Variation in gene expression within clones of the earthworm Dendrobaena octaedra

Abstract

Gene expression is highly plastic, which can help organisms to both acclimate and adapt to changing environments. Possible variation in gene expression among individuals with the same genotype (among clones) is not widely considered, even though it could impact the results of studies that focus on gene expression phenotypes, for example studies using clonal lines. We examined the extent of within and between clone variation in gene expression in the earthworm Dendrobaena octaedra, which reproduces through apomictic parthenogenesis. Five microsatellite markers were developed and used to confirm that offspring are genetic clones of their parent. After that, expression of 12 genes was measured from five individuals each from six clonal lines after exposure to copper contaminated soil. Variation in gene expression was higher over all genotypes than within genotypes, as initially assumed. A subset of the genes was also examined in the offspring of exposed individuals in two of the clonal lines. In this case, variation in gene expression within genotypes was as high as that observed over all genotypes. One gene in particular (chymotrypsin inhibitor) also showed significant differences in the expression levels among genetically identical individuals. Gene expression can vary considerably, and the extent of variation may depend on the genotypes and genes studied. Ensuring a large sample, with many different genotypes, is critical in studies comparing gene expression phenotypes. Researchers should be especially cautious inferring gene expression phenotypes when using only a single clonal or inbred line, since the results might be specific to only certain genotypes.

Polymorphic microsatellite markers demonstrate hybridization and interspecific gene flow between lumbricid earthworm species, Eisenia andrei and E. fetida

“…Genetic loci containing simple sequence repeats (SSRs, i.e. microsatellites) can be used as powerful markers in population genetics primarily because they are found throughout the nuclear genome, generally have several alleles per locus, and are inherited in a codominant way [11].…”

“…hybrid-derived spermatozoa is indicative of gene transfer from Ef to Ea. This might be exemplified by hypothetically polymorphic genes responsible for Ef-specific striped body pigmentation pattern of the 'tiger' fFF grandparent mated with aAA earthworm, through the aAF parents (1) to some Ef-like earthworms (11) with mixed pigmentation pattern but genotyped as aAA by species-specific sequences of COI/28S genes [7,8]…”

“…Microsatellites are highly polymorphic, very short nucleotide sequences inherited in a codominant way and repeated many times in the nuclear genome [11] that can be used for addressing questions concerning the mating systems, genetic diversity, and population structure of a diverse array of organisms [12]. Since next-generation sequencing (NGS) has become more and more accessible, the identification and characterization of species-specific microsatellites is currently faster and requires less effort.…”

“…Polymorphic microsatellite markers have been developed for several earthworm species, including Aporrectodea longa [13], Aporrectodea icterica [14,15], Allolobophora chlorotica [16,17], Hormogaster elisae [18], Dendrobaena octaedra [11], Amynthas cortices [19], several Lumbricus sp. [12,[20][21][22][23][24][25], Drawida gisti [26], and Eisenia fetida [27], but not for E. andrei.…”

Tolerance to climate change of the clonally reproducing endemic Baltic seaweed, Fucus radicans: is phenotypic plasticity enough?

“…Second, within-clone variation may arise due to environmental variation, that is, the environmental responses of clones may not be determined by their genotype alone, but also by their environmental history, which results in epigenetic changes (e.g., methylation and histone acetylation) that do not change the genome during ontogenesis (Joyce et al 2003). Epigenetic mechanisms can lead to differential gene expression among genetically identical individuals (Mather and Jinks 2012, Ong-Abdullah et al 2015, Evans et al 2016, Dub e et al 2017b, Mustonen et al 2017, Perez et al 2017). Furthermore, epigenetic variation can also be generated during mitotic cell divisions even in the absence of any specific environmental factors, due to stochastic events during somatic inheritance (Wong et al 2005).…”