Phylotranscriptomic Analyses of Mycoheterotrophic Monocots Show a Continuum of Convergent Evolutionary Changes in Expressed Nuclear Genes From Three Independent Nonphotosynthetic Lineages

作者：Prakash Raj Timilsena, Craig F. Barrett, Alma Piñeyro‐Nelson, Eric Wafula, Saravanaraj Ayyampalayam, Joel R. McNeal, Tomohisa Yukawa, Thomas J. Givnish, Sean W. Graham, J. Chris Pires, Jerrold I. Davis, Cécile Ané, Dennis Stevenson, Jim Leebens‐Mack, Esteban M. Martínez Salas, Elena Álvarez‐Buylla, Claude W. dePamphilis · 发表于：Genome Biology and Evolution · 年份：2022 · DOI：10.1093/gbe/evac183 · 被引用次数：23 · 研究领域：Plant and animal studies、Photosynthetic Processes and Mechanisms、Plant Gene Expression Analysis

Mycoheterotrophy is an alternative nutritional strategy whereby plants obtain sugars and other nutrients from soil fungi. Mycoheterotrophy and associated loss of photosynthesis have evolved repeatedly in plants, particularly in monocots. Although reductive evolution of plastomes in mycoheterotrophs is well documented, the dynamics of nuclear genome evolution remains largely unknown. Transcriptome datasets were generated from four mycoheterotrophs in three families (Orchidaceae, Burmanniaceae, Triuridaceae) and related green plants and used for phylogenomic analyses to resolve relationships among the mycoheterotrophs, their relatives, and representatives across the monocots. Phylogenetic trees based on 602 genes were mostly congruent with plastome phylogenies, except for an Asparagales + Liliales clade inferred in the nuclear trees. Reduction and loss of chlorophyll synthesis and photosynthetic gene expression and relaxation of purifying selection on retained genes were progressive, with greater loss in older nonphotosynthetic lineages. One hundred seventy-four of 1375 plant benchmark universally conserved orthologous genes were undetected in any mycoheterotroph transcriptome or the genome of the mycoheterotrophic orchid Gastrodia but were expressed in green relatives, providing evidence for massively convergent gene loss in nonphotosynthetic lineages. We designate this set of deleted or undetected genes Missing in Mycoheterotrophs (MIM). MIM genes encode not only mainly photo...