Data from: Transcriptome sequencing reveals genome-wide variation in molecular evolutionary rate among ferns

Background: Transcriptomics in non-model plant systems has recently reached a point where the examination of nuclear genome-wide patterns in understudied groups is an achievable reality. This progress is especially notable in evolutionary studies of ferns, for which molecular resources to date have been derived primarily from the plastid genome. Here, we utilize transcriptome data in the first genome-wide comparative study of molecular evolutionary rate in ferns. We focus on the ecologically diverse family Pteridaceae, which comprises about 10 % of fern diversity and includes the enigmatic vittarioid ferns—an epiphytic, tropical lineage known for dramatically reduced morphologies and radically elongated phylogenetic branch lengths. Using expressed sequence data for 2091 loci, we perform pairwise comparisons of molecular evolutionary rate among 12 species spanning the three largest clades in the family and ask whether previously documented heterogeneity in plastid substitution rates is reflected in their nuclear genomes. We then inquire whether variation in evolutionary rate is being shaped by genes belonging to specific functional categories and test for differential patterns of selection.

Results: We find significant, genome-wide differences in evolutionary rate for vittarioid ferns relative to all other lineages within the Pteridaceae, but we recover few significant correlations between faster/slower vittarioid loci and known functional gene categories. We demonstrate that the faster rates characteristic of the vittarioid ferns are likely not driven by positive selection, nor are they unique to any particular type of nucleotide substitution.

Conclusions: Our results reinforce recently reviewed mechanisms hypothesized to shape molecular evolutionary rates in vittarioid ferns and provide novel insight into substitution rate variation both within and among fern nuclear genomes.

背景：近年来，非模式植物系统的转录组学（transcriptomics）研究已发展至可实现对研究不足类群的全核基因组模式解析的阶段。这一进展在蕨类植物的进化研究中尤为显著——迄今为止，蕨类植物的分子资源主要来源于质体基因组（plastid genome）。本研究利用转录组数据，开展了首个蕨类植物全基因组水平的分子进化速率比较研究。本研究聚焦于生态多样性丰富的凤尾蕨科（Pteridaceae），该类群约占蕨类植物物种多样性的10%，包含神秘的书带蕨类（vittarioid ferns）——这是一类附生的热带演化支，以形态极度简化、系统发育分支长度极长为典型特征。本研究基于2091个基因座的表达序列数据，对该科3个最大演化支涵盖的12个物种的分子进化速率进行两两比较，并探究此前报道的质体基因组替换速率异质性是否在其核基因组中有所体现。随后，本研究进一步探讨进化速率的变异是否由特定功能类别的基因所驱动，并对选择作用的差异模式进行检验。
结果：研究发现，相较于凤尾蕨科内的其他所有演化支，书带蕨类的全基因组进化速率存在显著差异；但书带蕨类基因座的进化速率快慢与已知功能基因类别之间，仅存在极少显著的相关性。本研究证实，书带蕨类所特有的快速进化速率，既不太可能由正选择（positive selection）驱动，也并非特定类型的核苷酸替换所独有。
结论：本研究结果进一步支持了此前综述中提出的、可能塑造书带蕨类分子进化速率的相关机制，并为蕨类植物核基因组内部及类群间的替换速率变异研究提供了新的见解。