Whole-genome microsynteny-based phylogeny of angiosperms

Abstract

Plant genomes vary greatly in size, organization, and architecture. Such structural differences may be highly relevant for inference of genome evolution dynamics and phylogeny. Indeed, microsynteny—the conservation of local gene content and order—is recognized as a valuable source of phylogenetic information, but its use for the inference of large phylogenies has been limited. Here, by combining synteny network analysis, matrix representation, and maximum likelihood phylogenetic inference, we provide a way to reconstruct phylogenies based on microsynteny information. Both simulations and use of empirical data sets show our method to be accurate, consistent, and widely applicable. As an example, we focus on the analysis of a large-scale whole-genome data set for angiosperms, including more than 120 available high-quality genomes, representing more than 50 different plant families and 30 orders. Our ‘microsynteny-based’ tree is largely congruent with phylogenies proposed based on more traditional sequence alignment-based methods and current phylogenetic classifications but differs for some long-contested and controversial relationships. For instance, our synteny-based tree finds Vitales as early diverging eudicots, Saxifragales within superasterids, and magnoliids as sister to monocots. We discuss how synteny-based phylogenetic inference can complement traditional methods and could provide additional insights into some long-standing controversial phylogenetic relationships.

The Role of Ancestral Duplicated Genes in Adaptation to Growth on Lactate, a Non-Fermentable Carbon Source for the Yeast Saccharomyces cerevisiae

“…These works support the prevalence of duplicates and innovative potential as proposed more than fifty years ago by Ohno [14]. Since then, the molecular mechanisms behind this innovative potential and duplicate retention have become the target of many other researchers, involving the study of transcriptomic divergence between copies, functional specialization, adaptive potential, and evolvability of duplicates, among other parameters in all life kingdoms [15][16][17][18][19][20][21][22][23]. Some of these latest works show a relationship between duplicate transcriptional divergence and transcriptional plasticity in response to environmental challenges, which may link the evolvability of duplicates and their functional innovative potential in yeasts [23][24][25][26].…”

A non-duplicated magnoliid genome

“…In phylogenetics, such shared derived character is often used to define a monophyletic group, and thus in this case for magnoliids and monocots to share a common ancestor. Interestingly, a similar observation was made recently by Zhao et al 16 who also used collinearity and (micro)synteny information to infer phylogenetic relationships within angiosperms. Using a 'character matrix' derived from a network representation of pairwise (micro)synteny relations, and maximum likelihood inference, Zhao et al 16 found monocots and magnoliids also to be sister groups, to the exclusion of eudicots, and attributed the clustering of magnoliids and monocots to some syntenic blocks -other than the ones discovered by Qin et al 5 -that only seemed to exist in magnoliids and monocots.…”

“…Interestingly, a similar observation was made recently by Zhao et al 16 who also used collinearity and (micro)synteny information to infer phylogenetic relationships within angiosperms. Using a 'character matrix' derived from a network representation of pairwise (micro)synteny relations, and maximum likelihood inference, Zhao et al 16 found monocots and magnoliids also to be sister groups, to the exclusion of eudicots, and attributed the clustering of magnoliids and monocots to some syntenic blocks -other than the ones discovered by Qin et al 5 -that only seemed to exist in magnoliids and monocots. Again, as in the findings of Qin et al 5 , alternative explanations could not completely be ruled out, but both findings are worthy of further investigation.…”

Emergence of distinct syntenic density regimes is associated with early metazoan genomic transitions

“…Local gene order has been conserved across animal phyla over vast evolutionary time spans, and is referred to as microsynteny [ 1 – 5 ]. However, little is known about the loss of ancestrally inherited microsyntenies and the emergence of novel microsyntenies, due to genome rearrangements, gene gains and/or gene losses [ 1 , 6 – 8 ]. Determining the node of microsynteny loss or emergence can provide insights into the evolution of animal genome architecture and the extent of microsynteny conservation.…”