Sequence variability of the MspI satellite DNA family of the pinewood nematode Bursaphelenchus xylophilus at different geographic scales

Abstract

a b s t r a c tTandemly repeated sequences known as satellite DNA (satDNA) generally exhibit complex evolutionary patterns of concerted evolution in which mutations are homogenized and fixed in a stochastic process of molecular drive. Here, the nucleotidic variability of the MspI satDNA family of the pinewood nematode Bursaphelenchus xylophilus is analyzed in order to understand the evolutionary dynamics of satDNA at the intraspecific level. A total of 425 MspI monomer units, either PCR-amplified from isolates of local (Peninsula of Setúbal, Portugal) or worldwide origin, or retrieved from the B. xylophilus genome sequence, were characterized and compared. Whatever their origin, sliding window analysis of sequence variability patterns among monomers revealed low, moderate and highly variant domains, indicating that variable levels of evolutionary constraint may act upon the entire monomers. The phylogenetic inference based on the different sets of MspI satDNA family for this species shows a broad polymorphism of the individual monomers, which were distributed into four main clusters. However, such clustering appeared independent from the geographic origin of the nematodes, and could not discriminate isolates or groups of geographically close isolates. Rather, the formation of different phylogenetic groups within this satDNA family suggests an a priori embodying of a set of diverging repeats from a common ancestor satDNA library, which have been differently amplified along the evolutionary pathway of this species. The present work improves knowledge on the evolutionary dynamics of satDNA at the intraspecific level, and provides new information on satDNA sequence variability among natural populations sampled at a local geographic scale.

The satellite DNA AflaSAT-1 in the A and B chromosomes of the grasshopper Abracris flavolineata

“…Low variability was observed for AflaSAT-1, and additionally, almost no distinct or population-specific profile was observed, which has also been documented for other species consistent with the concerted evolution model for homogenization of repeats at the intragenomic level [ 53 – 57 ]. By contrast, chromosomal variability was observed for cluster number, size, distribution and abundance of repeats, depending on the population.…”

Satellite DNA as a Driver of Population Divergence in the Red Flour Beetle Tribolium castaneum

“…2003 , Kuhn and Sene 2004 ; de Franco et al . 2006 ) as well as in pinewood nematode Bursaphelenchus xylophilus ( Vieira et al . 2014 ) revealed no sequence characteristics or other features that could discriminate a population or groups of populations.…”

Protein markers of Bursaphelenchus xylophilus Steiner & Buhrer, 1934 (Nickle, 1970) populations using quantitative proteomics and character compatibility

“…Nematodes were unambiguously identified by microscopy, based on morphological and morphometrical features following the diagnostic protocols for regulated pests regarding the PWN (EPPO Standards PM7) . When the number of individuals was abundant, their identity was confirmed by ITS‐RFLP and when the number of individuals was small, their identification was based on species‐specific satellite DNA (satDNA) that have been shown to be excellent taxonomic markers for nematodes of agro‐forestry interest , which accomplish the criteria of high and versatile variability in the DNA sequences . To this end, the systematization of representative satDNA sequences of B. xylophilus isolates from the Iberian Peninsula has been carried out in order to define genetic or phylogenetics groups within this pest (reported to EU Comission, REPHRAME project, data not shown).…”

“…Although the taxonomic resolution at the species level is very stable, a wide range of B. xylophilus intraspecific differences have been demonstrated . The assessment of differences among populations through various DNA molecular marker approaches has been the main aspect of prospective studies on B. xylophilus ; however few results have been published on proteome differences regarding this important plant quarantine pathogen although its genome sequence has recently been made available . This is all the more surprising as new methodological developments in proteomics could be successfully applied to research into the genetic, pathogenic and evolutionary characteristics of parasites .…”