Haplotype-resolved genome assembly and resequencing analysis provide insights into genome evolution and allelic imbalance in Pinus densiflora

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; Jin Wook 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

doi:10.1038/s41588-024-01944-y

Haplotype-resolved genome assembly and resequencing analysis provide insights into genome evolution and allelic imbalance in Pinus densiflora

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, Jin Wook 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 KimMyung Shin Kim, Jae Heung Ko, Kyu Suk Kang, Doil Choi, Eung Jun Park, Seungill Kim

Department of Environmental Horticulture

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	2551-2561
Number of pages	11
Journal	Nature Genetics
Volume	56
Issue number	11
DOIs	https://doi.org/10.1038/s41588-024-01944-y
State	Published - Nov 2024

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Jang, M. J., Cho, H. J., Park, Y. S., Lee, H. Y., Bae, E. K., Jung, S., Jin, H., Woo, J., Park, E., Kim, S. J., Choi, J. W., Chae, G. Y., Guk, J. Y., Kim, D. Y., Kim, S. H., Kang, M. J., Lee, H., Cheon, K. S., Kim, I. S., ... Kim, S. (2024). Haplotype-resolved genome assembly and resequencing analysis provide insights into genome evolution and allelic imbalance in Pinus densiflora. Nature Genetics, 56(11), 2551-2561. https://doi.org/10.1038/s41588-024-01944-y

@article{98634cb209a04bf9ac8a6b5c22fa6772,

title = "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.",

author = "Jang, {Min Jeong} and Cho, {Hye Jeong} and Park, {Young Soo} and Lee, {Hye Young} and Bae, {Eun Kyung} and Seungmee Jung and Hongshi Jin and Jongchan Woo and Eunsook Park and Kim, {Seo Jin} and Choi, {Jin Wook} and Chae, {Geun Young} and Guk, {Ji Yoon} and Kim, {Do Yeon} and Kim, {Sun Hyung} and Kang, {Min Jeong} and Hyoshin Lee and Cheon, {Kyeong Seong} and Kim, {In Sik} and Kim, {Yong Min} and Kim, {Myung Shin} and Ko, {Jae Heung} and Kang, {Kyu Suk} and Doil Choi and Park, {Eung Jun} and Seungill Kim",

note = "Publisher Copyright: {\textcopyright} The Author(s), under exclusive licence to Springer Nature America, Inc. 2024.",

year = "2024",

month = nov,

doi = "10.1038/s41588-024-01944-y",

language = "English",

volume = "56",

pages = "2551--2561",

journal = "Nature Genetics",

issn = "1061-4036",

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Jang, MJ, Cho, HJ, Park, YS, Lee, HY, Bae, EK, Jung, S, Jin, H, Woo, J, Park, E, Kim, SJ, Choi, JW, Chae, GY, Guk, JY, Kim, DY, Kim, SH, Kang, MJ, Lee, H, Cheon, KS, Kim, IS, Kim, YM, Kim, MS, Ko, JH, Kang, KS, Choi, D, Park, EJ & Kim, S 2024, 'Haplotype-resolved genome assembly and resequencing analysis provide insights into genome evolution and allelic imbalance in Pinus densiflora', Nature Genetics, vol. 56, no. 11, pp. 2551-2561. https://doi.org/10.1038/s41588-024-01944-y

TY - JOUR

T1 - Haplotype-resolved genome assembly and resequencing analysis provide insights into genome evolution and allelic imbalance in Pinus densiflora

AU - Jang, Min Jeong

AU - Cho, Hye Jeong

AU - Park, Young Soo

AU - Lee, Hye Young

AU - Bae, Eun Kyung

AU - Jung, Seungmee

AU - Jin, Hongshi

AU - Woo, Jongchan

AU - Park, Eunsook

AU - Kim, Seo Jin

AU - Choi, Jin Wook

AU - Chae, Geun Young

AU - Guk, Ji Yoon

AU - Kim, Do Yeon

AU - Kim, Sun Hyung

AU - Kang, Min Jeong

AU - Lee, Hyoshin

AU - Cheon, Kyeong Seong

AU - Kim, In Sik

AU - Kim, Yong Min

AU - Kim, Myung Shin

AU - Ko, Jae Heung

AU - Kang, Kyu Suk

AU - Choi, Doil

AU - Park, Eung Jun

AU - Kim, Seungill

PY - 2024/11

Y1 - 2024/11

N2 - 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.

AB - 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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U2 - 10.1038/s41588-024-01944-y

DO - 10.1038/s41588-024-01944-y

M3 - Article

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AN - SCOPUS:85207019674

SN - 1061-4036

VL - 56

SP - 2551

EP - 2561

JO - Nature Genetics

JF - Nature Genetics

IS - 11

ER -

Haplotype-resolved genome assembly and resequencing analysis provide insights into genome evolution and allelic imbalance in Pinus densiflora

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