Satellitome evolution illuminates complex species history and satellite DNA transcriptomes show coordinated expression in Meloidogyne nematodes

Satellitome represents the collection of different satellite DNAs (satDNAs) in a genome. SatDNAs are tandemly repeated non-coding DNA sequences that constitute the most abundant and the fastest evolving part of the eukaryotic genome. Due to their extreme diversity and methodological difficulties to characterize and compare satDNA collection in complex genomes, knowledge on their putative functional constraints and capacity to participate in genome evolution remains rather elusive. SatDNA transcripts have been detected in many species. New studies have shown that deregulation of satDNA expression has role in cancer progression. However, how satDNA transcripts are regulated on the genome-wide scale is poorly understood. Here, we conducted a genome-wide survey and comparative analyses of satelitomes among different closely related Meloidogyne nematodes. The evolutionary trends of satDNA on the genome- wide scale show that each round of proposed polyploidization in the evolutionary history of the investigated species is concomitant with the addition of a new subset of satDNAs in the satellitome of any particular Meloidogyne species. Successive incorporation of new sets of satDNAs in the genome along the process of polyploidization suggests multiple hybridization events as the main factor in the formation of these species. In addition, comparative expression analyses of complete satDNA set show similar transcription profile of satDNAs among different Meloidogyne species which is not dependent on satDNA genome abundance indicating similar mechanisms that operate in regulation of satDNA expression in related genomes. Furthermore, stage-specific expression pattern of satDNAs through the Meloidogyne incognita development supports the view that satDNA expression is not a stochastic event but is subject to coordinated control. Comparative analyses of 83 satDNA sequences detected in Meloidogyne satelitomes revealed conserved sequence features indicative of evolution under selective pressure and their putative functional potential. Our results demonstrate the power of comparative analysis of the non-coding genome part for the successful elucidation of the origin of species with a complex history. Whereas satDNAs generally evolve extremely quickly and their functional role is largely difficult to be proved, comparative analyses of satellitomes and satDNA transcriptomes in related genomes could be a way to address satDNA regulation and their putative functional potential.