Academic Journal
A telomere-to-telomere Eucalyptus regnans genome: unveiling haplotype variance in structure and genes within one of the world’s tallest trees
| Title: | A telomere-to-telomere Eucalyptus regnans genome: unveiling haplotype variance in structure and genes within one of the world’s tallest trees |
|---|---|
| Authors: | Scott Ferguson, Yoav D Bar-Ness, Justin Borevitz, Ashley Jones |
| Source: | BMC Genomics, Vol 25, Iss 1, Pp 1-12 (2024) |
| Publisher Information: | BMC, 2024. |
| Publication Year: | 2024 |
| Collection: | LCC:Biotechnology LCC:Genetics |
| Subject Terms: | Eucalyptus regnans, Centurion, Diploid genome assembly, Haplotype-resolved, Telomere-to-telomere, Biotechnology, TP248.13-248.65, Genetics, QH426-470 |
| More Details: | Abstract Background Eucalyptus regnans (Mountain Ash) is an Australian native giant tree species which form forests that are among the highest known carbon-dense biomasses in the world. To enhance genomic studies in this ecologically important species, we assembled a high-quality, mostly telomere-to-telomere complete, chromosome-level, haplotype-resolved reference genome. We sampled a single tree, the Centurion, which is currently a contender for the world’s tallest flowering plant. Results Using long-read sequencing data (PacBio HiFi, Oxford Nanopore ultra-long reads) and chromosome conformation capture data (Hi-C), we assembled the most contiguous and complete Eucalyptus reference genome to date. For each haplotype, we observed contig N50s exceeding 36 Mbp, scaffold N50s exceeding 43 Mbp, and genome BUSCO completeness exceeding 99%. The assembled genome revealed extensive structural variations between the two haplotypes, consisting mostly of insertions, deletions, duplications and translocations. Analysis of gene content revealed haplotype-specific genes, which were enriched in functional categories related to transcription, energy production and conservation. Additionally, many genes reside within structurally rearranged regions, particularly duplications, suggesting that haplotype-specific variation may contribute to environmental adaptation in the species. Conclusions Our study provides a foundation for future research into E. regnans environmental adaptation, and the high-quality genome will be a powerful resource for conservation of carbon-dense giant tree forests. |
| Document Type: | article |
| File Description: | electronic resource |
| Language: | English |
| ISSN: | 1471-2164 |
| Relation: | https://doaj.org/toc/1471-2164 |
| DOI: | 10.1186/s12864-024-10810-4 |
| Access URL: | https://doaj.org/article/1c3a1a2d744b470cb822cd7a79cd0de3 |
| Accession Number: | edsdoj.1c3a1a2d744b470cb822cd7a79cd0de3 |
| Database: | Directory of Open Access Journals |
| Full text is not displayed to guests. | Login for full access. |
| ISSN: | 14712164 |
|---|---|
| DOI: | 10.1186/s12864-024-10810-4 |
| Published in: | BMC Genomics |
| Language: | English |