(A) Maximum likelihood (ML) tree based on concatenation of 354 proteins which are present in all species of the anemones and reference datasets. (Kashimoto et al., 2022)
Embedded Files
In my work, I have applied the transcriptomics dataset for phylogenetic study.
Why transcriptomic data is good for sea anemone phylogenetic tree reconstruction?
Obtaining high-quality transcriptomes, including complete marker genes, from tentacle samples in the open ocean is straightforward.
RNA-seq is cost-effective compared to whole-genome sequencing.
Wide data resources and pipeline availability.
Why do I consider this study important and for whom?
Identifying a small set of marker genes for precise species tree construction would significantly enhance both taxonomy efforts and fieldwork, particularly when distinguishing individuals becomes challenging due to morphological similarities (Photo images below).
Clownfish hosting Anemone Dataset is available here
You can download RNA-seq reads of giant sea anemone from PRJNA723429, PRJNA946267 and PRJNA877849.
Lineage D-
A. frenatus
Lineage A-
A. clarkii
Lineage A-
A. clarkii
Lineage A-
A. clarkii
Comprehensive approach for supporting taxonomy
Comprehensive approach for supporting taxonomy
The symbiosis between giant sea anemones, photosynthetic algae of the family Symbiodiniaceae, and anemonefish is an iconic example of a mutualistic “ménage à 3”. Recent molecular analyses, including phylogenetics, differential gene expression (DEGs), behavioral examinations, and positive gene selection, have revealed that Anemonefish (clownfish) are better taxonomists than humans when selecting giant sea anemone species as their hosts. This research is published in Current Biology (in press).
Optimal marker set for population genetics studies
Optimal marker set for population genetics studies
The relationship between anemonefish and sea anemones is one of the most emblematic examples of mutualistic symbiosis in coral reefs. Although this is a textbook example, the major aspects of this symbiosis are still not fully understood in mechanistic terms. In the previous mtDNA as a molecular maker, the placement of different species within these three groups of giant sea anemone was often poorly resolved. For example, within Heteractis, Heteractis crispa was found in three different clades, sometimes associated with other Heteractis, sometimes even closer to Macrodactyla doreensis (Titus et al., 2019; Nguyen et al., 2020). It is difficult to determine whether this result is linked to slowly evolving phylogenetic markers used in these studies or to deeper causes due to our still limited knowledge of the taxonomy of these animals. This clearly shows that more work is needed to identify phylogenetic markers that will improve our understanding of the taxonomy and phylogeny of giant sea anemones.
Maximum likelihood (ML) tree shown that giant sea anemones hosting anemonefish belong to three distinct clades: Entacmaea, Stichodactyla (Heteractis magnifica), and Heteractis based on the Orthologous gene sets (A).
The number of markers present in all 15 datasets (which correspond to nine species) increased to 6889 genes. From them, I selected 1365 orthogroups with a minimum of 86.7% of species having single-copy genes in any orthogroup (B).
The selection of markers for phylogenetic reconstructionmay influence the topology of the resulting trees considerably. Basic universal single-copy orthologs (BUSCO genes) Among 451 BUSCO genes, 226 genes had a sum of branch lengths ≥ the median value. This is a subset of genes with a higher evolutionary rate, which is good for distinguishing differences among closely related species or even within the species (D). Furthermore, 111 BUSCO proteins for which these sequences differ in all samples of our dataset are marked with red dots are used as final set of the marker gene. The remaining 340 genes are shown as black dots (E). Phylogenetic tree based on 111 BUSCO proteins for which these sequences are different in all 13 samples of the giant sea anemones (F). Identifying a small set of marker genes for precise species tree construction would significantly enhance both taxonomy efforts and fieldwork, particularly when distinguishing individuals becomes challenging due to morphological similarities.
Page updated
Google Sites
Report abuse