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，即灰藓亚纲Hypnanae）是一类物种丰富的陆生植物类群，包含约6000个物种，其共同特征为雌性生殖器官着生于短侧枝之上，属于苔藓植物中的衍生性状。灰藓目（Hypnales）是侧蒴藓类中最大的目，其下多数类群的起源可追溯至距今不足1亿年前的一次快速辐射演化，这一时间节点恰好紧随被子植物的兴起。因此，检验演化假说所需的灰藓目各科间系统发育分辨率，仅依靠单个或少数基因位点难以达成。本研究首次基于高通量测序数据（转录组序列）对侧蒴藓类开展系统发育推断。为检验基因家族演化假说，我们利用659个直系同源基因的超百万个位点，构建了包含21种侧蒴藓类与6种顶蒴藓类（acrocarpous mosses）的物种树。我们借助该物种树，探究了向侧蒴生长型转变带来的基因组效应，并验证了其他植物辐射演化中常见的模式——如基因家族扩张、全基因组复制，或是选择的分子特征改变——是否同样存在于本类群中。我们发现，相较于顶蒴藓类，侧蒴藓类中约6%的基因家族发生了扩张。这些扩张的基因家族富集了多项基因本体（gene ontology, GO）术语，其中包括与生物互作相关的功能项。基因拷贝数的增加与灰藓目的辐射演化时间相吻合，这表明在类群分化过程中可能发生了全基因组复制或是小规模复制事件的爆发。在超过500个基因家族中，我们发现了纯化选择减弱的证据。这类基因家族富集了多项隶属于基因本体层级中“tRNA代谢过程”相关的术语。本研究结果揭示了可能与侧蒴藓型生长型转变相关的候选基因与通路，阐明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。