Chromosome-level assembly of Pseudopodoces humilis genome: A resource for avian evolutionary studies
Abstract Pseudopodoces humilis is a small passerine bird predominantly found in the mid-latitude regions of the Tibetan Plateau in Asia. A chromosome-level reference genome assembly for P. humilis was generated using PacBio CLR with Hi-C. The final genome assembly spans approximately 1.096 Gb, consi...
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Nature Portfolio
2025-05-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-05171-w |
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| author | Xinwei Da Yanrui Liu Xun Jin Xin Lu |
| author_facet | Xinwei Da Yanrui Liu Xun Jin Xin Lu |
| author_sort | Xinwei Da |
| collection | DOAJ |
| description | Abstract Pseudopodoces humilis is a small passerine bird predominantly found in the mid-latitude regions of the Tibetan Plateau in Asia. A chromosome-level reference genome assembly for P. humilis was generated using PacBio CLR with Hi-C. The final genome assembly spans approximately 1.096 Gb, consisting of 1,968 contigs with a Contig N50 of 32.246 Mb, and was evaluated to be 95.60% complete using BUSCO. Hi-C chromosome mapping resulted in 33 chromosome sequences, which enabled the ordering and orientation of 329 contigs, with chromosome lengths ranging from 2.08 Mb to 152.13 Mb, covering 95.85% of the total genome sequence. Repetitive sequences comprised 144.91 Mb of the genome. A total of 381 tRNA, 507 non-coding RNA (ncRNA), and 205 rRNA were identified. In addition, we identified 17,108 protein-coding genes and 29,473 proteins, comprising a total of 17,236,726 amino acids. This high-quality genome assembly provides a strong genomic foundation for exploring critical questions in evolutionary genetics, phylogenomics, and the molecular mechanisms of adaptation - key areas for understanding biodiversity and species resilience amidst changing environments. |
| format | Article |
| id | doaj-art-4808849b2b1e4fd18d294efc766e95f4 |
| institution | Kabale University |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
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| series | Scientific Data |
| spelling | doaj-art-4808849b2b1e4fd18d294efc766e95f42025-08-20T03:53:57ZengNature PortfolioScientific Data2052-44632025-05-011211910.1038/s41597-025-05171-wChromosome-level assembly of Pseudopodoces humilis genome: A resource for avian evolutionary studiesXinwei Da0Yanrui Liu1Xun Jin2Xin Lu3Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau of the Ministry of Education, College of Life Sciences, Wuhan UniversityKey Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau of the Ministry of Education, College of Life Sciences, Wuhan UniversityDepartment of Ecology, College of Life Sciences, Henan Normal UniversityDepartment of Ecology, College of Life Sciences, Henan Normal UniversityAbstract Pseudopodoces humilis is a small passerine bird predominantly found in the mid-latitude regions of the Tibetan Plateau in Asia. A chromosome-level reference genome assembly for P. humilis was generated using PacBio CLR with Hi-C. The final genome assembly spans approximately 1.096 Gb, consisting of 1,968 contigs with a Contig N50 of 32.246 Mb, and was evaluated to be 95.60% complete using BUSCO. Hi-C chromosome mapping resulted in 33 chromosome sequences, which enabled the ordering and orientation of 329 contigs, with chromosome lengths ranging from 2.08 Mb to 152.13 Mb, covering 95.85% of the total genome sequence. Repetitive sequences comprised 144.91 Mb of the genome. A total of 381 tRNA, 507 non-coding RNA (ncRNA), and 205 rRNA were identified. In addition, we identified 17,108 protein-coding genes and 29,473 proteins, comprising a total of 17,236,726 amino acids. This high-quality genome assembly provides a strong genomic foundation for exploring critical questions in evolutionary genetics, phylogenomics, and the molecular mechanisms of adaptation - key areas for understanding biodiversity and species resilience amidst changing environments.https://doi.org/10.1038/s41597-025-05171-w |
| spellingShingle | Xinwei Da Yanrui Liu Xun Jin Xin Lu Chromosome-level assembly of Pseudopodoces humilis genome: A resource for avian evolutionary studies Scientific Data |
| title | Chromosome-level assembly of Pseudopodoces humilis genome: A resource for avian evolutionary studies |
| title_full | Chromosome-level assembly of Pseudopodoces humilis genome: A resource for avian evolutionary studies |
| title_fullStr | Chromosome-level assembly of Pseudopodoces humilis genome: A resource for avian evolutionary studies |
| title_full_unstemmed | Chromosome-level assembly of Pseudopodoces humilis genome: A resource for avian evolutionary studies |
| title_short | Chromosome-level assembly of Pseudopodoces humilis genome: A resource for avian evolutionary studies |
| title_sort | chromosome level assembly of pseudopodoces humilis genome a resource for avian evolutionary studies |
| url | https://doi.org/10.1038/s41597-025-05171-w |
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