Article Figures & Data
Figures
- Fig 1
Leaf-cutter ants forage on fresh foliar biomass (A) and use it as manure to cultivate symbiotic microbial gardens (B) that they consume for food. Fresh biomass is progressively degraded after it is integrated into the top strata of leaf-cutter ant gardens, creating a vertical gradient of biomass degradation (C). Photo credits: panel A, http://en.wikipedia.org/wiki/File:Leafcutter_ants_transporting_leaves.jpg (used under the GNU free documentation license, version 1.2); panel B, photo by Jarrod J. Scott; panel C, reprinted from reference 16 (based on original art by Cara Gibson and used under the Creative Commons attribution license).
- Fig 2
Heat map representing the relative numbers of mass spectra matching to the L. gongylophorus CAZyme (blue), FOLyme (magenta), and MEROPs (brown) protein families in the top, middle, and bottom strata of Ac. echinatior and At. cephalotes gardens. Rows have been normalized to unity. The dendrogram represents clustering based on the Pearson correlation of the spectral profiles for each protein family.
- Fig 3
Comparison of the spectral profiles recovered from mapping all mass spectra against the L. gongylophorus protein predictions.
- Fig 4
Bar chart showing the raw numbers of mass spectra that could be mapped to a subset of the most abundant lignocellulases identified in the six samples. Predicted FOLymes (A), cellulases (B), and hemicellulases and pectinases (C) are shown.
Tables
- Table 1
L. gongylophorus draft genome sequencing and annotation statistics
Statistic Value No. of contigs in the L. gongylophorus assembly 92,785 Total size (bp) in assembly 101,584,475 N50 contig size (bp) 1,793 No. of predicted proteins 12,132 No. of proteins verified by spectral mapping 4,567 % with KOG annotations 71.1 % with Pfam annotations 71.4 Total no. of mass spectra mapped onto proteins 484,059 - Table 2
Fungal lignocellulases with high spectral abundance in the metaproteomic data setsa
LAG ID Protein family Annotation No. of spectra mapped Ac. echinatior At. cephalotes CAZymes LAG_992 GH15 Glycoamylase, glycodextranase 3,812 1,428 LAG_4755 PL1 Pectin/pectate lyase 3,425 1,121 LAG_3581 CE5 Acetyl-xylan esterase, cutinase 305 1,440 LAG_1450 CE8 Pectin methylesterase 998 543 LAG_543 GH28 Polygalacturonase 1,050 387 LAG_3369 PL4 Rhamnogalacturonan lyase 889 462 LAG_3001 GH35 β-Galactosidase 495 557 LAG_81 PL4 Rhamnogalacturonan lyase 116 791 LAG_420 GH18 Chitinase, acetylglucosaminidase 186 688 LAG_2062 GH3 Glucosidase, xylosidase 325 252 LAG_1651 GH78 Rhamnosidase 163 403 LAG_2564 GH3 Glucosidase, xylosidase 116 445 LAG_2638 GH13, CBM20 Amylase, pollulanase, glucosidase 449 58 LAG_5098 GH3 Glucosidase, xylosidase 335 131 LAG_4224 GH10 Xylanase 249 146 FOLymes LAG_2404 LO1 Laccase 3,483 1,947 LAG_2639 LO1 Laccase 2,562 2,013 LAG_2522 LDA3 Glyoxal oxidase 1,356 641 LAG_5549 LO1 Laccase 264 373 Proteases LAG_2622 A01A Aspartyl protease 7,717 3,371 LAG_3716 M36 Metalloprotease 2,861 1,564 LAG_2011 S09X Serine protease 1,998 1,262 LAG_2465 S53 Serine protease 1,578 712 LAG_3735 S08A Serine protease 1,599 337 LAG_981 S10 Serine protease 1,038 310 LAG_5096 S08A Serine protease 471 783 LAG_439 A01A Aspartyl protease 433 693 LAG_7402 A01A Aspartyl protease 379 220 LAG_3725 M28E Metalloprotease 388 120 LAG_2527 S53 Serine protease 307 122 LAG_3512 S08A Serine protease 145 247 LAG_1757 S10 Serine protease 243 91 ↵a The spectral abundances shown represent the sum recovered from the top, middle, and bottom strata for both the Ac. echinatior and At. cephalotes samples.
- Table 3
Leucoagaricus gongylophorus isolates, their countries of origin, host ant species, and genes that were successfully amplified and sequenced from their purified DNA
Isolate IDa Country of origin Host ant species Sequencing successb CBHI CBHII XynI XynII LG_Peru1 Peru Acromyrmex sp. X X X X LG_CR1 Costa Rica Atta cephalotes X X X X LG_PN1 Panama Acromyrmex octospinosus X X X X LG_CR2 Costa Rica Atta cephalotes X X X X LG_CR3 Costa Rica Acromyrmex echinatior X X X X LG_CR4 Costa Rica Acromyrmex echinatior X X X X LG_CR5 Costa Rica Atta cephalotes X X X X LG_Pe2 Peru Acromyrmex sp. X X X X LG_CR6 Costa Rica Atta cephalotes X X X X LG_ARG1 Argentina Acromyrmex laticeps X X LG_ARG2 Argentina Acromyrmex niger X X X - Table 4
Nucleotide and amino acid similarities of four CAZymes sequenced from 11 L. gongylophorus isolates
Amplicon CAZy family Length of nucleotide alignment Length of amino acid alignment Avg nucleotide identity (%) Avg no. of gaps in nucleotide alignment Avg amino acid identity (%) Avg no. of gaps in amino acid alignment XynI GH10 647 94 99.1 0.92 99.17 0 XynII GH10 429 152 98.9 1.04 100 0 CBHI GH7 507 147 98.8 1.02 98.94 0 CBHII GH6 838 237 99.5 0.91 99.9 0
Supplemental material
Files in this Data Supplement:
- Supplemental file 1 -
Clustering of all lignocellulases identified in the Ac. echinatior (Fig. S1) and At. cephalotes (Fig. S2) metaproteomic samples with at least 10 mass spectra mapping; graph of % GC content and nucleotide length for contigs in the L. gongylophorus assembly (Fig. S3); flow chart outlining the processing of the metaproteomic samples (Fig. S4); maximum-likelihood phylogenetic trees created with FastTree from amino acid alignments of CAZymes amplified from L. gongylophorus isolates and sequenced (Fig. S5); annotation statistics for the 12,132 nonredundant protein predictions made from the draft L. gongylophorus genome (Table S1); list of CAZyme modules (Table S2) and FOLymes (Table S3) identified in the L. gongylophorus genome that were verified by spectral mapping of metaproteomic data; list of MEROPS proteases with signal peptides identified in the L. gongylophorus genome confirmed through spectral mapping of metaproteomic data (Table S4); primers used for the amplification of CAZyme-encoding genes in L. gongylophorus isolates (Table S5); supplemental text: protein prediction and annotation of the draft L. gongylophorus genome, proteomic sample preparation (Rapigest, FASP, high-pH RP C18 fractionation), mass spectometry analyses, protemic data analysis and data filtering.
PDF, 1.1M
- Supplemental file 2
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Annotation of all L. gongylophorus proteins that were identified in the draft genome and confirmed through spectral mapping (Data Set S2).
XLS, 3.0M
- Supplemental file 3
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Details regarding the spectra that mapped to lignocellulases encoded in the draft L. gongylophorus genome (Data Set S3).
XLS, 25K
- Supplemental file 4
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Annotation of bacterial proteins identified in the metaproteomic experiments of this work (Data Set S4).
XLS, 518K
- Supplemental file 5
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List of peptides mapping to lignocellulases for which only a single unique peptide could be mapped in our metaproteomic experiments (Data Set S5).
XLS, 9.0K
- Supplemental file 1 -
