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Keywords {🔍}

genome, giant, panda, chromosome, pubmed, genomes, cat, article, dog, google, scholar, ebrs, assembly, cas, evolution, chromosomes, chromosomelevel, genes, gene, genomics, carnivora, file, additional, table, sequencing, central, study, total, identified, analysis, results, scaffolds, reads, data, events, based, synteny, showed, published, comparative, species, size, content, studies, assemblies, largescale, regions, functional, located, conservation,

Topics {✒️}

evolutionary breakpoint region high-quality chromosome-level genome high-throughput linked-read sequencing full-length protein-coding genes fengtang yang chromosome-level genome assembly chromosome-level draft assembly everts-van der wind cn/search illumina x-ten platform high-quality draft genome cross-species chromosome painting published chromosome-level dog article download pdf large-scale hsbs junctions detecting large-scale hsbs build large-scale hsbs chromosome-level carnivora genomes chromosome-level giant panda high-purity sort option mate-pair reads data producing high-quality genomes chromosome-level reference genomes 10x genomics linked-reads yibo hu mate-pair sequencing reads determined large-scale hsbs linked-read sequencing combined single linked-read library evolutionary breakpoint regions orthologous protein-coding genes sweet-receptor gene accounts form large-scale hsbs reference-assisted chromosome assembly supplementary tables s4-s6 150 bp paired-end reads original author reference-assisted assembly strategies de novo predicted sweet-tasting compounds compared chromosome-level assembly chromosome-level genome genome-database management tool identified large-scale hsbs full access flow-sorting sequencing reads previously reported assemblies paired-end reads author correspondence de novo assembly

Questions {❓}

• Is mammalian chromosomal evolution driven by regions of genome fragility?
• Cn/search?

Schema {🗺️}

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         headline:Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution
         description: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. 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. 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.
         datePublished:2019-12-06T00:00:00Z
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      headline:Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution
      description: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. 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. 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.
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         Chromosome-level genome
         Chromosome evolution
         Evolutionary breakpoint region
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         Animal Genetics and Genomics
         Human Genetics
         Plant Genetics and Genomics
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         Evolutionary Biology
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