The developmental transcriptome of contrasting Arctic charr (Salvelinus alpinus) morphs

Arnar Pálsson, 13/11/2014

We just submitted a paper to G3, and deposited the manuscript on BioRxiv.

The developmental transcriptome of contrasting Arctic charr (Salvelinus alpinus) morphs
Jóhannes Gudbrandsson, Ehsan P Ahi, Kalina H Kapralova, Sigrídur R Franzdottir, Bjarni K Kristjánsson, Sophie S Steinhaeuser, Ísak M Jóhannesson, Valerie H Maier, Sigurdur S Snorrason, Zophonías O Jónsson, Arnar Pálsson

Species showing repeated evolution of similar traits can help illuminate the molecular and developmental basis of diverging traits and specific adaptations. Following the last glacial period, dwarfism and specialized bottom feeding morphology evolved rapidly in several landlocked Arctic charr (Salvelinus alpinus) populations in Iceland.
In order to study the genetic divergence between small benthic morphs and larger morphs with limnetic morphotype, we conducted an RNA-seq transcriptome analysis of developing charr. We sequenced mRNA from whole embryos at four stages in early development of two stocks with very different morphologies, the small benthic (SB) charr from Lake Thingvallavatn and Holar aquaculture (AC) charr. The data reveal significant differences in expression of several biological pathways during charr development. There is also a difference between SB- and AC-charr in mitochondrial genes involved in energy metabolism and blood coagulation genes. We confirmed expression difference of five genes in whole embryos with qPCR, including lysozyme and natterin which was previously identified as a fish-toxin of a lectin family that may be a putative immunopeptide. We verified differential expression of 7 genes in developing heads, and the expression associated consistently with benthic v.s. limnetic charr (studied in 4 morphs total). Comparison of Single nucleotide polymorphism (SNP) frequencies reveals extensive genetic differentiation between the SB- and AC-charr (60 fixed SNPs and around 1300 differing more than 50% in frequency). In SB-charr the high frequency derived SNPs are in genes related to translation and oxidative processes. Curiously, several derived SNPs reside in the 12s and 16s mitochondrial ribosomal RNA genes, including a base highly conserved among fishes.
The data implicate multiple genes and molecular pathways in divergence of small benthic charr and/or the response of aquaculture charr to domestication. Functional, genetic and population genetic studies on more freshwater and anadromous populations are needed to confirm the specific loci and mutations relating to specific ecological or domestication traits in Arctic charr.

Transcriptional dynamics of a conserved gene expression network associated with craniofacial divergence in Arctic charr

Arnar Pálsson, 03/11/2014
Background
Understanding the molecular basis of craniofacial variation can provide insights into key developmental mechanisms of adaptive changes and their role in trophic divergence and speciation. Arctic charr (Salvelinus alpinus) is a polymorphic fish species, and, in Lake Thingvallavatn in Iceland, four sympatric morphs have evolved distinct craniofacial structures. We conducted a gene expression study on candidates from a conserved gene coexpression network, focusing on the development ofcraniofacial elements in embryos of two contrasting Arctic charr morphotypes (benthic and limnetic).
Results
Four Arctic charr morphs were studied: one limnetic and two benthic morphs from Lake Thingvallavatn and a limnetic reference aquaculture morph. The presence of morphological differences at developmental stages before the onset of feeding was verified by morphometric analysis. Following up on our previous findings that Mmp2 and Sparc were differentially expressed between morphotypes, we identified a network of genes with conserved coexpression across diverse vertebrate species. A comparative expression study of candidates from this network in developing heads of the four Arctic charr morphs verified the coexpression relationship of these genes and revealed distinct transcriptional dynamics strongly correlated with contrasting craniofacial morphologies (benthic versus limnetic). A literature review and Gene Ontology analysis indicated that a significant proportion of the network genes play a role in extracellular matrix organization and skeletogenesis, and motif enrichment analysis of conserved noncoding regions of network candidates predicted a handful of transcription factors, including Ap1 and Ets2, as potential regulators of the gene network. The expression of Ets2 itself was also found to associate with network gene expression. Genes linked to glucocorticoid signalling were also studied, as both Mmp2 and Sparc are responsive to this pathway. Among those, several transcriptional targets and upstream regulators showed differential expression between the contrasting morphotypes. Interestingly, although selected network genes showed overlapping expression patterns in situ and no morph differences, Timp2 expression patterns differed between morphs.
Conclusion
Our comparative study of transcriptional dynamics in divergent craniofacial morphologies of Arctic charr revealed a conserved network of coexpressed genes sharing functional roles in structural morphogenesis. We also implicate transcriptional regulators of the network as targets for future functional studies.

(Icelandic) Getur verið að neanderdalsmaðurinn hafi ekki dáið út heldur blandast nútímamanninum?

Arnar Pálsson, 31/10/2014

Sorry, this entry is only available in Icelandic.

(Icelandic) Er hægt að klóna manneskju?

Arnar Pálsson, 31/10/2014

Sorry, this entry is only available in Icelandic.

(Icelandic) Er það rétt sem Dr. House segir í einum þætti að ef DNA okkar breytist um 1% þá verðum við höfrungar?

Arnar Pálsson, 31/10/2014

Sorry, this entry is only available in Icelandic.

(Icelandic) Vísindadagur Vonar: Nýjasta tækni og vísindi

Arnar Pálsson, 28/10/2014

Sorry, this entry is only available in Icelandic.

Submission of paper to Developmental dynamics

Arnar Pálsson, 27/10/2014

We co-authored a manuscript submitted recently to a special issue of Developmental dynamics.

Bones in motion: Ontogeny of craniofacial development in sympatric Arctic charr morphs Kalina H. Kapralova, Zophonías O. Jónsson, Arnar Palsson, Sigrídur Rut Franzdóttir, Soizic Le Deuff, Bjarni K. Kristjanson, Sigurður S. Snorrason

Paper on deletions of hunchback binding sites in eve covered by Global medical discovery

Arnar Pálsson, 14/10/2014

Our recent paper on deletion polymorphism in the eve stripe 3+7 enhancer was covered by the Global medical discovery website.

Palsson A, Wesolowska N, Reynisdóttir S, Ludwig MZ, Kreitman M (2014) Naturally Occurring Deletions of Hunchback Binding Sites in the Even-Skipped Stripe 3+7 Enhancer. PLoS ONE 9(5): e91924. doi:10.1371/journal.pone.0091924

Transcription factors (TF) bind to specific DNA sequence to regulate expression of genes. Evolutionary studies of enhancers show that some TF binding sites are well conserved while others are less constrained. The regulatory elements of the even-skipped (eve) gene in Drosophila are a textbook example of regulatory function, as specific activating and repressing TFs bind to specific binding sites and control the spatio-temporal expression of the gene. These enhancers are also a textbook example of TF binding site “turn-over” and compensatory evolution within regulatory elements.

In this study we examine natural sequence polymorphism in characterized enhancers in Drosophila melanogaster, and find the TF binding sites to be preserved by selection. Curiously we find two exceptions, both in the same enhancer of eve (that forms stripes 3 and 7 in the embryo). Both mutations are large deletions (larger than 45 bp) and both remove conserved binding sites for the same transcription factor. Hunchback is an important developmental regulator that affects expression of eve in the embryo. Both deletions are at high frequency in fly populations, and thus do not seem to be harmful for the flies. By analogy one might say that a tree is struck twice by lighting, but doesnt catch fire.

The most puzzling result of this study is that both Hb binding sites are conserved and the two deletions removing them are at up to 35% frequency in the population.

Furthermore, one of the Hb sites was not noticed earlier, because the Drosophila reference genome is homozygous for the deletion allele.

We postulate that coevolution between Hb function and its target sequences best explains the data. In other words, this could reflect compensatory evolution of cis and trans factors, that is developmental system drift in the gene regulatory network controlling stripe formation in fruitfly embryos.

Transcriptional dynamics of a conserved gene expression network

Arnar Pálsson, 25/09/2014

The charr group had one paper accepted in BMC EvoDevo last week. The title is:

Ehsan P Ahi, Kalina H Kapralova, Arnar Palsson, Valerie H Maier, Johannes Gudbrandsson, Sigurdur S Snorrason, Zophonias O Jonsson and Sigridur R Franzdottir Transcriptional dynamics of a conserved gene expression network associated with benthic-limnetic craniofacial divergence in Arctic charr. Abstract to follow.

(Icelandic) Stefnumót skilvirkni og breytileika – snertiflötur þroskunar og þróunar

Arnar Pálsson, 17/09/2014

A review article in Icelandic about the interface of development and evolution, published in the Icelandic Naturalist (Natturufraedingurinn).