单倍型解析的基因组组装和重测序分析为深入了解密花松树的基因组进化和等位

单倍型解析的基因组组装和重测序分析为深入了解密花松树的基因组进化和等位基因失衡提供了线索

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

摘要

单倍型水平的等位基因特征有助于研究超大型复杂植物基因组的功能、进化和育种相关特征。我们报告了一个 21.7 千兆字节的染色体级等位基因组装结果。我们发现了松属植物 1 号染色体和 3 号染色体之间涉及易位和倒位的基因组重排，以及特定长末端重复（LTR）反转座子（LTR-RTs）的扩散。进化分析表明，串联和 LTR-RT 介导的复制导致了 P. densiflora 中转录因子（TF）基因的增加。单倍型序列比较显示了等位基因的不平衡，包括基因（PAV基因）的存在-不存在变异，以及它们对丹顶鹤开花和非生物胁迫相关性状的功能贡献。等位基因感知的重测序分析揭示了不同登喜路品种中 PAV 基因的多样性。我们的研究深入揭示了松科植物基因组结构、LTR-RT 和 TFs 演化的关键机制，以及等位基因的不平衡和松科植物的多样性。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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

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. Chromosome-scale and haplotype-resolved assembly of Pinus densiflora sheds light on Pinus-specific genome enlargement. Comparison between haplotypes and resequencing of 30 wild accessions show allelic imbalance with roles in flowering regulation and stress resistance.

相关知识

单倍型解析的基因组组装和重测序分析为深入了解密花松树的基因组进化和等位
文献解读｜单倍型基因组和重测序揭示现代月季起源和育种历史
我国科研团队首次破译中国樱桃单倍型基因组
单倍型解析中国月季基因组揭示重要观赏性状的遗传基础
园艺作物基因组测序研究进展
JGG | 花楸树基因组的组装和转录组分析为花楸树种群进化和叶片晒伤反应提供新见解
两个早花樱桃（Cerasus × kanzakura）品种“河津樱”和“热海樱”的基因组测序和分析,DNA Research
园林学院科研团队完成紫薇基因组组装和群体重测序
分析染色体级别的基因组装配揭示了六倍体栽培菊花的起源和进化
两个单倍型解析的基因组揭示了大叶绣球花的重要花朵特征以及对紫苑进化的见解,Horticulture Research

网址: 单倍型解析的基因组组装和重测序分析为深入了解密花松树的基因组进化和等位 https://www.huajiangbk.com/newsview1733650.html