Grusz Amanda L, Rothfels Carl J, Schuettpelz Eric
Department of Botany, Smithsonian Institution, MRC 166 PO Box 37012, Washington, DC, 20013-7012, USA.
Department of Biology, University of Minnesota Duluth, 1035 Kirby Drive, Duluth, MN, 55812, USA.
BMC Genomics. 2016 Aug 30;17(1):692. doi: 10.1186/s12864-016-3034-2.
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.
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.
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.
非模式植物系统中的转录组学最近已发展到这样一个阶段,即对研究较少的类群进行全基因组范围的核模式研究已成为现实。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自质体基因组。在这里,我们在蕨类植物分子进化速率的首次全基因组比较研究中利用了转录组数据。我们关注生态多样的凤尾蕨科,该科约占蕨类植物多样性的10%,包括神秘的书带蕨类——一个附生的热带谱系,以形态显著简化和系统发育分支长度极度延长而闻名。利用2091个基因座的表达序列数据,我们对该科三个最大分支中的12个物种的分子进化速率进行了成对比较,并询问先前记录的质体替代率异质性是否反映在它们的核基因组中。然后,我们探究进化速率的变化是否由属于特定功能类别的基因所塑造,并测试选择的差异模式。
我们发现,相对于凤尾蕨科内的所有其他谱系,书带蕨类在进化速率上存在显著的全基因组差异,但我们发现较快/较慢的书带蕨类基因座与已知功能基因类别之间几乎没有显著相关性。我们证明,书带蕨类的较快进化速率可能不是由正选择驱动的,也不是任何特定类型的核苷酸替代所特有的。
我们的结果强化了最近被重新审视的、假设用于塑造书带蕨类分子进化速率的机制,并为蕨类植物核基因组内和核基因组间的替代率变化提供了新的见解。