Transcriptome sequencing of multiple species of Rosaceae. Rosaceae

Fruits are the defining feature of angiosperms, likely have contributed to angiosperm successes by protecting and dispersing seeds, and provide foods to humans and other animals, with many morphological types and important ecological and agricultural implications. Rosaceae is a family with ~3000 species and an extraordinary spectrum of distinct fruits, including fleshy peach, apple, and strawberry prized by their consumers, as well as dry achenetum and follicetum with features facilitating seed dispersal, excellent for studying fruit evolution. To address Rosaceae fruit evolution and other questions, we generated 125 new transcriptomic and genomic datasets and identified hundreds of nuclear genes to reconstruct a well-resolved Rosaceae phylogeny with highly supported monophyly of all subfamilies and tribes. Molecular clock analysis revealed an estimated age of ~101.6Ma for crown Rosaceae and divergence times of tribes and genera, providing a geological and climate context for fruit evolution. Phylogenomic analysis yielded strong evidence for numerous whole genome duplications (WGDs), supporting the hypothesis that the apple tribe had a WGD and revealing another one shared by fleshy fruit-bearing members of this tribe, with moderate support for WGDs in the peach tribe and other groups. Ancestral character reconstruction for fruit types supports independent origins of fleshy fruits from dry-fruit ancestors, including the evolution of drupes (e.g., peach) and pomes (e.g., apple) from follicetum, and drupetum (raspberry and blackberry) from achenetum. We propose that WGDs and environmental factors, including animals, contributed to the evolution of the many fruits in Rosaceae, which provide a foundation for understanding fruit evolution.果实是被子植物（angiosperms）的标志性特征，其通过保护与传播种子助力被子植物繁衍兴盛，同时为人类及其他动物提供食物来源；果实拥有多样的形态类型，在生态学与农业领域均具有重要研究价值。 蔷薇科（Rosaceae）包含约3000个物种，拥有种类极为丰富的果实类型：既有深受消费者青睐的肉质果实，如桃、苹果、草莓；也包括具备种子传播优势的干燥类果实，如瘦果群（achenetum）、蓇葖果群（follicetum），是研究果实演化的绝佳材料。 为解析蔷薇科果实演化等相关科学问题，本研究新增构建了125套转录组与基因组数据集，并筛选出数百个核基因位点，以此重建了分辨率极高的蔷薇科系统发育树，所有亚科与族的单系性均得到了高度支持。 分子钟（molecular clock）分析显示，冠群蔷薇科的起源时间约为1.016亿年（101.6Ma），同时明确了各族与属的分化时间，为果实演化研究提供了地质与气候背景参考。 系统基因组学分析为多次全基因组复制（whole genome duplications, WGD）事件提供了强有力的证据：支持苹果族曾发生全基因组复制的假说，并揭示该族肉质果实类群共享了另一次全基因组复制事件；同时为桃族及其他类群的全基因组复制事件提供了中等强度的支持证据。 果实类型的祖先性状重建结果表明，肉质果实独立起源于干燥果实的祖先类群：核果（drupes）如桃、梨果（pomes）如苹果由蓇葖果群演化而来，聚合核果（drupetum）如树莓、黑莓则由瘦果群演化而来。 本研究提出，全基因组复制事件与包括动物在内的环境因素共同推动了蔷薇科多样果实的演化，这一结论为理解果实演化机制奠定了重要基础。