Supporting Information Opperman et al. 10.1073/pnas.0805946105 SI Methods Library Construction. Meloidogyne hapla eggs were harvested from roots of tomato plants and DNA was isolated by using standard protocols. The one library sequenced at the Center for the Biology of Nematode Parasitism (CBNP), CHOHAP, was made by Orion. The CHOHAP library, made from sheared genomic DNA ligated into a modified pBluescript vector (Stratagene) had an average insert size of 3 kb. The FASU library, made from sheared DNA ligated into the vector pUC18, had an average insert size of 3 kb. The libraries FGHA and FGHB, made with sheared DNA ligated into the vector pMCL200, had average insert sizes of 6 and 8 kb, respectively. Two Fosmid libraries with average insert sizes of 40 kb were made by ligating sheared genomic DNA into the vector pCC1Fos. Details of library production can be found at http://www.jgi.doe.gov/sequencing/ protocols/index.html. Sequence Production. All sequencing was performed by using standard protocols on either ABI 3730 or MegaBase sequence analyzers. See supporting information (SI) Table S1 for a breakdown of sequence statistics. Sequence Analysis. Sequences were made available by the De- partment of Energy Joint Genome Institute (JGI) in SCF format. Quality scores were automatically generated at JGI by using either KB basecaller version 1.2 or Phred version 0.020425.c, depending on whether sequences were analyzed with an ABI 3730 or a MegaBase sequencer, respectively. All se- quencing at CBNP was performed on ABI 3730 DNA analyzers, and quality scores were generated by KB version 1.2. FastA and quality scores files were extracted from SCF files by using Phred. After extraction of FastA and quality files we used a series of tools to prepare the data for assembly. First, we used Crossmatch run on the Sun Grid Engine to compare all of the sequences with the cloning vectors, host Escherichia coli genome, and 14 com- plete nematode mitochondrial genomes available on the Na- tional Center for Biotechnology Information (NCBI) database. Accession numbers for the 14 mitochondrial genomes are AJ417718, X54253, NC004298, AC186293, AC186293, NC004806, AJ537512, AJ417719, AJ556134, NC001861, AY591323, AY591323, NC002681, and NC002681. Vector sequences were trimmed by using an algorithm developed at the CBNP. Sequences matching either mitochondrial or E. coli sequences were removed from our dataset. Sequences of 10 bp left after trimming were eliminated from further analysis. A series of ad hoc Perl scripts were used to prepare the data for Arachne. This included renaming individual sequence names to give each sequence a well ID, provide information about sequencing primer used, and provide insert size data for Arachne. Sequence data were assembled using Arachne 2.0.1 on a Dell workstation running Red Hat Enterprise Linux 5.0 with 16 GB of total RAM. The data were assembled by using a series of different parameters in an attempt to optimize assembly (data not shown). The current build included many of the parameters reported to enhance supercontig size and accuracy. We used the Arachne option removetinysupers to eliminate any supercontigs 2,000 bp in length. RepeatMasker. The assembled contig sequences were processed with RepeatMasker version 3.0.8 (1) with the cross-match engine, version 0.990329, using the RepBase Update repeat library, version 9.04, to identify any Transposable Elements (TEs). The options used were: poly, gff, ace, excln, and species. The ‘‘species’’ option was set to ‘‘elegans.’’ RepeatScout. The assembled contig sequences were processed with RepeatScout version 1.0.2 by using a standard protocol for the processing of data with RepeatScout that was developed in-house from the RepeatScout documentation. Step five of the protocol was repeated five times by using the threshold values of 10 (default), 20, 30, 40, and 50, and we did not use step six of the program. Glimmer. PASA (Program to Assemble Spliced Alignments) was run by using a combination of M. hapla genomic sequence and tylenchid EST data to produce a training set for gene modeling (2). ESTs with alignments 90% identity and 90% coverage with proper exon/intron boundaries were used to create EST assem- blies. After validation, there were 37,605 EST alignments that assembled into 5,887 assemblies representing 5,477 loci. Putative full-length assemblies with ORFs 100 aa and more than one exon were used as the training set for Glimmer. The gff file containing the PASA gene predictions was parsed for exon start and end positions for each gene. The exon positions and genome assembly were used as a training set for GlimmerHMM 3.0.1 (3). The trained data were then used to scan the entire assembly for predicted genes. Intron/Exon Statistics. Gene structure statistics were compiled by using 3,126 gene models that were unequivocally validated by using full-length EST assembly data. A Perl script was written to parse the gene model file produced by PASA. This script gathered statistics regarding the number and size of exons and introns for each of the tier 1 genes. The results were read into R and summary statistics were obtained. Merging M. hapla Genomic Sequence with Genetic Map. Integration of the genetic map with the draft sequence assembly was performed by comparing the sequences of the amplified frag- ment length polymorphism (AFLP) markers to the genomic contigs. Sequences of 30 AFLP marker sequences were com- pared with the contigs from the latest 10draft sequences by using BlastN. Marker sequences were used as query sequences, and true contigs from the 10draft assembly of the genomic sequence were used as target sequences. Low-complexity filter- ing was turned off for this blast job. An E value of E-10 was used as a cutoff. Up to 100 matches to the genomic sequence were returned. Operons and Synteny. A comparison was done between known operons in Caenorhabditis elegans and the M. hapla genomic dataset. A WormMart query provided 4,685 C. elegans proteins representing genes found in operons across the C. elegans genome. These proteins were used as queries in a GeneDetective search of the contigs from the M. hapla genomic assembly with a significance of 1.0E-05. Perl scripts were used to identify multiple members of C. elegans operons found on the same contig in the M. hapla assembly. Horizontal Gene Transfer. Genes from the Initial Freeze were used as queries in multiple homology searches by using the filtering methods described in Scholl et al. (4) Results of the filtering steps were manually curated for final analysis. Opperman et al. www.pnas.org/cgi/content/short/0805946105 1 of 14
Transcript
Supporting InformationOpperman et al. 10.1073/pnas.0805946105SI MethodsLibrary Construction. Meloidogyne hapla eggs were harvested fromroots of tomato plants and DNA was isolated by using standardprotocols. The one library sequenced at the Center for theBiology of Nematode Parasitism (CBNP), CHOHAP, was madeby Orion. The CHOHAP library, made from sheared genomicDNA ligated into a modified pBluescript vector (Stratagene) hadan average insert size of 3 kb. The FASU library, made fromsheared DNA ligated into the vector pUC18, had an averageinsert size of 3 kb. The libraries FGHA and FGHB, made withsheared DNA ligated into the vector pMCL200, had averageinsert sizes of 6 and 8 kb, respectively. Two Fosmid libraries withaverage insert sizes of �40 kb were made by ligating shearedgenomic DNA into the vector pCC1Fos. Details of libraryproduction can be found at http://www.jgi.doe.gov/sequencing/protocols/index.html.
Sequence Production. All sequencing was performed by usingstandard protocols on either ABI 3730 or MegaBase sequenceanalyzers. See supporting information (SI) Table S1 for abreakdown of sequence statistics.
Sequence Analysis. Sequences were made available by the De-partment of Energy Joint Genome Institute (JGI) in SCFformat. Quality scores were automatically generated at JGI byusing either KB basecaller version 1.2 or Phred version0.020425.c, depending on whether sequences were analyzed withan ABI 3730 or a MegaBase sequencer, respectively. All se-quencing at CBNP was performed on ABI 3730 DNA analyzers,and quality scores were generated by KB version 1.2. FastA andquality scores files were extracted from SCF files by using Phred.
After extraction of FastA and quality files we used a series oftools to prepare the data for assembly. First, we used Crossmatchrun on the Sun Grid Engine to compare all of the sequences withthe cloning vectors, host Escherichia coli genome, and 14 com-plete nematode mitochondrial genomes available on the Na-tional Center for Biotechnology Information (NCBI) database.Accession numbers for the 14 mitochondrial genomes areAJ417718, X54253, NC�004298, AC186293, AC186293,NC�004806, AJ537512, AJ417719, AJ556134, NC�001861,AY591323, AY591323, NC�002681, and NC�002681. Vectorsequences were trimmed by using an algorithm developed at theCBNP. Sequences matching either mitochondrial or E. colisequences were removed from our dataset. Sequences of �10 bpleft after trimming were eliminated from further analysis.
A series of ad hoc Perl scripts were used to prepare the datafor Arachne. This included renaming individual sequence namesto give each sequence a well ID, provide information aboutsequencing primer used, and provide insert size data forArachne. Sequence data were assembled using Arachne 2.0.1 ona Dell workstation running Red Hat Enterprise Linux 5.0 with16 GB of total RAM. The data were assembled by using a seriesof different parameters in an attempt to optimize assembly (datanot shown). The current build included many of the parametersreported to enhance supercontig size and accuracy. We used theArachne option remove�tiny�supers to eliminate any supercontigs�2,000 bp in length.
RepeatMasker. The assembled contig sequences were processedwith RepeatMasker version 3.0.8 (1) with the cross-matchengine, version 0.990329, using the RepBase Update repeatlibrary, version 9.04, to identify any Transposable Elements
(TEs). The options used were: poly, gff, ace, excln, and species.The ‘‘species’’ option was set to ‘‘elegans.’’
RepeatScout. The assembled contig sequences were processedwith RepeatScout version 1.0.2 by using a standard protocol forthe processing of data with RepeatScout that was developedin-house from the RepeatScout documentation. Step five of theprotocol was repeated five times by using the threshold values of10 (default), 20, 30, 40, and 50, and we did not use step six of theprogram.
Glimmer. PASA (Program to Assemble Spliced Alignments) wasrun by using a combination of M. hapla genomic sequence andtylenchid EST data to produce a training set for gene modeling(2). ESTs with alignments �90% identity and 90% coverage withproper exon/intron boundaries were used to create EST assem-blies. After validation, there were 37,605 EST alignments thatassembled into 5,887 assemblies representing 5,477 loci.
Putative full-length assemblies with ORFs �100 aa and morethan one exon were used as the training set for Glimmer. The gfffile containing the PASA gene predictions was parsed for exonstart and end positions for each gene. The exon positions andgenome assembly were used as a training set for GlimmerHMM3.0.1 (3). The trained data were then used to scan the entireassembly for predicted genes.
Intron/Exon Statistics. Gene structure statistics were compiled byusing 3,126 gene models that were unequivocally validated byusing full-length EST assembly data. A Perl script was written toparse the gene model file produced by PASA. This scriptgathered statistics regarding the number and size of exons andintrons for each of the tier 1 genes. The results were read intoR and summary statistics were obtained.
Merging M. hapla Genomic Sequence with Genetic Map. Integrationof the genetic map with the draft sequence assembly wasperformed by comparing the sequences of the amplified frag-ment length polymorphism (AFLP) markers to the genomiccontigs. Sequences of 30 AFLP marker sequences were com-pared with the contigs from the latest 10� draft sequences byusing BlastN. Marker sequences were used as query sequences,and true contigs from the 10� draft assembly of the genomicsequence were used as target sequences. Low-complexity filter-ing was turned off for this blast job. An E value of E-10 was usedas a cutoff. Up to 100 matches to the genomic sequence werereturned.
Operons and Synteny. A comparison was done between knownoperons in Caenorhabditis elegans and the M. hapla genomicdataset. A WormMart query provided 4,685 C. elegans proteinsrepresenting genes found in operons across the C. elegansgenome. These proteins were used as queries in a GeneDetectivesearch of the contigs from the M. hapla genomic assembly witha significance of 1.0E-05. Perl scripts were used to identifymultiple members of C. elegans operons found on the samecontig in the M. hapla assembly.
Horizontal Gene Transfer. Genes from the Initial Freeze were usedas queries in multiple homology searches by using the filteringmethods described in Scholl et al. (4) Results of the filtering stepswere manually curated for final analysis.
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Identification of Known Secretion Genes. A total of 80 sequenceswere obtained from GenBank by searching the literature forreported secreted proteins from various plant-parasitic nema-tode species. Some redundancy may exist in the list identified, asmultiple family members are listed for some genes. Redundancywas limited by using sequences from the most closely relatedspecies when genes were found described in several differentplant-parasitic nematode species. Sequences were translated insix frames and compared the entire set of 3,452 genomic contigstranslated in six frames by using Blast. A match was returned ifthe E value was less than E-03. The relatively high E value cutoffwas used to allow identification of the most complete set ofputative secreted proteins in M. hapla.
Identification of Putative Secreted Genes de Novo. For these anal-yses we used peptide sequences from HapPep3. First, we pre-dicted putative signal sequences by using SignalP. We used twoavailable methods to predict signal sequences, SignalP-NN (neu-ral networks) and SignalP-HMM (using hidden Markov models).Only predicted proteins that had a putative signal sequence byusing both methods were considered likely candidates. To ex-clude transmembrane proteins, we used the membrane topologyprediction program TM-HMM. Proteins determined to encodesecreted proteins were then compared with the proteins inWormPep version 185. All sequences that did not have a matchto C. elegans proteins were then compared with the NCBInonredundant protein dataset NR using BlastX to assign anno-tations to those predicted proteins. All Blast analyses requiredan E value of less than E-10 to be considered a significant match.
G Protein-Coupled Receptors. C. elegans G-Protein Coupled Re-ceptor (GPCR) protein sequences were collected from http://www.gpcr.org/7tm/. Sequence data were manually obtained byfollowing a trail of links for each entry until FASTA resourcescould be found. Entries with the following SWISS-PROT iden-tifiers were skipped, because their FASTA sequences could notbe found at the time of sequence collection: O45338�CAEEL,O45339�CAEEL, O45967�CAEEL, O45984�CAEEL,O62076�CAEEL, O62506�CAEEL, P91439�CAEEL,Q18687�CAEEL, Q21690 CAEEL, Q23265�CAEEL,Q3Y401�CAEEL, Q7M3K7�CAEEL, Q7M3K9�CAEEL,Q8MTW9�CAEEL, Q963E7�CAEEL, Q965H7�CAEEL,YWO4�CAEEL. The C. elegans GPCR protein sequence data-set contained 1,011 sequences.
The C. elegans GPCR protein sequences were used in a tera-blastp against the M. hapla gene freeze translated in all six framesat E values of 10E-05, 10E-10, 10E-15, and 10E-20 with and withouta low-complexity filter on. The resulting BLAST results sets wereimported into a spreadsheet where the number of top-hits andnon-hits were tabulated. Protein names of top- and non-hits wereplaced into categories based on common keywords. Any proteinname lacking descriptive text or containing the phrase ‘‘Tempo-rarily Assigned Gene name family member’’ was placed into the‘‘UNCHARACTERIZED/OTHER’’ category.
Nuclear Hormone Receptors. C. elegans Nuclear Hormone Recep-tor (NHR) protein sequences were collected from http://www.ncbi.nlm.nih.gov/. Duplicate entries and entries represent-ing proteins from nonunique genomic locations were eliminated.The C. elegans NHR protein sequence dataset, which contained170 sequences, was used in a tera-blastp against the M. haplagene freeze and processed as described for the GPCRs above.
Collagens. C. elegans collagen protein sequences were collectedfrom http://www.wormbase.org/. After duplicate entries andentries from nonunique genomic locations were eliminated, theC. elegans collagen protein sequence dataset contained 182sequences. This dataset was further reduced by removing allsequences that did not contain a minimum of one instance of a(Gly-X-Y)3 motif. Manually removing these entries resulted in aset of 165 C. elegans collagen protein sequences.
A Perl script was written that counts the number of sequenceswith a minimum of one instance of an uninterrupted (Gly-X-Y)nmotif, where Gly represents glycine, X represents any amino acid(including Glycine), and Y represents any amino acid exceptglycine. The restriction on Y was imposed to avoid findingsequences with only a very low complexity glycine repeat (i.e.,GGGGGGGGG). The number of sequences meeting the min-imum of one instance of an uninterrupted (Gly-X-Y)n motifcriterion was tabulated for three protein sets: C. elegans proteinset from http://www.sanger.ac.uk/Projects/C�elegans/Science98/,October1998 (19,099 proteins total); C. elegans collagen proteinset from Wormbase (http://www.wormbase.org/), cross-validated(165 proteins total); and M. hapla HapPepf1v1 (13,336 proteinstotal). Finding the n values for which all (or almost all) proteinsfrom the C. elegans reference set of 165 met the cutoff andfinding the corresponding number of M. hapla proteins that metthe cutoff was used as one line of evidence for the true numberof M. hapla collagen proteins. Second, a manual (visual) screenwas performed using n � {4, 5, 6, 7}, partitioning the proteinsinto ‘‘true collagens’’ and ‘‘questionable/false collagens.’’ The C.elegans collagen protein set of 165 was used as a reference for thevisual comparison. Third, tera-blastp was used with the C.elegans reference set of 165 collagen proteins as the query, usingE values of E-05, E-10, E-15, E-20, and E-25, with and withouta low-complexity filter on. Hits from selected resulting sets werecompared against the manually screened set of M. hapla proteinsthat were initially filtered down by using the ‘‘minimum of oneinstance of an uninterrupted (Gly-X-Y)n motif. Those proteinsidentified by tera-blastp which were not identified by the manualscreen were compared. The combined methods were used toarrive at a confident number and list of true M. hapla collagenproteins from HapPep.
GO Analysis. Each gene was used as a query in a GeneDetectivesearch against the Uniprot (swissprot � trembl) protein database.The top 10 results with a significance of 1.0E-15 were reported. Ascript was then used to query a database containing associationsbetween Uniprot identifiers and GO numbers. The script looks fora GO association for the best match to Uniprot. If it does not findone, it continues to the next match, until it finds the best availablematch to Uniprot that has an associated GO number. The GOnumbers are then used to re-create the GO tree, including countsfor each of the categories traversing the tree.
Protein Domain Analysis. A protein dataset was constructed from theM. hapla Freeze. These proteins were used as queries in an HMMsearch against the Pfam22 database. The top 10 matches with asignificance of E-05 were reported back. The top match for eachquery was used to examine the most common protein domainsidentified in the M. hapla protein dataset. The same analysis wasrepeated by using wormpep185 for comparison. In addition, byusing the top 10 matches, a distribution of the number of domainsidentified in each protein sequence was acquired.
1. Smit AFA, Hubley R, Green P (2004) RepeatMasker Open-3.0. Available at http://www.repeatmasker.org.
2. Haas BJ, et al. (2003) Improving the Arabidopsis genome annotation using maximaltranscript alignment assemblies. Nucleic Acids Res 31:5654–5666.
3. Salzberg SL, Pertea M, Delcher AL, Gardner MJ, Tettelin H (1999) Interpolated Markovmodels for eukaryotic gene finding. Genomics 59:24–31.
Fig. S1. Repetitive elements in the M. hapla genome consist of mostly low-complexity or simple repeats. �1% of the genome is classified as other, includingmobile elements.
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Fig. S2. G protein-coupled receptors are greatly reduced in M. hapla compared with C. elegans. Many have unknown function, and others encode typicalnervous system components involved in signal transduction.
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Fig. S4. Comparison of C. elegans and M. hapla genome organization reveals conserved macro- and microsynteny. (A) Gene order of dpy-30 and rnp-1 in C.elegans operon CEOP5328 is conserved in M. hapla, although Mh-dpy-30 has two additional introns compared to Ce-dpy-30, and apparent exon shuffling hasmoved the last exon of Mh-dpy-30 to within an Mh-rnp-1 intron. (B) Three operons from a 3-Mb span of C. elegans chromosome III have at least partialconservation on a 37-kb span of M. hapla contig 116. Four of the five genes in CEOP3272 have conserved order in M. hapla (dark blue) with the fifth found ona separate contig (light blue). Two genes of C. elegans operon CEOP3414 are conserved with M. hapla, and operon CEOP3508 is completely conserved. (C) Operonloss demonstrated by CEOP1388. Three of the four genes appear absent from the M. hapla genome.
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*Raw sequences were run through a series of software tools to remove contaminating sequences. See text for details.†Sequences excluded based on quality by using algorithm used by Arachne.‡Sequences excluded based on criteria provided to Arachne config files.
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Most repeats fragmented by insertions or deletions have been counted as one element. Runs of �20 Ns in querywere excluded in % calculated. The query species was assumed to be Caenorhabditis.RepeatMasker version open-3.0.8, default mode. Run with cross�match version 0.990329. RepBase Update 9.04,RM database version 20040702.
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Table S3. Known secretion genes found in the M. hapla genome
GenBank accession no. Description
DQ841123 M. hapla parasitism protein 16D10AY861685 M. incognita pectate lyase 3 (pel3)AJ557572 M. incognita putative cathepsin L protease (cpl-1 gene)AY515703 M. incognita pectate lyase 2 (pel2)AY515702 M. incognita pectate lyase 1 (pel1)AY422837 M. incognita cellulase (eng4)AY422836 M. incognita cellulase (eng3)AY422833 M. incognita putative esophageal gland cell secretory protein 40 (msp40)AY422832 M. incognita putative esophageal gland cell secretory protein 39 (msp39)AY422831 M. incognita putative esophageal gland cell secretory protein 38 (msp38)AY422830* M. incognita putative esophageal gland cell secretory protein 37 (msp37)AY422829 M. incognita putative esophageal gland cell secretory protein 36 (msp36)AY134435* M. incognita putative esophageal gland cell secretory protein 16 (msp16)AY142121 M. incognita putative esophageal gland cell secretory protein 31 (msp31)AY142120* M. incognita putative esophageal gland cell secretory protein 30 (msp30)AY142119 M. incognita putative esophageal gland cell secretory protein 35 (msp35)AY142118 M. incognita putative esophageal gland cell secretory protein 33 (msp33)AY142117 M. incognita putative esophageal gland cell secretory protein 34 (msp34)AY142116 M. incognita putative esophageal gland cell secretory protein 32 (msp32)AY135365 M. incognita putative esophageal gland cell secretory protein 29 (msp29)AY135364 M. incognita putative esophageal gland cell secretory protein 28 (msp28)AY135363 M. incognita putative esophageal gland cell secretory protein 27 (msp27)AY135362 M. incognita putative esophageal gland cell secretory protein 26 (msp26)AY134444 M. incognita putative esophageal gland cell secretory protein 25 (msp25)AY134443* M. incognita putative esophageal gland cell secretory protein 24 (msp24)AY134442 M. incognita putative esophageal gland cell secretory protein 23 (msp23)AY134441 M. incognita putative esophageal gland cell secretory protein 22 (msp22)AY134440 M. incognita putative esophageal gland cell secretory protein 21 (msp21)AY134439 M. incognita putative esophageal gland cell secretory protein 20 (msp20)AY134438 M. incognita putative esophageal gland cell secretory protein 19 (msp19)AY134437 M. incognita putative esophageal gland cell secretory protein 18 (msp18)AY134436 M. incognita putative esophageal gland cell secretory protein 17 (msp17)AY134434 M. incognita putative esophageal gland cell secretory protein 15 (msp15)AY134433 M. incognita putative esophageal gland cell secretory protein 14 (msp14)AY134432 M. incognita putative esophageal gland cell secretory protein 13 (msp13)AY134431 M. incognita putative esophageal gland cell secretory protein 12 (msp12)AF531170 M. incognita putative esophageal gland cell secretory protein 10 (msp10)AF531169 M. incognita putative esophageal gland cell secretory protein 9 (msp9)AF531168* M. incognita putative esophageal gland cell secretory protein 8 (msp8)AF531167 M. incognita putative esophageal gland cell secretory protein 11 (msp11)AF531166 M. incognita putative esophageal gland cell secretory protein 7 (msp7)AF531165 M. incognita putative esophageal gland cell secretory protein 6 (msp6)AF531164 M. incognita putative esophageal gland cell secretory protein 5 (msp5)AF531163 M. incognita putative esophageal gland cell secretory protein 4 (msp4)AF531162 M. incognita putative esophageal gland cell secretory protein 3 (msp3)AF531161 M. incognita putative esophageal gland cell secretory protein 2 (msp2)AF531160 M. incognita putative esophageal gland cell secretory protein 1 (msp1)AJ311902 G. rostochiensis EXPB2 proteinAY288520 H. schachtii ubiquitin extension protein 2AY286305 H. schachtii ubiquitin extension protein (Ubi1)AF502391* H. glycines putative gland protein G10A06AF500024 H. glycines putative gland protein G8H07AF469060 H. glycines ubiquitin extension proteinAF469059 H. glycines annexin 4C10AF469058* H. glycines cellulose binding proteinAF468679* H. glycines chitinaseAJ493677 G. rostochiensis secreted glutathione peroxidase (gpx1)AY098646 M. incognita polygalacturonaseAY026357 H. glycines pectinase precursorAF344862*. H. glycines putative salivary proline-rich glycoprotein precursor Hgg-15AF402771 M. incognita calreticulinAF402309 M. incognita 14–3-3 productAF402308 M. incognita myosin regulatory light chainAF374388 H. glycines vap-1
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AY033601 H. glycines venom allergen-like protein (vap-2)AF323086 M. incognita beta-1,4-endoglucanase (eng-2)AJ300178 G. pallida annexin 2 (nex-2 gene)AF273728* H. glycines hypothetical esophageal gland cell secretory protein 1 (hsp1)AJ251758* G. rostochiensis hypothetical protein (clone A41)AJ251757* G. rostochiensis hypothetical protein (clone A18)AF273735 H. glycines hypothetical esophageal gland cell secretory protein 8 (hsp8)AF224342 M. incognita xylanase (xyl-1)AJ271910* G. rostochiensis putative hypodermis secreted protein (sxp1 gene)AJ270995* G. rostochiensis putative amphid protein (ams1 gene)AF100549 M. incognita beta-1,4-endoglucanase (eng-1)AJ243736 G. rostochiensis peroxiredoxin (tpx gene)Y09293 G. pallida putative SEC-2 proteinAF095949 M. javanica chorismate mutase (NC30)AF013289 M. incognita secreted protein MSP-1 (msp-1)AF049139 M. incognita cellulose binding protein precursor cbp-1
*Gene not identified.
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Table S5. Operon conservation by C. elegans chromosome:Number of operons found on each of the C. eleganschromosomes and number of each of those found at leastpartially conserved in M. hapla
Operon name, location, and number of genes are based on C. elegans data found on WormBase. �M. haplatogether� indicates the number of genes from the C. elegans operon found in proximity to each other. �M. haplatotal� is the total number of genes found from the operon in the M. hapla dataset. Numbers split by a �/� indicatemore than one set of genes that are in proximity within the set, but not between sets (e.g., 2/2 indicates that forthe four genes in operon CEOP1552, there are two sets of 2 conserved genes, but those 2 sets are not in proximityto each other).
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