chrNS are obtained, and the intersection result and the union result are paired one by one, and the distance SD between the chromosomes is calculated by the number IN of the elements in each intersection and the number CN of the elements in the corresponding union. Further, SD=1-IN / CN.

[0038] It can be understood that, in an extreme case, for example, the number IN is 0, which represents that there is no overlapping fragment between the two chromosomes, and the value of SD obtained according to the formula is 1, which represents that the distance between the two chromosomes is the farthest, so the value range of SD is greater than or equal to 0 and less than or equal to 1.

[0039] In some embodiments, the Perl language is used to calculate SD by multi-process.

[0040] In some embodiments, the matrix SD is formed matrix , the rows of the matrix SD matrix represent rchr1S…rchrNS, the columns of the matrix SD matrix represent chr1S…chrNS, and the values in the matrix SD matrix represent the SD values corresponding to the rows and columns.

[0041] Exemplarily, the formed matrix is Matrix 1, as shown in Table 1.

[0042]

[0043]

[0044] ​In matrix 1, the allopolyploid species to be split is a tetraploid species, and AN=2, so there are four chromosomes (chr1S, chr2S, chr3S, chr4S), and the diploid species close to the allopolyploid species to be split exists as two chromosomes (rchr1S and rchr2S) as a diploid reference species In chr1S, chr2S, chr3S, chr4S, there are 2 chromosomes as homologous chromosomes of rchr1S, and 2 chromosomes as homologous chromosomes of rchr2S.

[0045] In S04, the SD value of rchr1S in the row of matrix 1 (SD In some embodiments, AN is the number of sources of different ancestors of the allopolyploid.

[0046] It can be understood that the number of chromosomes of the allopolyploid divided by the number of diploid chromosomes can obtain the number of sources of different ancestors of the allopolyploid.

[0047] It can also be understood that for each chromosome in the diploid, for example, chromosome rchr1, the chromosome has AN corresponding homologous chromosomes in the allopolyploid species, and the chromosome distance is much lower than that of non-homologous chromosomes.

[0048] Exemplarily, the SD values (SD 11 , SD 12 , SD 13 and SD 14 ) of rchr1S in the row of matrix 1 are sorted from small to large, and if the sorting result is SD 12 , SD 11 , SD 13 and SD 14 , it can be considered that SD 12 and SD 11 The chromosomes chr2S and chr1S in the corresponding column of matrix 1 are the 2 homologous chromosomes corresponding to rchr1S.

[0049] Similarly, the SD values (SD 21 , SD 22 , SD 23 and SD 24 ) of rchr2S in the row of matrix 1 are sorted from small to large, and if the sorting result is SD 23 , SD 24 , SD 22 and SD 21 , it can be considered that SD 23 and SD 24 The chromosomes chr3S and chr4S in the corresponding column of matrix 1 are the 2 homologous chromosomes corresponding to rchr2S.

[0050] In S05: In some embodiments, with diploid reference species chromosomes rchr1…rchrN in HG1…HGN as the abscissa, the chromosomes of the heterogenous polyploid species to be split in each homologous chromosome group are sorted in ascending order of SD value to obtain a queue, and the chromosome with the highest SD value in each queue is selected to form subgenome 1, the chromosome with the second highest SD value is selected to form subgenome 2, and so on, the chromosome with the nth highest SD value is selected to form subgenome n, until n equals AN, and finally the heterogenous polyploid species to be split is split into AN subgenomes.

[0051] Exemplarily, with 1 to 25 chromosomes of a diploid reference species in 25 homologous chromosome groups (HG1…HG25) as the abscissa, the chromosomes of a heterogenous tetraploid species to be split in each homologous chromosome group are sorted in ascending order of SD value to obtain a queue, and the chromosome with the highest SD value in each queue is selected to form subgenome 1 (subgenome 1), and the chromosome with the second highest SD value is selected to form subgenome 2 (subgenome 2), thereby completing the subgenome splitting of the heterogenous tetraploid species.

[0052] In a second aspect, the embodiments of the present application provide a system for splitting a heterogenous polyploid based on a perl language, which comprises: a diploid reference species obtaining module configured to select a diploid species close to a heterogenous polyploid species to be split as a diploid reference species; A set rchr1S…rchrNS and a set chr1S…chrNS obtaining module is configured to calculate the length of each chromosome of the diploid reference species and the heterogenous polyploid species to be split, respectively, to obtain the set rchr1S…rchrNS and the set chr1S…chrNS; A matrix obtaining module is configured to traverse each set from the set rchr1S…rchrNS, take the intersection and union of the set and chr1S…chrNS respectively, pair the intersection and union results one by one, calculate the distance SD value between the chromosomes, and form a matrix; A homologous chromosome group HG1..HGN obtaining module is configured to sort the SD values in each row in the matrix in ascending order, select the corresponding number of columns according to the AN value, and select the chromosomes in chr1S…chrNS corresponding to the columns, that is, the homologous chromosomes corresponding to each chromosome in rchr1S…rchrNS, to form a homologous chromosome group HG1..HGN; A subgenome obtaining module is configured to split the heterogenous polyploid to be split into AN subgenomes according to the homologous chromosome group HG1..HGN.

[0053] The diploid reference species obtaining module includes: In some embodiments, the allopolyploid is a combination of 2N chromosomes derived from N different diploid ancestors, and the gametic cell of the reproductive cell of the sexually reproducing polyploid population has a chromosome number of N.

[0054] For example, an allopolyploid species 1 has a total of A, A, B, B sets of chromosomes, wherein the same letter represents one chromosome from the father and the other from the mother, which are called the parental homologous chromosomes.

[0055] Because the sequences of the parental homologous chromosomes are highly similar, only one chimeric chromosome can be assembled.

[0056] For example, the allopolyploid species 1 has 100 chromosomes in somatic cells, and the zygote is developed from a combination of 50 gametes from the father and 50 gametes from the mother. The genome assembly can assemble 50 chromosomes, which can be divided into 25 A1-A25 and 25 B1-B25 subgenomes according to their derivation from two ancestors (A and B). A1 and B1 are called genome doubling homologous chromosomes.

[0057] For example, the allopolyploid species 1 selects a closely related diploid species 2 to assemble the chromosome sequences of species 2, which contain 25 (1-25).

[0058] The collection rchr1S…rchrNS and the collection chr1S…chrNS obtaining module includes: In some embodiments, the diploid reference species has chromosome numbers rchr1…rchrN, and the allopolyploid species to be split has chromosome numbers chr1…chrN; each chromosome of the diploid reference species has a length of rchr1L…rchrNL, and each chromosome of the allopolyploid species to be split has a length of chr1L…chrNL.

[0059] Further, K fragments of length L are taken from the first site of each chromosome of the diploid reference species and the allopolyploid species to be split, rchrNL-L+1 fragments of length K are taken from each chromosome of the diploid reference species, and chrNL-L+1 fragments of length K are taken from each chromosome of the allopolyploid species to be split. The fragments K from the same chromosome of the diploid reference species are defined as the collection rchr1S…rchrNS, and the fragments K from the same chromosome of the allopolyploid species to be split are defined as the collection chr1S…chrNS.

[0060] Further, 17≤L≤63, and L is an odd number.

[0061] The matrix obtaining module comprises: In some embodiments, the set of traversed elements is intersected and unioned with chr1S…chrNS respectively to obtain intersection results of rchr1S_chr1S…rchr1S_chrNS…rchrNS_chrNS and union results of rchr1S_chr1S…rchr1S_chrNS…rchrNS_chrNS, and the intersection results and the union results are paired one by one, and the distance SD between chromosomes is calculated according to the number of elements IN in each intersection and the number of elements CN in the corresponding union.

[0062] Further, SD = 1-IN / CN.

[0063] It can be understood that in an extreme case, for example, the number of IN is 0, which represents that there is no overlapping fragment between the two chromosomes, and the value of SD obtained according to the formula is 1, which represents that the distance between the two chromosomes is the farthest, so the value range of SD is greater than or equal to 0 and less than or equal to 1.

[0064] In some embodiments, the SD is calculated by using a multi-process Perl language.

[0065] In some embodiments, the matrix SD is formed matrix , the row of the matrix SD matrix represents rchr1S…rchrNS, the column of the matrix SD matrix represents chr1S…chrNS, and the value in the matrix SD matrix represents the SD value corresponding to the row and the column.

[0066] Exemplarily, the formed matrix is matrix 1, as shown in Table 1.

[0067] In the matrix 1, the heteromultiploid species to be split is a tetraploid species, and the AN=2, so there are four chromosomes (chr1S, chr2S, chr3S, chr4S), and the diploid species close to the heteromultiploid species to be split as the diploid reference species exists two chromosomes (rchr1S and rchr2S) In the chr1S, chr2S, chr3S, chr4S, there are 2 chromosomes as the homologous chromosomes of rchr1S, and 2 chromosomes as the homologous chromosomes of rchr2S.

[0068] The homologous chromosome group HG1..HGN obtaining module comprises: In some embodiments, the AN is the number of sources of different ancestors of the heteromultiploid.

[0069] It can be understood that the number of sources of different ancestors of the heteromultiploid can be obtained by dividing the number of chromosomes of the heteromultiploid by the number of diploid chromosomes.

[0070] It can also be understood that for each chromosome in the diploid, such as chromosome rchr1, which has AN corresponding homologous chromosomes in the allopolyploid species, the chromosome distance is much lower than that of non-homologous chromosomes.

[0071] Exemplarily, the SD values (SD 11 , SD 12 , SD 13 and SD 14 ) of rchr1S in the row of matrix 1 are sorted from small to large, and if the sorting result is SD 12 , SD 11 , SD 13 and SD 14 , it can be considered that SD 12 and SD 11 The chromosomes chr2S and chr1S in the corresponding columns in matrix 1 are the 2 homologous chromosomes corresponding to rchr1S.

[0072] Similarly, the SD values (SD 21 , SD 22 , SD 23 and SD 24 ) of rchr2S in the row of matrix 1 are sorted from small to large, and if the sorting result is SD 23 , SD 24 , SD 22 and SD 21 , it can be considered that SD 23 and SD 24 The chromosomes chr3S and chr4S in the corresponding columns in matrix 1 are the 2 homologous chromosomes corresponding to rchr2S.

[0073] In the sub-genome obtaining module: In some embodiments, taking the diploid reference species chromosomes rchr1…rchrN in HG1…HGN as the abscissa, the allopolyploid species chromosomes to be split in each homologous chromosome group are sorted according to the SD value from small to large to obtain a queue, and the chromosome with the highest SD value in each queue is selected to form sub-genome 1, the chromosome with the second highest SD value is selected to form sub-genome 2, and so on, the chromosome with the nth highest SD value is selected to form sub-genome n, until n equals AN, and finally the allopolyploid species to be split is split into AN sub-genomes.

[0074] Exemplarily, taking 1 to 25 chromosomes of a diploid reference species in 25 homologous chromosome groups (HG1…HG25) as the horizontal coordinates, the chromosomes of the heterologous tetraploid species to be split in each homologous chromosome group are sorted in ascending order of the SD values to obtain a queue, and the chromosome with the first highest SD value in each queue is selected to form subgenome 1 (subgenomel), and the chromosome with the second highest SD value is selected to form subgenome 2 (subgenomme2), thereby completing the subgenome splitting of the heterologous tetraploid species.

[0075] In a third aspect, the present application provides a computer device, comprising a memory and a processor, wherein the memory stores a computer program, and the computer program, when executed by the processor, causes the processor to perform the steps of the method for splitting a heterologous polyploid based on a perl language.

[0076] The computer device can be a desktop computer, a notebook computer, a palm computer, a cloud server, or the like. The computer device can interact with a user through a keyboard, a mouse, a remote controller, a touchpad, a voice control device, or the like.

[0077] The memory comprises at least one type of readable storage medium, such as a flash memory, a hard disk, a multimedia card, a card-type memory (e.g., an SD or D interface display memory, etc.), a random access memory (RAM), a static random access memory (SRAM), a read-only memory (ROM), an electrically erasable programmable read-only memory (EEPROM), a programmable read-only memory (PROM), a magnetic memory, a magnetic disk, an optical disk, or the like. In some embodiments, the memory can be an internal storage unit of the computer device, such as a hard disk or a memory of the computer device. In other embodiments, the memory can also be an external storage device of the computer device, such as a plug-in hard disk, a smart media card (SMC), a secure digital (SD) card, a flash card, or the like. Of course, the memory can also include both the internal storage unit and the external storage device of the computer device. In the present embodiment, the memory is usually used to store an operating system and various application software installed in the computer device, such as program codes of the method for splitting a heterologous polyploid based on a perl language, and the like. In addition, the memory can also be used to temporarily store various data that have been output or will be output.

[0078] The processor in some embodiments can be a central processing unit (CPU), a controller, a microcontroller, a microprocessor, or other data processing chip. The processor is generally used to control the overall operation of the computer device. In the present embodiment, the processor is used to run program codes or process data stored in the memory, for example, program codes of the method for splitting allopolyploid based on perl language.

[0079] In a fourth aspect, the present application provides a computer readable storage medium storing a computer program, which, when executed by a processor, causes the steps of the method for splitting allopolyploid based on perl language to be performed.

[0080] The computer readable storage medium stores an interface display program, which can be executed by at least one processor to cause the at least one processor to perform the steps of the method for splitting allopolyploid based on perl language as described above.

[0081] Application example The present application provides an example of splitting subgenome, please refer to Figure 2 In the family of Cyprinidae Carassius carassius (Carassius auratus), there are 50 chromosomes, while in the closely related diploid species Labeo rohita (Rhodeus sericeus), 25 chromosomes are assembled. By the method described in the present application, the corresponding Carassius auratus chromosomes of each chromosome in Rhodeus sericeus are found in turn. For example, the 1st chromosome of Rhodeus sericeus (x-axis label in the example figure) corresponds to the 6th and 7th chromosomes of Carassius auratus, and the 2nd chromosome of Rhodeus sericeus (x-axis label in the example figure) corresponds to the 12th and 20th chromosomes of Carassius auratus.

[0082] The smaller SD (standard deviation) values of the two corresponding chromosomes of Carassius auratus for each chromosome in Rhodeus sericeus are connected by a line to form a broken line. For example, the 7th, 20th, 1st, 26th, 5th, 17th, 3rd, 21st, 19th, 45th, 44th, 40th, 14th, 29th, 28th, 15th, 32nd, 23rd, 8th, 27th, 36th, 16th, 37th, 35th, and 43rd chromosomes of Carassius auratus are connected together to form subgenome 1. The remaining chromosomes form subgenome 2. In this way, the subgenome of Carassius auratus is successfully split into two sets (subgenome 1 and subgenome 2).

[0083] Figure 2In the figure, the x-axis represents the chromosome number of the rohu, and the y-axis represents the SD value. The line chart in the figure shows the SD value variation between each rohu chromosome and the corresponding crucian carp chromosome. This visualization method allows for a more intuitive understanding of the correspondence between chromosomes and the results of subgenome segmentation.

[0084] The method presented here matches crucian carp chromosomes with those of rohu through precise chromosome correspondence analysis. The relationship between the chromosomes is visually displayed using a line graph of SD values, successfully splitting the crucian carp subgenome into two sets. This method offers advantages such as high accuracy, excellent visualization, ease of use, strong applicability, reliable data support, and the ability to facilitate genomic research, providing an effective approach for subgenome splitting and related research.

[0085] The above is a detailed introduction to the method for splitting allopolyploids based on the Perl language provided in the embodiment. Specific examples are used in this article to illustrate the principles and implementation methods of the present application. The description of the above embodiments is only used to help understand the method of the present application and its core idea. At the same time, for those skilled in the art, according to the ideas of the present application, there may be changes in the specific implementation methods and application scope. In summary, the content of this specification should not be understood as limiting the present application.

Claims

1. A method for splitting allopolyploids based on the Perl language, characterized by: The steps include: Select a diploid species closely related to the allopolyploid species to be split as the diploid reference species; The length of each chromosome of the diploid reference species and the allopolyploid species to be split is calculated respectively to obtain the set rchr1S…rchrNS and the set chr1S…chrNS; Starting from the set rchr1S…rchrNS, traverse each set, take the intersection and union of the traversed set with chr1S…chrNS respectively, pair the intersection and union results one by one, and calculate the distance SD value between chromosomes to form a matrix; In the matrix, sort the SD values ​​of each row from small to large, and select the chromosomes in chr1S…chrNS corresponding to the corresponding number of columns according to the AN value, which are the homologous chromosomes corresponding to rchr1S…rchrNS. Construct the homologous chromosomes corresponding to each chromosome in rchr1S…rchrNS to form the homologous chromosome groups HG1..HGN; According to the homologous chromosome groups HG1..HGN, the allopolyploid to be split is split into AN subgenomes.

2. The method for splitting allopolyploids based on the Perl language according to claim 1, wherein: The chromosomes of the diploid reference species are numbered rchr1…rchrN, and the chromosomes of the allopolyploid species to be split are numbered chr1…chrN; the length of each chromosome of the diploid reference species is rchr1L…rchrNL, and the length of each chromosome of the allopolyploid species to be split is chr1L…chrNL; for each chromosome of the diploid reference species and the allopolyploid species to be split, a fragment K of length L is taken from the first site, rchrNL-L+1 fragments K are taken from each chromosome of the diploid reference species, and chrNL-L+1 fragments K are taken from each chromosome of the allopolyploid species to be split. The fragments K from the same chromosome of the diploid reference species are defined as the set rchr1S…rchrNS, and the fragments K from the same chromosome of the allopolyploid species to be split are defined as the set chr1S…chrNS, 17≤L≤63, and L is an odd number.

3. The method for splitting allopolyploids based on the Perl language according to claim 1, wherein: Take the intersection and union of the traversed set with chr1S…chrNS respectively, and obtain rchr1S_chr1S…rchr1S_chrNS…rchrNS_chrNS intersection results and rchr1S_chr1S…rchr1S_chrNS…rchrNS_chrNS union results. Pair the intersection and union results one by one, and calculate the distance SD between chromosomes through the number of elements IN in each intersection and the number of elements CN in the corresponding union.

4. The method for splitting allopolyploids based on the Perl language according to claim 3, characterized in that: SD=1-IN / CN.

5. The method for splitting allopolyploids based on the Perl language according to claim 1 or 4, characterized in that: SD is calculated using multi-process Perl language.

6. The method for splitting allopolyploids based on the Perl language according to claim 1, characterized in that: Forming matrix SD matrix , matrix SD matrix The rows represent rchr1S…rchrNS, and the matrix SD matrix The columns represent chr1S…chrNS, the matrix SD matrix The values ​​in represent the SD values ​​of the corresponding rows and columns.

7. The method for splitting allopolyploids based on the Perl language according to claim 1, characterized in that: Taking the diploid reference species chromosomes rchr1…rchrN in HG1…HGN as the horizontal coordinates, the chromosomes of the allopolyploid species to be split in each homologous chromosome group are sorted from small to large according to the SD value to obtain a queue. From each queue, the chromosome with the first highest SD value is selected to form subgenome 1, the chromosome with the second highest SD value is selected to form subgenome 2, and so on. The chromosome with the nth highest SD value forms subgenome n, until n equals AN. Finally, the allopolyploid species to be split is split into AN subgenomes, where AN is the number of sources of different ancestors of the allopolyploid.

8. Splitting allopolyploid system based on Perl language, characterized by: include: A diploid reference species acquisition module, used to select a diploid species closely related to the allopolyploid species to be split as a diploid reference species; A module for obtaining the set rchr1S…rchrNS and the set chr1S…chrNS, for respectively calculating the length of each chromosome of the diploid reference species and the allopolyploid species to be split, to obtain the set rchr1S…rchrNS and the set chr1S…chrNS; The matrix acquisition module is used to traverse each set starting from the set rchr1S…rchrNS, take the intersection and union of the traversed set with chr1S…chrNS respectively, pair the intersection and union results one by one, and calculate the distance SD value between chromosomes to form a matrix; The module for obtaining the homologous chromosome groups HG1..HGN is to sort the SD values ​​of each row in the matrix from small to large, and select the chromosomes in chr1S…chrNS corresponding to the corresponding number of columns according to the AN value, which are the homologous chromosomes corresponding to rchr1S…rchrNS. The homologous chromosomes corresponding to each chromosome in rchr1S…rchrNS are constructed to form the homologous chromosome groups HG1..HGN. The subgenome acquisition module is used to split the allopolyploid to be split into AN subgenomes according to the homologous chromosome groups HG1..HGN.

9. Computer device, characterized in that The device comprises a memory and a processor, wherein the memory stores a computer program, and when the computer program is executed by the processor, the processor executes the steps of the method according to any one of claims 1 to 7.

10. A computer-readable storage medium, characterized in that A computer program is stored, and when the computer program is executed by a processor, the processor is caused to perform the steps of the method according to any one of claims 1 to 7.

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