DOI: 10.5061/dryad.f1vhhmh72
title: Endogenous glycoside hydrolases reveal foraminiferal capacity to degrade terrestrial and marine polysaccharides

description: Foraminifera, a major component of sediment biomass, play a critical role
 in sedimentary food webs. In this study, we identified and characterized
 endogenous glycoside hydrolases (GHs) in Cymbaloporetta bradyi,
 demonstrating their capacity to degrade both terrestrial and marine
 polysaccharides. Through transcriptomic and in silico analyses,
 prokaryotic and eukaryotic contamination was minimized, ensuring the
 identified GHs were of foraminiferal origin. Our results revealed that
 cellulases, chitinases, and mannanases are the most highly expressed GHs,
 even under nutrient-rich conditions. Xylanases, pectinases, and
 fucosidases are also verified being possessed by C. bradyi. The presence
 of signal peptides in cellulases and cellulosome-related genes suggests an
 extracellular cellulose-degrading system in C. bradyi. These findings
 indicate that C. bradyi can metabolize polysaccharides from terrestrial
 plants and marine algae, reflecting adaptability to diverse sedimentary
 environments. As foraminifera serve as prey for various deposit feeders
 and predators, their ability to degrade complex polysaccharides highlights
 their key role in sedimentary food webs and the carbon cycle. This study
 underscores the ecological significance of foraminifera in linking primary
 producers to higher trophic levels within marine sediments.
description: # Endogenous glycoside hydrolases reveal foraminiferal capacity to degrade
 terrestrial and marine polysaccharides Dataset DOI:
 [10.5061/dryad.f1vhhmh72](10.5061/dryad.f1vhhmh72) ## Description of the
 data and file structure This dataset contains the assembled transcripts of
 *C. bradyi*, and extracted transcripts that have similarities to
 cellulase, xylanase, pectinase, chitinase, mannanase, fucosidase, and
 laminarinase.  ### Files and variables #### File:
 Assembled_transcripts_of_C.bradyi.fasta **Description:** FASTA file
 containing assembled transcripts of *Cymbaloporetta bradyi*. #### File:
 Annotation.csv **Description:** Annotated transcripts analyzed by
 Trinotate, integraging BLASTp, Pfam(HMM), SignalP and Gene Ontology (GO)
 results. | Column name | Definition | | :---------------------- |
 :-------------------------------------------- | | gene\_id | IDs of each
 gene generated by Trinity | | transcript\_id | IDs of each isoform
 generated by Trinity | | prot\_id | IDs of each isoform generated by
 TransDecoder | | prot\_coords | ORF amino acid coordinates of each isoform
 | | sprot\_Top\_BLASTP\_hit | Blastp search result | | Pfam | Pfam search
 result | | SignalP | Signal peptide result | | gene\_ontology\_BLASTX |
 Gene ontology result (Blastx) of each ORF | | gene\_ontology\_BLASTP |
 Gene ontology result (Blastp) of each ORF | | gene\_ontology\_Pfam | Gene
 ontology result (Pfam) of each ORF | #### File:
 CAZy_database_BlastP_results.zip **Description:** Annotated transcripts
 obtained by performing BLASTp against the full CAZy database. These
 results were merged with annotations from Trinotate to facilitate the
 identification of GH-related transcripts of interest. | Column name |
 Definition | | :---------- | :------------------------------ | | qseqid |
 IDs of query sequences | | sseqid | IDs of searched sequences | | pident |
 Percentage of identical matches | | length | Alignment length | | mismatch
 | Number of mismatches | | gapopen | Number of gap openings | | qstart |
 Start of alignment in query | | qend | End of alignment in query | |
 sstart | Start of alignment in subject | | send | End of alignment in
 subject | | evalue | Expect value | | bitscore | Bit score | | annotation
 | Annotation | #### File: Sequences_of_GHs_for_PhylogeneticTree.zip
 **Description:** A compressed archive containing reference sequences of
 each GH type used in alignment. #### File: Extracted_GHs.csv
 **Description:** A comprehensive list of transcripts showing similarity to
 glycoside hydrolases targeted in this study, including cellulase,
 xylanase, pectinase, chitinase, mannanase, fucosidase, and laminarinase.
 The file includes BLASTp results, UniProt and Pfam domain annotations,
 SignalP predictions, Gene Ontology assignments, and transcript expression
 levels (TPM). Raw RSEM results used for TPM calculation are available as
 the uploaded file "RSEM.isoforms.results". | Column name |
 Definition | | :------------------------------------------- |
 :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Category | Category of isoforms of each origin; (Foraminiferal Genome aligned, Eukaryotic origin detected by phylogenetic analysis, Prokaryotic origin detected by phylogenetic analysis, Eukaryotic origin found in CAZY Database Blastp & detected by phylogenetic analysis, Prokaryotic origin found in CAZY Database Blastp & detected by phylogenetic analysis) | | GHF decision by BLASTp | GHF category analyzed and determined by phylogenetic analysis. Numbers after "-" are counts of each GHF | | Counts of each origin | Counts of each category | | gene\_id | IDs of each gene generated by Trinity | | transcript\_id | IDs of each isoform generated by Trinity | | prot\_id | IDs of each isoform generated by TransDecoder | | prot\_coords | ORF amino acid coordinates of each isoform | | sprot\_Top\_BLASTP\_hit | Blastp search result | | Pfam | Pfam search result | | SignalP | Signal peptide result | | Signal Peptide | Hit = 1, Not hit = 0 | | gene\_ontology\_BLASTP | Gene ontology result (Blastp) of each ORF | | gene\_ontology\_Pfam | Gene ontology result (Pfam) of each ORF | | Foraminiferal genome hit (Globobulimina sp.) | "Hit" = aligned by *Globobulimina* sp. genome; blank = no hits | | genome hit (Reticulomyxa filosa) | "Hit" = aligned by *Reticulomyxa filosa* genome; blank = no hits | | genome hit (Astrammina rara) | "Hit" = aligned by *Astrammina rara* genome; blank = no hits | | count (gene scale) | Counts of each category in gene-scale | | TPM | Transcripts Per Million. It is a relative measure of transcript abundance. The sum of all transcripts' TPM is 1 million | | Log~2~TPM | Log~2~ of TPM | #### File: RSEM.isoform.results.txt **Description:** TPM expression data for all assembled transcripts (isoforms), generated via RSEM. | Column name | Definition | | :---------------- | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | transcript\_id | IDs of each isoform generated by Trinity | | gene\_id | IDs of each gene generated by Trinity | | length | transcript's sequence length (poly(A) tail is not counted) | | effective\_length | counts only the positions that can generate a valid fragment. If no poly(A) tail is added, 'effective\_length' is equal to transcript length | | expected\_count | the sum of the posterior probability of each read comes from this transcript over all reads | | TPM | Transcripts Per Million. It is a relative measure of transcript abundance. The sum of all transcripts' TPM is 1 million | | FPKM | Fragments Per Kilobase of transcript per Million mapped reads. It is another relative measure of transcript abundance | | IsoPct | Isoform percentage. It is the percentage of this transcript's abundance over its parent gene's abundance. If its parent gene has only one isoform or the gene information is not provided, this field will be set to 100 | ## Code/software Bioedit Sequence Alignment Editor