To sequence a genome or not to sequence a genome, that is the question

In a paper out last month in the Journal of Phycology, Bhattacharya et al. (2015) provide a perspective on the need for more algal genomes.

[A] relevant question on the minds of many phycologists might be: do we really need more algal genomes or, should we stop and focus on the hard job of developing genetic tools and other resources for already sequenced taxa?

Chondrus crispus, one of the first macroalgal genomes (Collén et al. 2013) © SA Krueger-Hadfield

Chondrus crispus, one of the first macroalgal genomes (Collén et al. 2013) © SA Krueger-Hadfield

Algal molecular work has historically lagged a bit behind similar work in other taxonomic groups even though algae are important primary producers in marine environments.

The authors provide four main reasons why genome sequencing should still be a focus in phycological research, some of which can probably be extended to other taxonomic groups as well:

1. Transcriptomes that aim to create gene inventories or study gene expression differences … may not be sufficient for in-depth study of genomes.

RNAseq data support the gene discovery, but these data can be greatly improved by the availability of reference genomes. Bhattacharya et al. (2015) point to the pitfalls in using transcriptome sequences in isolation which can lead to assembly artifacts.

2. Much of natural biodiversity is still unstudied, necessitating approaches such as single cell genomics (SCG) that, although still challenging when applied to algae, can sample taxa directly from the environment.

For example, one problem in the study population genetic structure of many microalgae is the necessity of initiating and maintaining extensive culture collections initiated from a single cell obtained from the environment. There is often loss of cells from the field to the lab and this could bias population genetic estimates when clonal cultures are treated analogously to single genets of macroscopic organisms (Krueger-Hadfield et al. 2014). There are also many unicellular forms which cannot be maintained in the laboratory, so as phycologists, we are left to work with species that do not represent the “full extent of microbial genetic capacity.” Single cell isolations will benefit all molecular work, including population genetics and genome sequencing, on well described species, but also those elusive ones.

Algal genomes have also played an important role in the study of the evolution of life cycles. Many macroalage undergo an alternation of free-living diploid individuals, called sporophytes, and free-living haploid individuals, called gametophytes (more about these complexities that are near and dear to my heart in a later post). Coelho et al. (2011) described a mutation, aptly named ouroboros after the symbol of the cycle of life, that causes the sporophyte to develop as a gametophyte.

Ouroboros © Wikipedia

Ouroboros © Wikipedia

This mutation is similar to homeotic mutations found in other organisms, such as the mutation that turns antenna into legs in fruit flies. But, in Ectocarpus, this mutation doesn’t just occur at the level of an organ, but at the whole organism.

3. Horizontal gene transfer (HGT) in algae is no longer controversial, but rather a major contributor to the evolution of photosynthetic lineages, and its study benefits greatly from completed (or draft) genomes.

HGT has been found to play significant roles in algal adaptation to different environments (e.g., Qiu et al. 2013). Genomic data will enable the description of how and when foreign genes were acquired.

4. Epigenetic and genome evolution among populations are best studied using assembled genome data.

Epigenetic patterns, such as changed in DNA methylation, have not been well documented in algal groups, but genomic data will advance these types of questions. This is an important avenue as there are many invasive seaweeds in which clonal fragmentation is common or in which genetic diversity is limited. Epigenetic patterns have been shown to facilitate the invasion of an introduced songbird in which methylation was suggested to increase phenotypic variation enabling short-term adaptation following the demographic and genetic bottlenecks of invasions (Liebl et al. 2013).

5. … the opportunity to reconstruct the eukaryotic tree of life using validated nuclear gene data.

Recent work has demonstrated a complex history of algal evolution and increased genomic data will offer a glimpse of how natural selection has shaped algal lineages.

References

Bhatacharya et al. (2015) Why we need more algal genomes. Journal of Phycology 51, 1-5. dpi: 10.1111/jpy.12267

Coelho et al. (2011) OUROBOROS is a master regulator of the gametophyte to sporophyte life cycle transition in the brown alga Ectocarpus. PNAS 108, 11518–11523. doi:10.1073/pnas.1102274108

Collén et al. (2013) Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida. PNAS 110, 5247–5252. doi: 10.1073/pnas.1221259110

Krueger-Hadfield et al. (2014) Genotyping an Emiliania hyxleyi (Prymnesiophyceae) bloom event in the North Sea reveals evidence of asexual reproduction.  Biogeosciences 11, 5215-5234. doi:10.5194/bg-11-5215-2014

Liebl et al. (2013) Patterns of DNA methylation throughout a range expansion of an introduced songbird. Integrative and Comparative Biology 53, 351-358. doi: 10.1093/icb/ict007

Qui et al. (2013) Adaptation through horizontal gene transfer in the cryptoendolithic red alga Galdieria phlegrea. Current Biology 23, R865-866. doi:10.1016/j.cub.2013.08.046

Share

About Stacy Krueger-Hadfield

I am a marine evolutionary ecologist interested in the impacts of seascapes and complex life cycles on marine population dynamics. I use natural history, manipulative field experiments and population genetic and genomic approaches with algal and invertebrate models in temperate rocky shores,estuaries and the open ocean.
This entry was posted in bioinformatics, evolution, genomics, horizontal gene transfer, mutation, next generation sequencing, selection and tagged , , , , . Bookmark the permalink.