Transcriptional profiles associated with Context dependent behavior in Rock X Sand F1 in Lake Malawi Cichlids
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ABSTRACT:
PROVIDER: PRJNA505424 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8187020_1.fastq.gz | Fastqsanger.gz | |||
| SRR8187020_2.fastq.gz | Fastqsanger.gz | |||
| SRR8187021_1.fastq.gz | Fastqsanger.gz | |||
| SRR8187021_2.fastq.gz | Fastqsanger.gz | |||
| SRR8187022_1.fastq.gz | Fastqsanger.gz |
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Project description:We sought to evaluate the brain gene expression profiles of male courtship display. To assess male display and courtship behavior, we designed a courtship preference assay. We evaluated social interactions between males and females using a 40 gallon tank design with a ‘rock’ habitat at one end and ‘sand’ at the other, separated by glass bottom. When parental rock species (Petrotilapia nigra (TaxId 526958), Maylandia zebra (TaxId 106582), Labeotropheus feulliborni) are placed in this tank paradigm, males court females over the rocks. Males of sand species (Mchenga conophorus, Aulonocara baenschi (TaxId 143496), Tramitichromis intermedius (TaxId 323801)) court females over sand and construct species appropriate bowers. When single rock x sand F1 males were placed in this set up with F1 females, males invariably courted females over the ‘rock’ habitat, suggesting genetic dominance. When two rock x sand F1 males were allowed to compete for F1 females in this tank paradigm, something interesting happened. One male, typically the larger, courted females over the rock habitat, and the other simultaneously constructed bowers to court females in the sand. We detected no difference in GSI (gonadal somatic index) between F1 males behaving as ‘socially rock’ vs. ‘socially sand.’ This observation of divergent behavior among interacting F1 brothers suggests an interaction between the genome and the social environment in these males.
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Project description:Most behaviors are associated with heritable genetic variation. Genetic mapping has revealed genomic regions or, in a few cases, specific genes explaining part of this variation. However, understanding how genetic divergence shapes behavioral evolution remains unclear. Here we analyze the evolution of an innate extended phenotype: bower building among male cichlid fish of Lake Malawi, which build bowers of two types, pits and castles. F1 hybrids of pit-digging and castle-building species perform sequential construction of first pit and then castle bowers. Analysis of brain gene expression in these hybrids showed that genes near behavior-associated variants display behavior-dependent allele-specific expression with preferential expression of the pit-species allele during pit digging, and of the castle-species allele during castle building. These genes are highly enriched for functions and pathways involved in neurodevelopment and neural plasticity. Our results suggest that natural behaviors can be associated with complex genetic architectures that alter behavior via cis-regulatory differences whose effects on gene expression are specific to the behavior itself.
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Project description:Whole-genome methylomes and total transcriptomes for muscle and liver tissues of Lake Malawi cichlid species characterised in the context of phenotypic diversification.
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Project description:A laboratory colony of Phlebotomus perniciosus sand flies was maintained. Sand flies were infected with cultured Leishmania infantum promastigotes in stationary phase. Ten infected sand flies were dissected after 5 days and promastigotes within the gut pooled. The cells were immediately washed in PBS once and lysed in TRIzol reagent (Life Technologies). RNA isolation was completed according to the manufacturer's instructions, obtaining 63ng. RNA-seq libraries were generated using the spliced leader sequence for second strand synthesis (Cuypers et al., 2017; Haydock et al., 2015), thus allowing for specific amplification of sequences from L. infantum promastigotes, thus avoiding contamination with material from the sand fly gut. Single-end sequencing was performed in an Illumina HiSeq2500 instrument and data analysis was conducted using bowtie2, samtools, featureCounts and Geneious. The main findings are: i) substantial differences in differential gene expression between sand fly-derived (sfPro) and cultured (acPro) promastigotes; and ii) over-expression of genes involved in metacyclogenesis in sfPro vs. acPro, including gp63 genes, autophagy genes, etc.
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Project description:East African cichlid fishes have radiated in an explosive fashion. The (epi)genetic basis for the abundant phenotypic diversity of these fishes remains largely unknown. As transposable elements (TEs) contribute extensively to genome evolution, we reasoned that TEs may have fuelled cichlid radiations. While TE-derived genetic and epigenetic variability has been associated with phenotypic traits, TE expression and epigenetic silencing remain unexplored in cichlids. Here, we profiled TE expression in African cichlids, and describe dynamic expression patterns during embryogenesis and according to sex. Most TE silencing factors are conserved and expressed in cichlids. We describe an expansion of two truncated Piwil1 genes in Lake Malawi/Nyasa cichlids, encoding a Piwi domain with catalytic potential. To further dissect epigenetic silencing of TEs, we focused on small RNA-driven epigenetic silencing. We detect a small RNA population in gonads consistent with an active Piwi-interacting RNA (piRNA) pathway targeting TEs. We uncover fluid genomic origins of piRNAs in closely related cichlid species. This, along with signatures of positive selection in piRNA pathway factors, points towards fast co-evolution of TEs and the piRNA pathway. Our study is the first step to understand the contribution of ongoing TE-host arms races to the cichlid radiations in Africa.
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Project description:Purpose: The goal of this study is to identify genes that showed a pattern of differential expression between species within activated neurons during mirror-elicited aggression between two species of Lake Malawi cichlid fish which differ in aggressive behaviors, Mchenga conophoros (MC, sand-dwelling) and Petrotilapia chitimba (PC, rock-dwelling). To do this, we use antibodies to phosphorylated ribosomal protein S6 (pS6) to enrich for transcripts bound to phosphorylated ribosomes followed by RNA-seq (PhosphoTRAP). In neurons, this phosphorylation occurs downstream of the binding of neurotransmitters and, thus, pS6 antibodies are increasingly being used as markers of neural activity, similar to immediate early genes (IEGs) like c-fos or egr-1. Methods: Whole brain mRNA samples were collected from 8 adult male cichlids (4 MC, 4 PC) 90min following either 15min exposure to mirror in home tank (Mirror Test) or a Control condition. RNA-immunoprecipitation using antibodies to pS6 were performed and RNA was extracted from immunoprecipitated (IP) RNA samples. We also collected total RNA (input), prior to immunoprecipitation. For details see extraction protocol below. RNA from both input and IP samples was reverse transcribed using the SMART-Seq v4 Ultra Low Input RNA kit. Libraries were prepped using the NEBNext Ultra II FS DNA library Prep Kit for Illumina and sequenced. Sequence reads that passed quality filters were aligned to the Metriaclima zebra (Malawi cichlid) reference genome UMD2A using HiSat2. Transcripts were quantified using StringTie and differential expressional analyses were performed using DESeq2. Results: We identified a large number of genes showing differential expression in mirror-elicited aggression, as well as many genes that differ between ecotypes. These genes, which may underly species differences in behavior, include several neuropeptides, genes involved in the synthesis of steroid hormones, and neurotransmitter activity. Conclusions: This work lays the foundation for future experiments using this emerging genetic model system to investigate the genomic basis of evolved species differences in both brain and behavior.
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