Tandem-running is a recruitment behavior in ants that has been described as a form of teaching, where spatial information possessed by a leader is conveyed to following nestmates. Within Temnothorax ants, tandem-running is used within a variety of contexts, from foraging and nest relocation to – in the case of slavemaking species – slave raiding. Here, we elucidate the transcriptomic basis of scouting, tandem-leading, and tandem-following behavior across two species with divergent lifestyles: the slavemaking Temnothorax americanus and its primary, non-parasitic host T. longispinosus. Analysis of gene expression data from brains revealed that only a small number of unique differentially-expressed genes are responsible for scouting and tandem-running. Comparison of orthologous genes between T. americanus and T. longispinosus suggests that tandem-running is characterized by species-specific patterns of gene usage. However, within both species, tandem-leaders showed gene expression patterns median to those of scouts and tandem-followers, which was expected, as leaders can be recruited from either of the other two behavioral states. Most importantly, a number of differentially-expressed behavioral genes were found, with functions relating to learning and memory formation in other social and non-social insects. This includes a number of up-regulated receptor genes such as a glutamate and dopamine receptor, as well as serine/threonine protein phosphatases and kinases. Learning and memory genes were specifically up-regulated within scouts and tandem-followers, not only reinforcing previous behavioral studies into how Temnothorax navigate novel environments and share information, but also providing insight into the molecular underpinnings of teaching and learning within social insects.
Script_S1
This is code to replicate the analysis from Alleman et al. "Tandem-Running and Scouting Behavior is Characterized by Up-Regulation of Learning and Memory formation genes within the Ant Brain": DESeq2 analysis of T. americanus, Transcriptome constructed using Trinity and filtered for those contigs that contain an open reading frame, Expected read counts created using RSEM
Script_S2
This is code to replicate the analysis from Alleman et al. "Tandem-Running and Scouting Behavior is Characterized by Up-Regulation of Learning and Memory formation genes within the Ant Brain": DESeq2 analysis of T. longispinosus, Transcriptome constructed using Trinity and filtered for those contigs that contain an open reading frame, Expected read counts created using RSEM.
Script_S3
This is code to replicate the analysis from Alleman et al. "Tandem-Running and Scouting Behavior is Characterized by Up-Regulation of Learning and Memory formation genes within the Ant Brain": Weighted Gene Co-expression Analysis (WGCNA) of T. americanus, Transcriptome constructed using Trinity and filtered for those contigs that contain an open reading frame, Expected read counts created using RSEM and filtered for contigs with at least 10 count in at least 4 samples and maximum Cook's distance below 38. Script modified from Tutorials provided on https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/
Script_S4
This is code to replicate the analysis from Alleman et al. "Tandem-Running and Scouting Behavior is Characterized by Up-Regulation of Learning and Memory formation genes within the Ant Brain": Weighted Gene Co-expression Analysis (WGCNA) of T. longispinosus, Transcriptome constructed using Trinity and filtered for those contigs that contain an open reading frame, Expected read counts created using RSEM and filtered for contigs with at least 10 count in at least 4 samples and maximum Cook's distance below 38. Script modified from Tutorials provided on https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/
Script_S5
This is code to replicate the analysis from Alleman et al. "Tandem-Running and Scouting Behavior is Characterized by Up-Regulation of Learning and Memory formation genes within the Ant Brain": GO enrichment analysis of T. americanus, Transcriptome constructed using Trinity, Differentially expressed contigs obtained using DESeq2, Modules of contigs obtained using WGCNA.
Script_S6
This is code to replicate the analysis from Alleman et al. "Tandem-Running and Scouting Behavior is Characterized by Up-Regulation of Learning and Memory formation genes within the Ant Brain": GO enrichment analysis of T. longispinosus, Transcriptome constructed using Trinity, Differentially expressed contigs obtained using DESeq2, Modules of contigs obtained using WGCNA.
Script_S7
This is code to replicate the analysis from Alleman et al. "Tandem-Running and Scouting Behavior is Characterized by Up-Regulation of Learning and Memory formation genes within the Ant Brain": Homologue analysis between T. americanus and T. longispinosus, Transcriptomes constructed using Trinity, DEGs obtained by using DESeq2, Orthogroups created using Orthofinder.
Table_S1
Expression matrix of T. americanus, generated using RSEM v.1.3.0.
Table_S2
Expression matrix T. longispinosus generated using RSEM v.1.3.0.
Table_S3
Differentially expressed genes of T. americanus generated using R packages DESeq2 v.1.16.1. This table consists of six sub-tables, one for each pairwise comparison between behaviors with only over-expressed contigs with a adjusted p-value<0.05 and Dunn p-value<0.05 shown.
Table_S4
Differentially expressed genes of T. longispinosus generated using R packages DESeq2 v.1.16.1. This table consists of six sub-tables, one for each pairwise comparison between behaviors with only over-expressed contigs with a adjusted p-value<0.05 and Dunn p-value<0.05 shown.
Table_S5
Contigs in significant modules of WGCNA in T. americanus generated using R packages WGCNA v.1.64-1, ggpubr v.0.1.8, DESeq2 v.1.16.1.
Table_S6
Contigs in significant modules of WGCNA in T. longispinosus generated using R packages WGCNA v.1.64-1, ggpubr v.0.1.8, DESeq2 v.1.16.1.
Table_S7
Enriched GO terms in DEGs and modules of T. americanus generated using InterProScan v.5.25-64.0, R package topGO v.2.28.0.
Table_S8
Enriched GO terms in DEGs and modules of T. longispinosus generated using InterProScan v.5.25-64.0, R package topGO v.2.28.0.
Table_S9
Enriched KEGG pathways in DEGs and modules of T. americanus generated using InterProScan v.5.25-64.0.
Table_S10
Enriched KEGG pathways in DEGs and modules of T. longispinosus generated using InterProScan v.5.25-64.0.
Table_S11
Orthogroups found between transcriptomes of T. americanus and T. longispinosus generated using Orthofinder v.1.1.8.
Table_S12
Orthogroups found between DEGs of T. americanus and T. longispinosus generated using Orthofinder v.1.1.8.
Table_S13
Orthogroups found between DEGs of T. longispinosus and T. americanus generated using Orthofinder v.1.1.8.
Tamer_BLAST_transcriptome
BLAST annotations of all contigs in the Trinity transcriptome of T. americanus generated using blastx, NCBI BLAST v2.6.0.
Tamer_Interproscan_GO
Gene ontology annotations of all contigs of the transcriptome of T. americanus generated using InterProScan v.5.25-64.0.
Tamer_Interproscan_KEGG
KEGG pathways of all contigs of the transcriptome of T. americanus generated using InterProScan v.5.25-64.0.
Tamer_transcriptome_filtered
Transcriptome of T. americanus after all filtering steps prior to gene expression analysis generated using Trinity v.2.4.0, TransDecoder TransDecoder v.3.0.1, R package DESeq2 v.1.16.1.
Tamer_Trinity_Transcriptome
Transcriptome of T. americanus created by Trinity without any filtering steps generated using Trinity v.2.4.0.
Tlongi_BLAST_transcriptome
BLAST annotations of all contigs in the Trinity transcriptome of T. longispinosus generated using blastx, NCBI BLAST v2.6.0.
Tlongi_Interproscan_GO
Gene ontology annotations of all contigs of the transcriptome of T. longispinosus generated using InterProScan v.5.25-64.0.
Tlongi_Interproscan_KEGG
KEGG pathways of all contigs of the transcriptome of T. longispinosus generated using InterProScan v.5.25-64.0.
Tlongi_transcriptome_filtered
Transcriptome of T. longispinosus after all filtering steps prior to gene expression analysis generated using Trinity v.2.4.0, TransDecoder TransDecoder v.3.0.1, R package DESeq2 v.1.16.1.
Tlongi_Trinity_Transcriptome
Transcriptome of T. longispinosus created by Trinity without any filtering steps generated using Trinity v.2.4.0.
ReadMe
This file describes all supplementary material provided alongside: Tandem-Running and Scouting Behavior is Characterized by Up-Regulation of Learning and Memory formation genes within the Ant Brain
(A. Alleman, M. Stoldt, B. Feldmeyer, S. Foitzik) 2019