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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.

Authors’ original file for figure 1

Additional file of Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita

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Authors’ original file for figure 2

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.

Summary Meloidogyne paranaensis is one of the most destructive root-knot nematode species affecting coffee cultivation. This species presents different esterase phenotypes (Est): P1, P2 and P2a, previous studies showing that Est P2 and P2a populations were more aggressive to susceptible coffee cultivars than populations with Est P1, and local producers have even asked if they may be described as other species. The objective of this study was to characterise M. paranaensis populations of different esterase phenotypes (Est P1, P2 and P2a), regarding morphological, morphometric and phylogenetic relationships in distinct regions of ribosomal DNA (rDNA), mitochondrial gene cytochrome c oxidase II (COII) and nuclear protein coding gene HSP90. All populations were identified by esterase phenotype and SCAR-specific markers. Regarding morphology/morphometrics, the three populations were very similar to the description of the species, differing only in the morphology of the male stylet and second-stage juvenile hyaline tail length. Based on the phylogenetic analysis, a low intraspecific variability was detected among M. paranaensis Est P1 and Est P2 populations from Brazil; the Guatemalan population Est P2a, however, showed a genetic differentiation from the Brazilian populations, confirming the geographic genetic distance of this aggressive population. According to this multi-source approach study, in spite of the intraspecific variation, the phylogenetic position of M. paranaensis is absolute, regardless of the enzymatic phenotype and SCAR markers.

La bactérie Xylella fastidiosa, sous-espèce multiplex, a été identifiée pour la première fois en France en 2015. Aujourd’hui, elle est établie dans certaines communes du littoral méditerranéen de la région Provence-Alpes-Côte d’Azur et dans la région Corse, pour laquelle une stratégie d’enrayement est en place depuis janvier 2018.La décision d’exécution 2015/789/UE modifiée précise les dispositions visant à empêcher d’autres introductions de la bactérie Xylella fastidiosa ainsi que sa propagation dans l’UE. Conformément à l'article 9.1 de cette décision, les mouvements de végétaux spécifiés (la liste des espèces spécifiées est précisée en annexe I de la décision d’exécution 2015/789/UE) en dehors des zones délimitées (la définition d’une zone délimitée est précisée à l’article 4 de la décision d’exécution 2015/789/UE), sont interdits. Par dérogation, l’article 9.2 définit des conditions permettant à l'autorité compétente d’autoriser un opérateur à déplacer des végétaux spécifiés hors de zones délimitées. Parmi ces dispositions1, l’obligation de maintenir sous protection matérielle (en conditions « insect-proof » permanentes) le site de production du végétal spécifié pendant toute la durée de culture pose des difficultés de mise en œuvre. De ce fait, aucune dérogation n’a été délivrée, à ce jour, en France. Cela se traduit notamment par des pertes de marchés et des baisses du chiffre d'affaires chez les professionnels concernés pouvant aller jusqu'à 50 %.

Population genetics have been greatly beneficial to improve knowledge about biological invasions. Quantitative genetic methods, such as Approximate Bayesian Computation (ABC), have brought this improvement up a notch and are now essential tools to decipher the invasion routes of any invasive species. In this paper, we performed ABC analyses to shed light on the pinewood nematode (PWN) worldwide invasion routes and identify the source of the European populations. Originating from North America, this microscopic worm has been invading Asia since 1905 and Europe since 1999, causing tremendous damage on pine forests. Using microsatellite data, we demonstrated the existence of multiple independent events of introduction in Japan (one from the USA and one with an unknown origin) and China (one from the USA and one from Japan). We also found an American origin of the Portuguese samples. Although, we observed some discrepancies between traditional genetic methods and the ABC method, which are worth investigating and are discussed here, the ABC approach definitely helped clarify the worldwide history of the PWN invasion.