Loss of all plastid ndh genes in Gnetales and conifers: extent and evolutionary significance for the seed plant phylogeny

Abstract

The exact phylogenetic position of Gnetales, a small, highly modified group of gymnosperms with an accelerated rate of molecular evolution, is one of the most challenging issues for seed plant systematics. Recent results from entire plastid genome (ptDNA) sequencing revealed the absence of the entire suite of plastid ndh genes in several species of Gnetales and the pine family (Pinaceae) potentially highlighting a major structural feature linking these two groups-concerted loss of all plastid genes for the NADH dehydrogenase complex. However, the precise extent of ndh gene loss in gymnosperms has not been surveyed. Using a slot-blot hybridization method, we probed all 11 ndh genes in 162 species from 70 of 85 gymnosperm genera. We find that all ndh genes are absent across Gnetales and Pinaceae, but not in any other group of gymnosperms. This feature represents either a major synapomorphy for a clade consisting of these two lineages or, less likely, a convergent loss. Our survey substantially extends previous inferences based on more limited sampling and, if the former evolutionary interpretation is correct, it provides additional support for the contentious "gnepine" hypothesis, which places Gnetales as sister to Pinaceae.

Evolutionary loss of light‐harvesting proteins Lhcb6 and Lhcb3 in major land plant groups – break‐up of current dogma

“…It is also important to mention that in contrast to all other land plant groups, Pinaceae and Gnetales have also lost an entire set of plastid genes for NAD(P)H dehydrogenase (NDH) (Braukmann et al, 2009). The NDH enzyme participates in one of two main pathways of cyclic electron flow (CEF) around PSI.…”

Recent loss of plastid-encoded ndh genes within Erodium (Geraniaceae)

“…In these two lineages, as in parasitic plants, the entire suite of 11 plastid-encoded ndh genes is lost together. Both of these losses of plastid-encoded ndh genes are relatively ancient-the divergence of Pinaceae has been estimated at approximately 140 million years ago (MYA) (Wang et al 2000), and loss of ndh genes necessarily predates this divergence, especially if it represents a synapomorphy for Pinaceae and Gnetales (Braukmann et al 2009). The sister relationship between Pinaceae and Gnetales-the so-called ''gnepine'' hypothesis-is still controversial (Zhong et al 2010).…”

Characteristics of guaiacyl-syringyl lignin in reaction wood in the gymnosperm Gnetum gnemon L.

“…However, based on molecular genetics studies Gnetales species are more closely related to gymnosperms than angiosperms (Winter et al 1999;Bowe et al 2000;Chaw et al 2000;Soltis et al 2002;Wang 2004;Zhong et al 2010). Interestingly, some molecular phylogenetic studies placed Gnetales within conifers as the sister group of Pinaceae based on the analyses of structural alteration of the plastid genome ("gnepine" hypothesis) (Braukmann et al 2009), whereas some studies using the large set of nuclear genes supports a "gnetifer" hypothesis, in which Gnetales are categorized as the sister group of all conifers (Chaw et al 1997(Chaw et al , 2000Wickett et al 2014).…”