Low genetic variation is associated with low mutation rate in the giant duckweed

Abstract

Mutation rate and effective population size (Ne) jointly determine intraspecific genetic diversity, but the role of mutation rate is often ignored. Here we investigate genetic diversity, spontaneous mutation rate and Ne in the giant duckweed (Spirodela polyrhiza). Despite its large census population size, whole-genome sequencing of 68 globally sampled individuals reveals extremely low intraspecific genetic diversity. Assessed under natural conditions, the genome-wide spontaneous mutation rate is at least seven times lower than estimates made for other multicellular eukaryotes, whereas Ne is large. These results demonstrate that low genetic diversity can be associated with large-Ne species, where selection can reduce mutation rates to very low levels. This study also highlights that accurate estimates of mutation rate can help to explain seemingly unexpected patterns of genome-wide variation.

Duckweed (Lemnaceae): Its Molecular Taxonomy

“…The extension of this method to clones belonging to other duckweed species requires the availability of whole genome sequences of those species. It should be mentioned here that from whole genome sequencing it is known that the intraspecific variation in Spirodela polyrhiza is extremely low (Michael et al, 2017;Hoang et al, 2018;Ho et al, 2019;Xu et al, 2019). Therefore, demonstrating differences between clones of this species is a kind of "toughness test" for the method employed.…”

“…et al, 2015) and Lemna minor 8627, Lemna gibba 7742a, and Wolffia australiana 8730 (www.lemna.org/; for a review see An et al, 2018). Further, 68 clones of Spirodela polyrhiza were recently sequenced by Xu et al (2019) and 38 by Ho et al (2019).…”

Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries

“…Between the chromosomes of seven cytogenetically investigated S. polyrhiza clones so far no BAC-sized structural rearrangements were found 24 . In addition, population genomics studies suggested a considerably low genetic diversity between world-wide distributed S. polyrhiza clones 26,27 . Sequence assignment to distinct chromosomes based on cross-hybridization of genomic sequences between related species represents a novel cytogenomic approach.…”

Marine and Freshwater Plants: Challenges and Expectations

“…(Gachon et al, 2007). A monocot, Spirodela polyrhiza , needs also to be added to this list, to comprehend angiosperm adaptation to aquatic habitats (Wang et al, 2014; Xu et al, 2019). Each model is key to address questions in relation with specific clades of algae and plants.…”