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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.

Additional file 1: Fig. S1. Different genome coverages (0,125X, 0,25X and 0,5X) applied in graph-based clustering analysis by Repeat Explorer with number of total obtained clusters on isolates used for comparative analysis; M. incognita L19 (SRR4242479), M. javanica VW4 (SRR4242459), equal parts of three isolates (HarA, L32, L28) for M. arenaria (SRR4242477, SRR4242480, SRR4242481) and M. floridensis SJF1 (SRR4242475). Fig. S2. Comparative analysis of satellitomes in three different isolates of (A) M. incognita (isolates 56, 61, 79), (B) M. javanica (isolates 59, 71, 78), and (C) M. arenaria (isolates 77, 80, 81). Each column represents putative satDNA, while the areas of the colored rectangles are proportional to the abundance of individual satDNA in the genome ranging from 0-0.594% in M. incognita, 0-0.649% in M. javanica and 0-0.694% in M arenaria. Fig. S3. Comparison of MelSat transcripts of the two different transcriptome data sets from M. incognita using the Bowtie2 and BBMap mapper. Fig. S4. Alignments of six MelSat groups which show significant mutual repeat unit similarity (A-F). MelSat60, MelSat65 and MelSat76 (E) represent previously published MARJA, MPA1 and AJL satDNAs respectively [12, 38, 39]. MV1, LV1, MV2, LV2 and HV indicate domains of MEL 172 satDNA described previously [12]. CENP-B box-like sequence (F) previously found in distant M. chitwoodi and M. fallax [10]. Fig. S5. (A) Identity matrix of CENP-B box containing satDNAs (MelSat 72/02/36/42/61/83 from MIG species and from M. chitwoodi and M. fallax (ChFa) previous published in [10]) and (B) identity matrix of MelSat01 in different Meloidogyne species (Minc-M. incognita, Mflo-M. floridensis, Mare-M. arenaria, Mjav-M. javanica, Ment-M. enterolobii and Mhap-M. haplanaria). Fig. S6. Electrophoresis of FISH probes after PCR labeling and purification; (A) biotin-labeled probe for MelSat01 (spliced leader) amplified from a cloned dimer [33] (B) six MelSat probes (CENP-B box containing) amplified and labeled with Cy3 from M. arenaria genomic DNA (MelSat02, 36, 61, 72, 83) and from a cloned dimer of MelSat42. Table S1. Main characteristics of the 83 satDNAs found in the genomes of Meloidogyne species by RepeatExplorer based on consensus sequences of satDNA family found in each of the analyzed species. The slash symbol in the divergency column indicates that this satDNA family is only present in one species. Table S2. Statistics of satDNAs from M. incognita satellitome mapped on genome assembly [42] and unplaced reads. Table S3. Satellite DNA transcription data of Meloidogyne species. SatDNA transcription was obtained with Bowtie2 mapping and normalization using RPKM (reads per kilobase of transcript per million mapped reads) method. SatDNA are ordered based on their catalog number as shown in Fig. 2. Other details are described in Methods section Analysis of the whole transcriptome data. Table S4. Expression analyses of 4 house-keeping genes in M. incognita based on previously validated candidates [65]. For mapping of two juvenile (J2) transcriptome databases (ERR790027 and ERR790028), coding sequences (CDS) of reference genes downloaded from WormBase ParaSite ( https://parasite.wormbase.org/index.html ) were used as listed M. incognita loci for each gene. Table S5. Consensus sequences of 83 satDNAs found in the genomes of the Meloidogyne species by RepeatExplorer. Table S6. Primers pairs used for MelSat amplification and labeling.

Root-knot nematodes (RKN) (Meloidogyne spp.) represent a relatively small but economically important group of obligate plant parasites. Several RKN species belong to the ‘tropical’ RKN group which can cause significant economic losses in agriculture, especially in vegetable crops. The species of this group reproduce by mitotic parthenogenesis and are pests of important food crops, vegetables, fruits and ornamentals grown in tropical, subtropical and temperate climates. The damage and yield losses caused by this group are greater in tropical regions than in temperate regions because of more favourable environmental conditions for pest colonization, development, reproduction and dispersal. However, climate change will influence the spread of these pests and their dispersal across temperate regions. The project aimed to organise surveys in several partnering countries to map the occurrence and distribution of tropical RKN species, to validate biochemical and/ or molecular diagnostic tests and to study the survival ability of RKN species at the open field conditions in the continental climate and Mediterranean/ Atlantic conditions. Data on the distribution of tropical RKN species in partner countries were obtained focussing on sites of field cultivation and ornamental production and by summing national record data on the occurrence of tropical RKN. In total, 107 locations from France, Portugal, Serbia and Slovenia were covered. The most frequently identified species was Meloidogyne incognita, recorded at 47 locations. The second most common species was M. arenaria (21 locations), followed by M. javanica (11 locations), M. hispanica (7 locations), M. luci (6 locations) and of M. enterolobii (2 locations). Mixed species were also found at 13 sites. Forty-three different host species were recorded. Tropical RKN species in the open areas was predominantly distributed in areas with Mediterranean climatic conditions, but a small proportion of sites were recorded in areas with semi-continental climates and mild winter conditions. Five laboratories from partner institutions participated in the test performance study to identify RKN species using biochemical and molecular tests. For isozyme phenotyping, the average agreement of results was 85.1%, while successful identification among laboratories ranged from 58.3 to 100%. Not all species were identified with the same success. The species that were correctly identified 100% of the time were M. arenaria and M. enterolobii. For M. hispanica, M. javanica and M. luci, 90% agreement was achieved, while 80% for M. incognita, 70% for M. ethiopica and 60% for M. inornata. A modified DNA barcoding method, in which four mtDNA coding regions were sequenced, did not prove to be a successful method for identifying all eight selected species. Only 36% of the samples were correctly identified by all laboratories involved in the test performance study. Sequencing of additional mtDNA regions as well as having valid reference data for more species in public nucleotide sequences databases (e.g. Genbank, ENA, Q-bank) could achieve better resolution and correct species identification, but the success rate of identification among laboratories remains to be tested. The survival ability of M. incognita and M. arenaria in the field under continental climatic conditions was studied. Both species survived and maintained their infectivity in a micro-plot (semi-field conditions) filled with soil during three consecutive winters at the Ljubljana site, defined as continental conditions. The potential suitability of European territory for survival and development of selected tropical RKN species was assessed with CLIMEX software and simulation of the influences of climate change scenario were performed., Report of the Euphresco project 2016-A-199 'Global warming and distribution of root-knot nematode species of the tropical group (MeloTrop)'

Centromeres are chromosomal regions essential for kinetochore attachment to mitotic spindle and proper chromosome segregation during cell divisions. They are determined epigenetically with centromere-specific variant of histone H3 (CenH3). While centromere function is conserved, CenH3 and underlying DNA evolve rapidly. Most research has been done on sexual species with monocentric chromosomes characterized by a single CenH3-containing region. In contrast, holocentromeres have their function dispersed throughout the entire length of chromosome. In this study, we used holocentric nematodes of the genus Meloidogyne as a model organism for the centromere study [1]. CenH3 characterization is done for three closely related, polyploid mitotic parthenogenetic species together with distantly related meiotic parthenogen species. We found that ancestral duplication of CenH3 gene resulted in one conserved CenH3 (αCenH3) and other gene that evolved rapidly into four different CenH3 variants. Immunofluorescence performed on mitotic M. incognita revealed a dominant role of αCenH3 histone on its centromere (Figure 1) while the other CenH3s have lost their function. In addition, ChIP-Seq analysis showed that αCenH3-associated DNA is comprised of tandem repeats with divergent monomers but completely conserved 19-bp long box. Preservation of αCenH3 and DNA constituents is also proven for other investigated species. These results elucidate unique characteristics where CenH3 and associated DNA are maintained over long period of time in holocentromeres of exclusively mitotic species. Our findings of centromere evolution in asexual, holocentric organisms thus help building an integrated view on the centromere (epi)genomics.

V prispevku obravnavamo borovo ogorčico (Bursaphelenchus xylophilus), ki je v Evropi (tudi v Sloveniji) uvrščena na karantensko listo A1. Vrsta je izredno napadalna, povzroča hitro propadanje iglavcev - predvsem vrst rodu Pinus, redko Picea, Abies in Larix. Prikazan je njen areal, ekološke zahteve, gostitelji, bionomija ter simptomi napada na borih. V okviru bionomije borove ogorčice so posebej predstavljeni njeni potrjeni vektorji (Insecta: Cerambycidae - rod Monochamus) in tudi njeni potencialni vektorji (Insecta: Curculionidae - rod Pissodes in Scolytidae). Podajamo razširjenost potencialnih gostiteljskih rastlin borove ogorčice pri nas, podnebne razmere ter kritične točke za vnos in širjenje škodljivca. Ocenjujemo stopnjo fitosanitarnega tveganja pojava borove ogorčice v Sloveniji. The present paper deals with the pine wood nematode (Bursaphelenchus xylophilus), which has been placed on the A1 quarantine list in both Europe and Slovenia. The species is extremely offensive, causing fast-paced deterioration in conifers, particularly in those of the Pinus genus and more rarely in those of the Picea, Abies, and Larix genera. The areal, ecological demands, hosts, ecology, and the symptoms of attack on pines of the pine wood nematode are shown. The confirmed vectors (Insecta: Cerambycidae - genus Monochamus) and potential vectors (Insecta: Curculionidae - genus Pissodes andScolytidae) of the pine wood nematode are presented within the framework ofits ecology. The range of potential host plants of the pine wood nematode inSlovenia, climatic conditions, and critical points for the entry and spread of pests are also given. The level of phytosanitary risk presented by the appearance of the pine wood nematode in Slovenia is also evaluated.

Satellite DNAs (satDNAs) are tandemly repeated non-coding DNA sequences, and the most common constituents of every functional centromere. Holocentric chromosomes and multiple genome copies establish nematodes of the genus Meloidogyne as an attractive model for studying centromere- associated DNA sequences. In order to identify a pool of satDNAs that may be involved in genomics of the holocentromere, we have analyzed the satellitome (whole-genome complement of satDNAs) in four different publicly available Meloidogyne genomes using RepeatExplorer computational tool. Our results of genome-wide analyses revealed the presence of a remarkable collection of 38-80 different satDNAs in each examined genome. In addition, comparative analyses of satellitomes show three main groups of satDNAs ; common for all four studied species, and shared by subsets of three or only two species. This distribution of satDNAs supports a recent hypothesis based on comparative analyses of coding regions, that speciation processes in Meloidogyne may be a result of additive interspecific hybridizations. Our preliminary analysis of satDNA distribution on chromosomes of studied species also speaks in favor of such unusual genome evolution in Meloidogyne.

V prispevku obravnavamo borovo ogorčico (Bursaphelenchus xylophilus), ki je v Evropi (tudi v Sloveniji) uvrščena na karantensko listo A1. Vrsta je izredno napadalna, povzroča hitro propadanje iglavcev - predvsem vrst rodu Pinus, redko Picea, Abies in Larix. Prikazan je njen areal, ekološke zahteve, gostitelji, bionomija ter simptomi napada na borih. V okviru bionomije borove ogorčice so posebej predstavljeni njeni potrjeni vektorji (Insecta: Cerambycidae - rod Monochamus) in tudi njeni potencialni vektorji (Insecta: Curculionidae - rod Pissodes in Scolytidae). Podajamo razširjenost potencialnih gostiteljskih rastlin borove ogorčice pri nas, podnebne razmere ter kritične točke za vnos in širjenje škodljivca. Ocenjujemo stopnjo fitosanitarnega tveganja pojava borove ogorčice v Sloveniji. The present paper deals with the pine wood nematode (Bursaphelenchus xylophilus), which has been placed on the A1 quarantine list in both Europe and Slovenia. The species is extremely offensive, causing fast-paced deterioration in conifers, particularly in those of the Pinus genus and more rarely in those of the Picea, Abies, and Larix genera. The areal, ecological demands, hosts, ecology, and the symptoms of attack on pines of the pine wood nematode are shown. The confirmed vectors (Insecta: Cerambycidae - genus Monochamus) and potential vectors (Insecta: Curculionidae - genus Pissodes andScolytidae) of the pine wood nematode are presented within the framework ofits ecology. The range of potential host plants of the pine wood nematode inSlovenia, climatic conditions, and critical points for the entry and spread of pests are also given. The level of phytosanitary risk presented by the appearance of the pine wood nematode in Slovenia is also evaluated.

The present paper deals with the pine wood nematode (Bursaphelenchus xylophilus), which has been placed on the A1 quarantine list in both Europe and Slovenia. The species is extremely offensive, causing fast-paced deterioration in conifers, particularly in those of the Pinus genus and more rarely in those of the Picea, Abies, and Larix genera. The areal, ecological demands, hosts, ecology, and the symptoms of attack on pines of the pine wood nematode are shown. The confirmed vectors (Insecta: Cerambycidae - genus Monochamus) and potential vectors (Insecta: Curculionidae - genus Pissodes andScolytidae) of the pine wood nematode are presented within the framework ofits ecology. The range of potential host plants of the pine wood nematode inSlovenia, climatic conditions, and critical points for the entry and spread of pests are also given. The level of phytosanitary risk presented by the appearance of the pine wood nematode in Slovenia is also evaluated. V prispevku obravnavamo borovo ogorčico (Bursaphelenchus xylophilus), ki je v Evropi (tudi v Sloveniji) uvrščena na karantensko listo A1. Vrsta je izredno napadalna, povzroča hitro propadanje iglavcev - predvsem vrst rodu Pinus, redko Picea, Abies in Larix. Prikazan je njen areal, ekološke zahteve, gostitelji, bionomija ter simptomi napada na borih. V okviru bionomije borove ogorčice so posebej predstavljeni njeni potrjeni vektorji (Insecta: Cerambycidae - rod Monochamus) in tudi njeni potencialni vektorji (Insecta: Curculionidae - rod Pissodes in Scolytidae). Podajamo razširjenost potencialnih gostiteljskih rastlin borove ogorčice pri nas, podnebne razmere ter kritične točke za vnos in širjenje škodljivca. Ocenjujemo stopnjo fitosanitarnega tveganja pojava borove ogorčice v Sloveniji.

The present paper deals with the pine wood nematode (Bursaphelenchus xylophilus), which has been placed on the A1 quarantine list in both Europe and Slovenia. The species is extremely offensive, causing fast-paced deterioration in conifers, particularly in those of the Pinus genus and more rarely in those of the Picea, Abies, and Larix genera. The areal, ecological demands, hosts, ecology, and the symptoms of attack on pines of the pine wood nematode are shown. The confirmed vectors (Insecta: Cerambycidae - genus Monochamus) and potential vectors (Insecta: Curculionidae - genus Pissodes andScolytidae) of the pine wood nematode are presented within the framework ofits ecology. The range of potential host plants of the pine wood nematode inSlovenia, climatic conditions, and critical points for the entry and spread of pests are also given. The level of phytosanitary risk presented by the appearance of the pine wood nematode in Slovenia is also evaluated.