TY - JOUR
T1 - Proteome-Based Clustering Approaches Reveal Phylogenetic Insights into Amphistegina
AU - Stuhr, Marleen
AU - Blank-Landeshammer, Bernhard
AU - Meyer, Achim
AU - Baumeister, Vera
AU - Rahnenführer, Jörg
AU - Sickmann, Albert
AU - Westphal, Hildegard
N1 - KAUST Repository Item: Exported on 2022-09-14
Acknowledgements: This project was funded by the Leibniz Association (No. SAW-2014-ISAS-2) awarded to Hildegard Westphal, Albert Sickmann and Jörg Rahnenführer. Sampling in the Florida Keys was conducted under the Research Permit (No. FKNMS2015-026). Samples from Zanzibar were collected under the Revolutionary Government of Zanzibar 434 (S.M.Z.) Research Permit (No. 0671). We sincerely thank Pamela Hallock and Gi- ta R. Narayan for their sampling support, and the staff of the MAREE at ZMT for help with foraminifera cultures.
PY - 2022/7/19
Y1 - 2022/7/19
N2 - Foraminifera are highly diverse and have a long evolutionary history. As key bioindicators, their phylogenetic schemes are of great importance for paleogeographic applications, but may be hard to recognize correctly. The phylogenetic relationships within the prominent genus Amphistegina are still uncertain. Molecular studies on Amphistegina have so far only focused on genetic diversity within single species and suggested a cryptic diversity that demands for further investigations. Besides molecular sequencing-based approaches, different mass spectrometry-based proteomics approaches are increasingly used to give insights into the relationship between samples and organisms, especially as these do not require reference databases. To better understand the relationship of amphisteginids and test different proteomics-based approaches we applied de novo peptide sequencing and similarity clustering to several populations of Amphistegina lobifera, A. lessonii and A. gibbosa. We also analyzed the dominant photosymbiont community to study their influence on holobiont proteomes. Our analyses indicate that especially de novo peptide sequencing allows to reconstruct the relationship among foraminiferal holobionts, although the detected separation of A. gibbosa from A. lessonii and A. lobifera may be partly influenced by their different photosymbiont types. The resulting dendrograms reflect the separation in two lineages previously suggested and provide a basis for future studies.
AB - Foraminifera are highly diverse and have a long evolutionary history. As key bioindicators, their phylogenetic schemes are of great importance for paleogeographic applications, but may be hard to recognize correctly. The phylogenetic relationships within the prominent genus Amphistegina are still uncertain. Molecular studies on Amphistegina have so far only focused on genetic diversity within single species and suggested a cryptic diversity that demands for further investigations. Besides molecular sequencing-based approaches, different mass spectrometry-based proteomics approaches are increasingly used to give insights into the relationship between samples and organisms, especially as these do not require reference databases. To better understand the relationship of amphisteginids and test different proteomics-based approaches we applied de novo peptide sequencing and similarity clustering to several populations of Amphistegina lobifera, A. lessonii and A. gibbosa. We also analyzed the dominant photosymbiont community to study their influence on holobiont proteomes. Our analyses indicate that especially de novo peptide sequencing allows to reconstruct the relationship among foraminiferal holobionts, although the detected separation of A. gibbosa from A. lessonii and A. lobifera may be partly influenced by their different photosymbiont types. The resulting dendrograms reflect the separation in two lineages previously suggested and provide a basis for future studies.
UR - http://hdl.handle.net/10754/679788
UR - https://link.springer.com/10.1007/s12583-022-1609-1
U2 - 10.1007/s12583-022-1609-1
DO - 10.1007/s12583-022-1609-1
M3 - Article
SN - 1674-487X
JO - Journal of Earth Science
JF - Journal of Earth Science
ER -