Detailed Record
Haplotype-resolved genome assembly and resequencing analysis provide insights into genome evolution and allelic imbalance in Pinus densiflora
| Abstract | Haplotype-level allelic characterization facilitates research on the functional, evolutionary and breeding-related features of extremely large and complex plant genomes. We report a 21.7-Gb chromosome-level haplotype-resolved assembly in Pinus densiflora. We found genome rearrangements involving translocations and inversions between chromosomes 1 and 3 of Pinus species and a proliferation of specific long terminal repeat (LTR) retrotransposons (LTR-RTs) in P. densiflora. Evolutionary analyses illustrated that tandem and LTR-RT-mediated duplications led to an increment of transcription factor (TF) genes in P. densiflora. The haplotype sequence comparison showed allelic imbalances, including presence–absence variations of genes (PAV genes) and their functional contributions to flowering and abiotic stress-related traits in P. densiflora. Allele-aware resequencing analysis revealed PAV gene diversity across P. densiflora accessions. Our study provides insights into key mechanisms underlying the evolution of genome structure, LTR-RTs and TFs within the Pinus lineage as well as allelic imbalances and diversity across P. densiflora. |
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| Authors |
Min‐Jeong Jang  , Hye Jeong Cho , Young-Soo Park , Hye‐Young Lee , Eun‐Kyung Bae , Seungmee Jung  , Hongshi Jin , Jongchan Woo , Eunsook Park , Seo‐Jin Kim , Jinwook Choi , Geun Young Chae , Ji‐Yoon Guk , Do Yeon Kim , Sun-Hyung Kim , Min‐Jeong Kang , Hyoshin Lee , Kyeong-Seong Cheon , In Sik Kim , Yong‐Min Kim , Myung‐Shin Kim , Jae‐Heung Ko , Kyu‐Suk Kang , Doil Choi , Eung‐Jun Park , Seungill Kim
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| Journal Info | Nature Portfolio | Nature Genetics , vol: 56 , iss: 11 , pages: 2551 - 2561 |
| Publication Date | 10/20/2024 |
| ISSN | 1061-4036 |
Type |
article |
| Open Access |
closed
|
| DOI | https://doi.org/10.1038/s41588-024-01944-y |
| Keywords |
Pinus densiflora (Score: 0.8300762) |