Genome collinearity analysis illuminates the evolution of donkey chromosome 1 and horse chromosome 5 in perissodactyls: A comparative study
Abstract Background It is important to resolve the evolutionary history of species genomes as it has affected both genome organization and chromosomal architecture. The rapid innovation in sequencing technologies and the improvement in assembly algorithms have enabled the creation of highly contiguo...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2021-09-01
|
| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-021-07984-6 |
| _version_ | 1818738674017239040 |
|---|---|
| author | Shaohua Li Gaoping Zhao Hongmei Han Yunxia Li Jun Li Jinfeng Wang Guifang Cao Xihe Li |
| author_facet | Shaohua Li Gaoping Zhao Hongmei Han Yunxia Li Jun Li Jinfeng Wang Guifang Cao Xihe Li |
| author_sort | Shaohua Li |
| collection | DOAJ |
| description | Abstract Background It is important to resolve the evolutionary history of species genomes as it has affected both genome organization and chromosomal architecture. The rapid innovation in sequencing technologies and the improvement in assembly algorithms have enabled the creation of highly contiguous genomes. DNA Zoo, a global organization dedicated to animal conservation, offers more than 150 chromosome-length genome assemblies. This database has great potential in the comparative genomics field. Results Using the donkey (Equus asinus asinus, EAS) genome provided by DNA Zoo as an example, the scaffold N50 length and Benchmarking Universal Single-Copy Ortholog score reached 95.5 Mb and 91.6%, respectively. We identified the cytogenetic nomenclature, corrected the direction of the chromosome-length sequence of the donkey genome, analyzed the genome-wide chromosomal rearrangements between the donkey and horse, and illustrated the evolution of the donkey chromosome 1 and horse chromosome 5 in perissodactyls. Conclusions The donkey genome provided by DNA Zoo has relatively good continuity and integrity. Sequence-based comparative genomic analyses are useful for chromosome evolution research. Several previously published chromosome painting results can be used to identify the cytogenetic nomenclature and correct the direction of the chromosome-length sequence of new assemblies. Compared with the horse genome, the donkey chromosomes 1, 4, 20, and X have several obvious inversions, consistent with the results of previous studies. A 4.8 Mb inverted structure was first discovered in the donkey chromosome 25 and plains zebra chromosome 11. We speculate that the inverted structure and the tandem fusion of horse chromosome 31 and 4 are common features of non-caballine equids, which supports the correctness of the existing Equus phylogeny to an extent. |
| first_indexed | 2024-12-18T01:12:41Z |
| format | Article |
| id | doaj.art-91a4412554af4217bd83defa305afb97 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-18T01:12:41Z |
| publishDate | 2021-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-91a4412554af4217bd83defa305afb972022-12-21T21:26:02ZengBMCBMC Genomics1471-21642021-09-0122111010.1186/s12864-021-07984-6Genome collinearity analysis illuminates the evolution of donkey chromosome 1 and horse chromosome 5 in perissodactyls: A comparative studyShaohua Li0Gaoping Zhao1Hongmei Han2Yunxia Li3Jun Li4Jinfeng Wang5Guifang Cao6Xihe Li7Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia UniversityInner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic AnimalDepartment of Physical Education, Hohhot Minzu CollegeResearch Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia UniversityInner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic AnimalCollege of Basic Medicine, Inner Mongolia Medical UniversityCollege of Veterinary Science, Inner Mongolia Agricultural UniversityResearch Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia UniversityAbstract Background It is important to resolve the evolutionary history of species genomes as it has affected both genome organization and chromosomal architecture. The rapid innovation in sequencing technologies and the improvement in assembly algorithms have enabled the creation of highly contiguous genomes. DNA Zoo, a global organization dedicated to animal conservation, offers more than 150 chromosome-length genome assemblies. This database has great potential in the comparative genomics field. Results Using the donkey (Equus asinus asinus, EAS) genome provided by DNA Zoo as an example, the scaffold N50 length and Benchmarking Universal Single-Copy Ortholog score reached 95.5 Mb and 91.6%, respectively. We identified the cytogenetic nomenclature, corrected the direction of the chromosome-length sequence of the donkey genome, analyzed the genome-wide chromosomal rearrangements between the donkey and horse, and illustrated the evolution of the donkey chromosome 1 and horse chromosome 5 in perissodactyls. Conclusions The donkey genome provided by DNA Zoo has relatively good continuity and integrity. Sequence-based comparative genomic analyses are useful for chromosome evolution research. Several previously published chromosome painting results can be used to identify the cytogenetic nomenclature and correct the direction of the chromosome-length sequence of new assemblies. Compared with the horse genome, the donkey chromosomes 1, 4, 20, and X have several obvious inversions, consistent with the results of previous studies. A 4.8 Mb inverted structure was first discovered in the donkey chromosome 25 and plains zebra chromosome 11. We speculate that the inverted structure and the tandem fusion of horse chromosome 31 and 4 are common features of non-caballine equids, which supports the correctness of the existing Equus phylogeny to an extent.https://doi.org/10.1186/s12864-021-07984-6Chromosome-length genome assembliesComparative genomesChromosome evolutionDNA zoo |
| spellingShingle | Shaohua Li Gaoping Zhao Hongmei Han Yunxia Li Jun Li Jinfeng Wang Guifang Cao Xihe Li Genome collinearity analysis illuminates the evolution of donkey chromosome 1 and horse chromosome 5 in perissodactyls: A comparative study BMC Genomics Chromosome-length genome assemblies Comparative genomes Chromosome evolution DNA zoo |
| title | Genome collinearity analysis illuminates the evolution of donkey chromosome 1 and horse chromosome 5 in perissodactyls: A comparative study |
| title_full | Genome collinearity analysis illuminates the evolution of donkey chromosome 1 and horse chromosome 5 in perissodactyls: A comparative study |
| title_fullStr | Genome collinearity analysis illuminates the evolution of donkey chromosome 1 and horse chromosome 5 in perissodactyls: A comparative study |
| title_full_unstemmed | Genome collinearity analysis illuminates the evolution of donkey chromosome 1 and horse chromosome 5 in perissodactyls: A comparative study |
| title_short | Genome collinearity analysis illuminates the evolution of donkey chromosome 1 and horse chromosome 5 in perissodactyls: A comparative study |
| title_sort | genome collinearity analysis illuminates the evolution of donkey chromosome 1 and horse chromosome 5 in perissodactyls a comparative study |
| topic | Chromosome-length genome assemblies Comparative genomes Chromosome evolution DNA zoo |
| url | https://doi.org/10.1186/s12864-021-07984-6 |
| work_keys_str_mv | AT shaohuali genomecollinearityanalysisilluminatestheevolutionofdonkeychromosome1andhorsechromosome5inperissodactylsacomparativestudy AT gaopingzhao genomecollinearityanalysisilluminatestheevolutionofdonkeychromosome1andhorsechromosome5inperissodactylsacomparativestudy AT hongmeihan genomecollinearityanalysisilluminatestheevolutionofdonkeychromosome1andhorsechromosome5inperissodactylsacomparativestudy AT yunxiali genomecollinearityanalysisilluminatestheevolutionofdonkeychromosome1andhorsechromosome5inperissodactylsacomparativestudy AT junli genomecollinearityanalysisilluminatestheevolutionofdonkeychromosome1andhorsechromosome5inperissodactylsacomparativestudy AT jinfengwang genomecollinearityanalysisilluminatestheevolutionofdonkeychromosome1andhorsechromosome5inperissodactylsacomparativestudy AT guifangcao genomecollinearityanalysisilluminatestheevolutionofdonkeychromosome1andhorsechromosome5inperissodactylsacomparativestudy AT xiheli genomecollinearityanalysisilluminatestheevolutionofdonkeychromosome1andhorsechromosome5inperissodactylsacomparativestudy |