NDLI: Distribution rules of 8-mer spectra and characterization of evolution state in animal genome sequences

Content Provider	Springer Nature : BioMed Central
Author	Li, Xiaolong Li, Hong Yang, Zhenhua Wang, Lu
Abstract	Background Studying the composition rules and evolution mechanisms of genome sequences are core issues in the post-genomic era, and k-mer spectrum analysis of genome sequences is an effective means to solve this problem. Result We divided total 8-mers of genome sequences into 16 kinds of XY-type due to XY dinucleotides number in 8-mers. Previous works explored that the independent unimodal distributions observed only in three CG-type 8-mer spectra, while non-CG type 8-mer spectra have not the universal phenomenon from prokaryotes to eukaryotes. On this basis, we analyzed the distribution variation of non-CG type 8-mer spectra across 889 animal genome sequences. Following the evolutionary order of animals from primitive to more complex, we found that the spectrum distributions gradually transition from unimodal to tri-modal. The relative distance from the average frequency of each non-CG type 8-mers to the center frequency is different within a species and among different species. For the 8-mers contain CG dinucleotides, we further divided these into 16 subsets, where each 8-mer contains both CG and XY dinucleotides, called XY1_CG1 subsets. We found that the separability values of XY1_CG1 spectra are closely related to the evolution and specificity of animals. Considering the constraint of Chargaff’s second parity rule, we finally obtained 10 separability values as the feature set to characterize the evolution state of genome sequences. In order to verify the rationality of the feature set, we used 14 common classification algorithms to perform binary classification tests. The results showed that the accuracy (Acc) ranged between 98.70% and 83.88% among birds, other vertebrates and mammals. Conclusion We proposed a credible feature set to characterizes the evolution state of genomes and obtained satisfied results by the feature set on large scale classification of animals.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-024-10786-1.pdf
Ending Page	14
Page Count	14
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-024-10786-1
Journal	BMC Genomics
Issue Number	1
Volume Number	25
Language	English
Publisher	BioMed Central
Publisher Date	2024-09-12
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Animal genomes 8-mer spectra Feature set Evolution state of genome Species classification
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Exploring objective feature sets in constructing the evolution relationship of animal genome sequences

Evolution of mitochondrial genomes in Baikalian amphipods

Chloroplast genomes of five Oedogonium species: genome structure, phylogenetic analysis and adaptive evolution

Minimal regulatory spaces in yeast genomes

Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes

Evolution of myxozoan mitochondrial genomes: insights from myxobolids

Melanoma genome evolution across species

Complete sequences of organelle genomes from the medicinal plant Rhazya stricta(Apocynaceae) and contrasting patterns of mitochondrial genome evolution across asterids

Do the human gut metagenomic species possess the minimal set of core functionalities necessary for life?

Distribution rules of 8-mer spectra and characterization of evolution state in animal genome sequences

Similar Documents

Exploring objective feature sets in constructing the evolution relationship of animal genome sequences

Evolution of mitochondrial genomes in Baikalian amphipods

Chloroplast genomes of five Oedogonium species: genome structure, phylogenetic analysis and adaptive evolution

Minimal regulatory spaces in yeast genomes

Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes

Evolution of myxozoan mitochondrial genomes: insights from myxobolids

Melanoma genome evolution across species

Complete sequences of organelle genomes from the medicinal plant Rhazya stricta(Apocynaceae) and contrasting patterns of mitochondrial genome evolution across asterids

Do the human gut metagenomic species possess the minimal set of core functionalities necessary for life?

Distribution rules of 8-mer spectra and characterization of evolution state in animal genome sequences