Data from: A phylotranscriptomic analysis of gene family expansion and evolution in the largest order of pleurocarpous mosses (Hypnales, Bryophyta)

The pleurocarpous mosses (i.e., Hypnanae) are a species-rich group of land plants comprising about 6,000 species that share the development of female sex organs on short lateral branches, a derived trait within mosses. Many of the families within Hypnales, the largest order of pleurocarpous mosses, trace their origin to a rapid radiation less than 100 million years ago, just after the rise of the angiosperms. As a result, the phylogenetic resolution among families of Hypnales, necessary to test evolutionary hypotheses, has proven difficult using one or few loci. We present the first phylogenetic inference from high-throughput sequence data (transcriptome sequences) for pleurocarpous mosses. To test hypotheses of gene family evolution, we built a species tree of 21 pleurocarpous and six acrocarpous mosses using over one million sites from 659 orthologous genes. We used the species tree to investigate the genomic consequences of the shift to pleurocarpy and to identify whether patterns common to other plant radiations (gene family expansion, whole genome duplication, or changes in the molecular signatures of selection) could be observed. We found that roughly six percent of all gene families have expanded in the pleurocarpous mosses, relative to acrocarpous mosses. These gene families are enriched for several gene ontology (GO) terms, including interaction with other organisms. The increase in copy number coincident with the radiation of Hypnales suggests that a process such as whole genome duplication or a burst of small-scale duplications occurred during the diversification. In over 500 gene families we found evidence of a reduction in purifying selection. These gene families are enriched for several terms in the GO hierarchy related to “tRNA metabolic process.” Our results reveal candidate genes and pathways that may be associated with the transition to pleurocarpy, illustrating the utility of phylotranscriptomics for the study of molecular evolution in non-model species.侧蒴藓类（pleurocarpous mosses，即灰藓亚目Hypnanae）是一类物种丰富的陆生植物类群，共计包含约6000个物种，其共同衍征为雌性生殖器官着生于短侧枝之上，该性状是藓类植物中的衍生演化特征。灰藓目（Hypnales）作为侧蒴藓类中最大的目，其多数科的起源可追溯至被子植物兴起后不足1亿年前的一次快速辐射事件。此前，仅依靠单个或少量基因座难以解析灰藓目各科间的系统发育关系，而这正是检验演化假说的必要前提。本研究首次利用高通量测序数据——转录组序列（transcriptome sequences），对侧蒴藓类开展系统发育推断。为检验基因家族演化相关假说，我们基于659个同源基因（orthologous genes）的超百万个变异位点，构建了包含21种侧蒴藓与6种顶蒴藓（acrocarpous mosses）的物种树。我们借助该物种树探究了向侧蒴藓生长型转变的基因组效应，并验证是否存在其他植物辐射类群共有的演化模式：如基因家族扩张、全基因组复制，或选择作用的分子特征改变。研究结果显示，相较于顶蒴藓类，侧蒴藓类中约6%的基因家族发生了扩张。这类扩张的基因家族富集了多个基因本体（Gene Ontology，GO）术语，涵盖与其他生物相互作用相关的功能类别。基因拷贝数的增加与灰藓目的辐射事件同步发生，这表明在类群分化过程中，可能发生了全基因组复制或小规模复制爆发等演化过程。我们在超过500个基因家族中发现了纯化选择（purifying selection）减弱的分子证据，这些基因家族富集了多个与“tRNA代谢过程”相关的基因本体层级术语。本研究揭示了可能与侧蒴藓型生长型转变相关的候选基因及调控通路，证实了系统发育转录组学（phylotranscriptomics）在非模式物种分子演化研究中的应用价值。