A phylogenomic approach reveals a low somatic mutation rate in a long-lived plant

Orr, Adam J.; Padovan, Amanda; Kainer, David; Külheim, Carsten; Bromham, Lindell; Bustos‐Segura, Carlos; Foley, William J.; Haff, Tonya M.; Hsieh, Ji-Fan; Morales-Suarez, Alejandro; Cartwright, Reed A.; Lanfear, Robert

doi:10.1101/727982

Cited by 15 publications

(41 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our estimate of the mutation rate in S. polyrhiza (8.39E-11 per bp per gen.) is similar to the estimates reported by (Xie et al 2016;Hanlon et al 2019;Orr et al 2020). However, duckweeds do appear to exhibit a low mutation rate compared to animals which have limited cell divisions between meiotic events due to a segregated germline.…”

Section: Discussionsupporting

confidence: 87%

“…Duckweed estimated highlighted by red box. References: (Ossowski et al 2010;Lynch 2010;Denver et al 2012;Schrider et al 2013;Weller et al 2014;Zhu et al 2014;Venn et al 2014;Keightley et al 2015;Uchimura et al 2015;Yang et al 2015;Farlow et al 2015;Ness et al 2015;Smeds et al 2016;Xie et al 2016;Besenbacher et al 2016 p.;Feng et al 2017;Liu et al 2017;Oppold and Pfenninger 2017;Flynn et al 2017;Krasovec et al 2017Krasovec et al , 2018Krasovec et al , 2019Hanlon et al 2019;Orr et al 2020)…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Estimation of the SNP Mutation Rate in Two Vegetatively Propagating Species of Duckweed

Sandler

Bartkowska

Agrawal

et al. 2020

G3 Genes|Genomes|Genetics

View full text Add to dashboard Cite

Mutation rate estimates for vegetatively reproducing organisms are rare, despite their frequent occurrence across the tree of life. Here we report mutation rate estimates in two vegetatively reproducing duckweed species, Lemna minor and Spirodela polyrhiza. We use a modified approach to estimating mutation rates by taking into account the reduction in mutation detection power that occurs when new individuals are produced from multiple cell lineages. We estimate an extremely low per generation mutation rate in both species of duckweed and note that allelic coverage at de novo mutation sites is very skewed. We also find no substantial difference in mutation rate between mutation accumulation lines propagated under benign conditions and those grown under salt stress. Finally, we discuss the implications of interpreting mutation rate estimates in vegetatively propagating organisms.

show abstract

Section: Discussionsupporting

confidence: 87%

Section: Discussionmentioning

confidence: 99%

Estimation of the SNP Mutation Rate in Two Vegetatively Propagating Species of Duckweed

Sandler

Bartkowska

Agrawal

et al. 2020

G3 Genes|Genomes|Genetics

View full text Add to dashboard Cite

show abstract

“…First, direct observations of plant development at the cellular level indicate that cells destined to form axillary meristems undergo much fewer divisions than other cells from the moment they are produced in the apical meristem, which suggests that the number of cell divisions per branching event, and therefore the number of opportunities for mutations to accumulate, may be lower than previously thought (Burian et al, 2016). Second, estimates of somatic mutation rates per unit of growth tend to be low (Orr et al, 2020). Third, to our knowledge, the only experiment comparing the mutagenicity of meiosis and mitosis was performed by Magni and Von Borstel (1962) in yeast.…”

Section: Evolutionarily Stable Mutation Ratementioning

confidence: 97%

“…Consistent with this view, it was shown at the cellular level that axillary meristems cells are set aside early during the growth of a shoot (Burian et al, 2016), resulting in a number of cell divisions increasing linearly with the number of branching events in trees although the number of terminal branches increases exponentially. Furthermore, multiple studies showed that somatic mutation rates tend to be considerably lower in taller, more long-lived species (Schmid-Siegert et al, 2017;Plomion et al, 2018;Hofmeister et al, 2019;Orr et al, 2020;Wang et al, 2019;Hanlon et al, 2019). For instance, Orr et al (2020) found the somatic mutation rate per generation to be only ten times higher in Eucalyptus melliodora than in Arabidopsis, despite being > times larger in size.…”

Section: Introductionmentioning

confidence: 99%

“…Furthermore, multiple studies showed that somatic mutation rates tend to be considerably lower in taller, more long-lived species (Schmid-Siegert et al, 2017;Plomion et al, 2018;Hofmeister et al, 2019;Orr et al, 2020;Wang et al, 2019;Hanlon et al, 2019). For instance, Orr et al (2020) found the somatic mutation rate per generation to be only ten times higher in Eucalyptus melliodora than in Arabidopsis, despite being > times larger in size.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Population-level consequences of inheritable somatic mutations and the evolution of mutation rates in plants

Lesaffre

2020

Preprint

View full text Add to dashboard Cite

Inbreeding depression, that is the decrease in fitness of inbred relative to outbred individuals, was shown to increase strongly as life expectancy increases in plants. Because plants are thought to not have a separated germline, it was proposed that this pattern could be generated by somatic mutations accumulating during growth, since larger and more long-lived species have more opportunities for mutations to accumulate. A key determinant of the role of somatic mutations is the rate at which they occur, which likely differs between species because mutation rates may evolve differently in species with constrasting life-histories. In this paper, we study the evolution of the mutation rates in plants, and consider the population-level consequences of inheritable somatic mutations given this evolution. We show that despite substantially lower per year mutation rates, more long-lived species still tend to accumulate larger amounts of deleterious mutations because of higher per generation, leading to higher levels of inbreeding depression in these species. However, the magnitude of this increase depends strongly on how mutagenic meiosis is relative to growth.

show abstract

Accumulation of somatic mutations leads to genetic mosaicism in cannabis

2021

View full text Add to dashboard Cite

Cannabis (Cannabis sativa L.) is typically propagated using stem cuttings taken from mother plants to produce genetically uniform propagules. However, producers anecdotally report that clonal lines deteriorate over time and eventually produce clones with less vigor and lower cannabinoid levels than the original mother plant. While the cause of this deterioration has not been investigated, one potential contributor is the accumulation of somatic mutations within the plant. To test this, we used deep sequencing of whole genomes (>50×) to compare the variability within an individual cannabis cultivar Honey Banana plant sampled at the bottom, middle, and top. We called over six million sequence variants based on a reference genome and found that the top had the most by a sizable amount. Comparing the variants among the samples uncovered that nearly 600,000 (34%) were unique to the top while the bottom only contained 148,000 (12%), and middle with 77,000 (9%) unique variants. Bioinformatics tools were used to identify mutations in critical cannabinoid–terpene biosynthesis pathways. While none were identified as high impact, four genes contained more than double the average level of nucleotide diversity (π) in or near the gene. Two genes code for essential enzymes required for the cannabinoid pathway while the other two are in the terpene pathways, demonstrating that mutations were accumulating within these pathways and could influence their function. Overall, a measurable number of intraplant genetic diversity was discovered that could impact long‐term genetic fidelity of clonal lines and potentially contribute to the observed decline in vigor and cannabinoid content.

show abstract

A phylogenomic approach reveals a low somatic mutation rate in a long-lived plant

Cited by 15 publications

References 39 publications

Estimation of the SNP Mutation Rate in Two Vegetatively Propagating Species of Duckweed

Estimation of the SNP Mutation Rate in Two Vegetatively Propagating Species of Duckweed

Population-level consequences of inheritable somatic mutations and the evolution of mutation rates in plants

Accumulation of somatic mutations leads to genetic mosaicism in cannabis

Contact Info

Product

Resources

About