Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution
Abstract Background Chromosome evolution is an important driver of speciation and species evolution. Previous studies have detected chromosome rearrangement events among different Carnivora species using chromosome painting strategies. However, few of these studies have focused on chromosome evoluti...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2019-12-01
|
| Series: | Genome Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13059-019-1889-7 |
| _version_ | 1818353245626564608 |
|---|---|
| author | Huizhong Fan Qi Wu Fuwen Wei Fengtang Yang Bee Ling Ng Yibo Hu |
| author_facet | Huizhong Fan Qi Wu Fuwen Wei Fengtang Yang Bee Ling Ng Yibo Hu |
| author_sort | Huizhong Fan |
| collection | DOAJ |
| description | Abstract Background Chromosome evolution is an important driver of speciation and species evolution. Previous studies have detected chromosome rearrangement events among different Carnivora species using chromosome painting strategies. However, few of these studies have focused on chromosome evolution at a nucleotide resolution due to the limited availability of chromosome-level Carnivora genomes. Although the de novo genome assembly of the giant panda is available, current short read-based assemblies are limited to moderately sized scaffolds, making the study of chromosome evolution difficult. Results Here, we present a chromosome-level giant panda draft genome with a total size of 2.29 Gb. Based on the giant panda genome and published chromosome-level dog and cat genomes, we conduct six large-scale pairwise synteny alignments and identify evolutionary breakpoint regions. Interestingly, gene functional enrichment analysis shows that for all of the three Carnivora genomes, some genes located in evolutionary breakpoint regions are significantly enriched in pathways or terms related to sensory perception of smell. In addition, we find that the sweet receptor gene TAS1R2, which has been proven to be a pseudogene in the cat genome, is located in an evolutionary breakpoint region of the giant panda, suggesting that interchromosomal rearrangement may play a role in the cat TAS1R2 pseudogenization. Conclusions We show that the combined strategies employed in this study can be used to generate efficient chromosome-level genome assemblies. Moreover, our comparative genomics analyses provide novel insights into Carnivora chromosome evolution, linking chromosome evolution to functional gene evolution. |
| first_indexed | 2024-12-13T19:06:28Z |
| format | Article |
| id | doaj.art-296ceaf25020496097f6111729cec984 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-13T19:06:28Z |
| publishDate | 2019-12-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-296ceaf25020496097f6111729cec9842022-12-21T23:34:31ZengBMCGenome Biology1474-760X2019-12-0120111210.1186/s13059-019-1889-7Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolutionHuizhong Fan0Qi Wu1Fuwen Wei2Fengtang Yang3Bee Ling Ng4Yibo Hu5CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of SciencesCAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of SciencesCAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of SciencesWellcome Sanger Institute, Wellcome Genome CampusWellcome Sanger Institute, Wellcome Genome CampusCAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of SciencesAbstract Background Chromosome evolution is an important driver of speciation and species evolution. Previous studies have detected chromosome rearrangement events among different Carnivora species using chromosome painting strategies. However, few of these studies have focused on chromosome evolution at a nucleotide resolution due to the limited availability of chromosome-level Carnivora genomes. Although the de novo genome assembly of the giant panda is available, current short read-based assemblies are limited to moderately sized scaffolds, making the study of chromosome evolution difficult. Results Here, we present a chromosome-level giant panda draft genome with a total size of 2.29 Gb. Based on the giant panda genome and published chromosome-level dog and cat genomes, we conduct six large-scale pairwise synteny alignments and identify evolutionary breakpoint regions. Interestingly, gene functional enrichment analysis shows that for all of the three Carnivora genomes, some genes located in evolutionary breakpoint regions are significantly enriched in pathways or terms related to sensory perception of smell. In addition, we find that the sweet receptor gene TAS1R2, which has been proven to be a pseudogene in the cat genome, is located in an evolutionary breakpoint region of the giant panda, suggesting that interchromosomal rearrangement may play a role in the cat TAS1R2 pseudogenization. Conclusions We show that the combined strategies employed in this study can be used to generate efficient chromosome-level genome assemblies. Moreover, our comparative genomics analyses provide novel insights into Carnivora chromosome evolution, linking chromosome evolution to functional gene evolution.https://doi.org/10.1186/s13059-019-1889-7Giant pandaChromosome-level genomeChromosome evolutionEvolutionary breakpoint regionCarnivora |
| spellingShingle | Huizhong Fan Qi Wu Fuwen Wei Fengtang Yang Bee Ling Ng Yibo Hu Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution Genome Biology Giant panda Chromosome-level genome Chromosome evolution Evolutionary breakpoint region Carnivora |
| title | Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution |
| title_full | Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution |
| title_fullStr | Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution |
| title_full_unstemmed | Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution |
| title_short | Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution |
| title_sort | chromosome level genome assembly for giant panda provides novel insights into carnivora chromosome evolution |
| topic | Giant panda Chromosome-level genome Chromosome evolution Evolutionary breakpoint region Carnivora |
| url | https://doi.org/10.1186/s13059-019-1889-7 |
| work_keys_str_mv | AT huizhongfan chromosomelevelgenomeassemblyforgiantpandaprovidesnovelinsightsintocarnivorachromosomeevolution AT qiwu chromosomelevelgenomeassemblyforgiantpandaprovidesnovelinsightsintocarnivorachromosomeevolution AT fuwenwei chromosomelevelgenomeassemblyforgiantpandaprovidesnovelinsightsintocarnivorachromosomeevolution AT fengtangyang chromosomelevelgenomeassemblyforgiantpandaprovidesnovelinsightsintocarnivorachromosomeevolution AT beelingng chromosomelevelgenomeassemblyforgiantpandaprovidesnovelinsightsintocarnivorachromosomeevolution AT yibohu chromosomelevelgenomeassemblyforgiantpandaprovidesnovelinsightsintocarnivorachromosomeevolution |