NDLI: A telomere-to-telomere Eucalyptus regnans genome: unveiling haplotype variance in structure and genes within one of the world’s tallest trees

Content Provider	Springer Nature : BioMed Central
Author	Ferguson, Scott Bar-Ness, Yoav D Borevitz, Justin Jones, Ashley
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.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-024-10810-4.pdf
Ending Page	12
Page Count	12
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-024-10810-4
Journal	BMC Genomics
Issue Number	1
Volume Number	25
Language	English
Publisher	BioMed Central
Publisher Date	2024-09-30
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Eucalyptus regnans Centurion Diploid genome assembly Haplotype-resolved Telomere-to-telomere
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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Correction: A telomere-to-telomere Eucalyptus regnans genome: unveiling haplotype variance in structure and genes within one of the world’s tallest trees

A diploid chromosome-level genome of Eucalyptus regnans: unveiling haplotype variance in structure and genes within one of the world’s tallest trees

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phasebook: haplotype-aware de novo assembly of diploid genomes from long reads

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A telomere-to-telomere Eucalyptus regnans genome: unveiling haplotype variance in structure and genes within one of the world’s tallest trees

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Correction: A telomere-to-telomere Eucalyptus regnans genome: unveiling haplotype variance in structure and genes within one of the world’s tallest trees

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A telomere-to-telomere Eucalyptus regnans genome: unveiling haplotype variance in structure and genes within one of the world’s tallest trees