Additional file 1 of Satellitome analyses in nematodes illuminate complex species history and show conserved features in satellite DNAs
Creators: name: Despot-Slade, Evelin
name: Širca, Saša
name: Mravinac, Brankica
name: Castagnone-Sereno, Philippe
name: Plohl, Miroslav
name: Meštrović, Nevenka
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: 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.