Abstract Detail


Doyle, Jeff [1], Xian, Wenfei [2], Cheng, Shifeng [2].

Conserved noncoding sequences in the genomes of nodulating angiosperms and their potential for homology assessment.

All flowering plant genomes are composed largely of noncoding DNAs, among them regulatory sequences. Some of these are highly conserved even among very distantly related taxa, but the function and evolutionary dynamics of these “conserved noncoding sequences” (CNSs) remain poorly understood. In particular, the relationship of CNSs to novel phenotypes is only beginning to be studied in plants, for example in nodulation—the symbiotic relationship in which plants host nitrogen-fixing bacteria in novel structures called nodules. Here we discuss the use of CNSs to test hypotheses of the number of independent origins of this ecologically and economically important symbiosis. Nodulation is confined to a single subclade comprising four orders of rosid angiosperms, the Nitrogen-Fixing Nodulation Clade (NFNC). Nodulation is best known in Fabales, where in the only nodulating family (Fabaceae) nodulation is characteristic of thousands of species in the crown group of subfamily Papilionoideae and in the large mimosoid clade of nested within Caesalpinioideae, but is absent from other subfamilies. The distribution of nodulating species is even more sparse in the other three NFNC orders, Fagales, Rosales, and Cucurbitales. In these orders nodule morphology and anatomy are highly variable, and differ from legumes. Also, legume microsymbionts are diverse gram negative bacteria collectively termed “rhizobia” whereas in the remaining orders only Parasponia (Rosales) nodulates with rhizobia; elsewhere the microsymbionts are gram positive actinorhizal bacteria. The phylogenetic distribution and variability of nodulation have led to competing hypotheses, ranging from a single origin and massive parallel losses to numerous independent gains and fewer losses. The diversity of nodule morphologies and anatomies argues for multiple origins, as does the phylogenetic diversity of bacterial microsymbionts. The difficulty of independently evolving a syndrome as complex as nodulation, compared the presumed ease of loss, argues for fewer origins. Individual genes and networks involved in nodulation likely were recruited from pre-existing—and current—functions, creating deep homologies that complicate homology assessment of the overall process of nodulation. CNSs represent an untapped resource for testing competing hypotheses of nodulation origin and evolution. Here we discuss assumptions underlying these tests, including those involving the evolution of regulatory elements during gene recruitment. We compare reference-guided and reference-free approaches to identifying CNSs, particularly those relevant to nodulation, resulting in the identification of hundreds of thousands of CNSs in 88 species of NFC and outgroups. We explore the dynamics of CNSs evolution in papilionoid legume species that are considered to have lost the ability to nodulate.

1 - Cornell University, School of Integrative Plant Science, Plant Biology Section, 404 Mann Library Building, Ithaca, NY, 14853, USA
2 - Chinese Academy of Agricultural Sciences, Agricultural Genomics Institute at Shenzhen, Shenzhen, 518124, China

conserved noncoding sequences

Presentation Type: Oral Paper
Number: SYST I009
Abstract ID:516
Candidate for Awards:None

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