韩国首尔大学Seungill Kim等研究人员合作发现，单倍型解析基因组组装和重测序分析为赤松的基因组演化和等位基因不平衡提供见解。该研究于2024年10月20日在线发表于国际一流学术期刊《自然—遗传学》。

研究人员报告了赤松（Pinus densiflora）21.7 Gb染色体水平的单倍型解析组装。研究人员发现物种间染色体1和3之间存在基因组重排，包括易位和倒位，并且P. densiflora中特定的长末端重复（LTR）逆转录转座子（LTR-RT）繁殖增加。

演化分析表明，串联重复和LTR-RT介导的复制导致P. densiflora中转录因子（TF）基因的增加。单倍型序列比较显示出等位基因不平衡，包括基因的存在–缺失变异（PAV基因）及其对P. densiflora中开花和抗逆境性状的功能贡献。

等位基因识别的重测序分析揭示了P. densiflora不同种质中的PAV基因多样性。该研究为揭示松属物种中基因组结构、LTR-RT和TF的演化机制以及P. densiflora中的等位基因不平衡和多样性提供了见解。

研究人员表示，单倍型水平的等位基因表征有助于研究极其庞大和复杂的植物基因组的功能、演化和育种相关特征。

附：英文原文

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

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

Issue&Volume: 2024-10-20

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.

DOI: 10.1038/s41588-024-01944-y

Source: https://www.nature.com/articles/s41588-024-01944-y