Reconstructing the last common ancestor of all eukaryotes

Thomas A Richards; Laura Eme; John M Archibald; Guy Leonard; Susana M Coelho; Alex de Mendoza; Christophe Dessimoz; Pavel Dolezal; Lillian K Fritz-Laylin; Toni Gabaldón; Vladimír Hampl; Geert J P L Kops; Michelle M Leger; Purificacion Lopez-Garcia; James O McInerney; David Moreira; Sergio A Muñoz-Gómez; Daniel J Richter; Iñaki Ruiz-Trillo; Alyson E Santoro; Arnau Sebé-Pedrós; Berend Snel; Courtney W Stairs; Eelco C Tromer; Jolien J E van Hooff; Bill Wickstead; Tom A Williams; Andrew J Roger; Joel B Dacks; Jeremy G Wideman

doi:10.1371/journal.pbio.3002917

Reconstructing the last common ancestor of all eukaryotes

Thomas A Richards^*, Laura Eme^*, John M Archibald^*, Guy Leonard, Susana M Coelho, Alex de Mendoza, Christophe Dessimoz, Pavel Dolezal, Lillian K Fritz-Laylin, Toni Gabaldón, Vladimír Hampl, Geert J P L Kops, Michelle M Leger, Purificacion Lopez-Garcia, James O McInerney, David Moreira, Sergio A Muñoz-Gómez, Daniel J Richter, Iñaki Ruiz-Trillo, Alyson E SantoroArnau Sebé-Pedrós, Berend Snel, Courtney W Stairs, Eelco C Tromer, Jolien J E van Hooff, Bill Wickstead, Tom A Williams, Andrew J Roger^*, Joel B Dacks^*, Jeremy G Wideman^*

^*Corresponding author for this work

Cell Biochemistry

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Abstract

Understanding the origin of eukaryotic cells is one of the most difficult problems in all of biology. A key challenge relevant to the question of eukaryogenesis is reconstructing the gene repertoire of the last eukaryotic common ancestor (LECA). As data sets grow, sketching an accurate genomics-informed picture of early eukaryotic cellular complexity requires provision of analytical resources and a commitment to data sharing. Here, we summarise progress towards understanding the biology of LECA and outline a community approach to inferring its wider gene repertoire. Once assembled, a robust LECA gene set will be a useful tool for evaluating alternative hypotheses about the origin of eukaryotes and understanding the evolution of traits in all descendant lineages, with relevance in diverse fields such as cell biology, microbial ecology, biotechnology, agriculture, and medicine. In this Consensus View, we put forth the status quo and an agreed path forward to reconstruct LECA's gene content.

Original language	English
Article number	e3002917
Number of pages	24
Journal	PLOS BIOLOGY
Volume	22
Issue number	11
DOIs	https://doi.org/10.1371/journal.pbio.3002917
Publication status	E-pub ahead of print - 25-Nov-2024

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Richards, T. A., Eme, L., Archibald, J. M., Leonard, G., Coelho, S. M., de Mendoza, A., Dessimoz, C., Dolezal, P., Fritz-Laylin, L. K., Gabaldón, T., Hampl, V., Kops, G. J. P. L., Leger, M. M., Lopez-Garcia, P., McInerney, J. O., Moreira, D., Muñoz-Gómez, S. A., Richter, D. J., Ruiz-Trillo, I., ... Wideman, J. G. (2024). Reconstructing the last common ancestor of all eukaryotes. PLOS BIOLOGY, 22(11), Article e3002917. Advance online publication. https://doi.org/10.1371/journal.pbio.3002917

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title = "Reconstructing the last common ancestor of all eukaryotes",

abstract = "Understanding the origin of eukaryotic cells is one of the most difficult problems in all of biology. A key challenge relevant to the question of eukaryogenesis is reconstructing the gene repertoire of the last eukaryotic common ancestor (LECA). As data sets grow, sketching an accurate genomics-informed picture of early eukaryotic cellular complexity requires provision of analytical resources and a commitment to data sharing. Here, we summarise progress towards understanding the biology of LECA and outline a community approach to inferring its wider gene repertoire. Once assembled, a robust LECA gene set will be a useful tool for evaluating alternative hypotheses about the origin of eukaryotes and understanding the evolution of traits in all descendant lineages, with relevance in diverse fields such as cell biology, microbial ecology, biotechnology, agriculture, and medicine. In this Consensus View, we put forth the status quo and an agreed path forward to reconstruct LECA's gene content.",

author = "Richards, {Thomas A} and Laura Eme and Archibald, {John M} and Guy Leonard and Coelho, {Susana M} and {de Mendoza}, Alex and Christophe Dessimoz and Pavel Dolezal and Fritz-Laylin, {Lillian K} and Toni Gabald{\'o}n and Vladim{\'i}r Hampl and Kops, {Geert J P L} and Leger, {Michelle M} and Purificacion Lopez-Garcia and McInerney, {James O} and David Moreira and Mu{\~n}oz-G{\'o}mez, {Sergio A} and Richter, {Daniel J} and I{\~n}aki Ruiz-Trillo and Santoro, {Alyson E} and Arnau Seb{\'e}-Pedr{\'o}s and Berend Snel and Stairs, {Courtney W} and Tromer, {Eelco C} and {van Hooff}, {Jolien J E} and Bill Wickstead and Williams, {Tom A} and Roger, {Andrew J} and Dacks, {Joel B} and Wideman, {Jeremy G}",

note = "Copyright: {\textcopyright} 2024 Richards et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.",

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month = nov,

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Richards, TA, Eme, L, Archibald, JM, Leonard, G, Coelho, SM, de Mendoza, A, Dessimoz, C, Dolezal, P, Fritz-Laylin, LK, Gabaldón, T, Hampl, V, Kops, GJPL, Leger, MM, Lopez-Garcia, P, McInerney, JO, Moreira, D, Muñoz-Gómez, SA, Richter, DJ, Ruiz-Trillo, I, Santoro, AE, Sebé-Pedrós, A, Snel, B, Stairs, CW, Tromer, EC, van Hooff, JJE, Wickstead, B, Williams, TA, Roger, AJ, Dacks, JB & Wideman, JG 2024, 'Reconstructing the last common ancestor of all eukaryotes', PLOS BIOLOGY, vol. 22, no. 11, e3002917. https://doi.org/10.1371/journal.pbio.3002917

TY - JOUR

T1 - Reconstructing the last common ancestor of all eukaryotes

AU - Richards, Thomas A

AU - Eme, Laura

AU - Archibald, John M

AU - Leonard, Guy

AU - Coelho, Susana M

AU - de Mendoza, Alex

AU - Dessimoz, Christophe

AU - Dolezal, Pavel

AU - Fritz-Laylin, Lillian K

AU - Gabaldón, Toni

AU - Hampl, Vladimír

AU - Kops, Geert J P L

AU - Leger, Michelle M

AU - Lopez-Garcia, Purificacion

AU - McInerney, James O

AU - Moreira, David

AU - Muñoz-Gómez, Sergio A

AU - Richter, Daniel J

AU - Ruiz-Trillo, Iñaki

AU - Santoro, Alyson E

AU - Sebé-Pedrós, Arnau

AU - Snel, Berend

AU - Stairs, Courtney W

AU - Tromer, Eelco C

AU - van Hooff, Jolien J E

AU - Wickstead, Bill

AU - Williams, Tom A

AU - Roger, Andrew J

AU - Dacks, Joel B

AU - Wideman, Jeremy G

N1 - Copyright: © 2024 Richards et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

PY - 2024/11/25

Y1 - 2024/11/25

N2 - Understanding the origin of eukaryotic cells is one of the most difficult problems in all of biology. A key challenge relevant to the question of eukaryogenesis is reconstructing the gene repertoire of the last eukaryotic common ancestor (LECA). As data sets grow, sketching an accurate genomics-informed picture of early eukaryotic cellular complexity requires provision of analytical resources and a commitment to data sharing. Here, we summarise progress towards understanding the biology of LECA and outline a community approach to inferring its wider gene repertoire. Once assembled, a robust LECA gene set will be a useful tool for evaluating alternative hypotheses about the origin of eukaryotes and understanding the evolution of traits in all descendant lineages, with relevance in diverse fields such as cell biology, microbial ecology, biotechnology, agriculture, and medicine. In this Consensus View, we put forth the status quo and an agreed path forward to reconstruct LECA's gene content.

AB - Understanding the origin of eukaryotic cells is one of the most difficult problems in all of biology. A key challenge relevant to the question of eukaryogenesis is reconstructing the gene repertoire of the last eukaryotic common ancestor (LECA). As data sets grow, sketching an accurate genomics-informed picture of early eukaryotic cellular complexity requires provision of analytical resources and a commitment to data sharing. Here, we summarise progress towards understanding the biology of LECA and outline a community approach to inferring its wider gene repertoire. Once assembled, a robust LECA gene set will be a useful tool for evaluating alternative hypotheses about the origin of eukaryotes and understanding the evolution of traits in all descendant lineages, with relevance in diverse fields such as cell biology, microbial ecology, biotechnology, agriculture, and medicine. In this Consensus View, we put forth the status quo and an agreed path forward to reconstruct LECA's gene content.

U2 - 10.1371/journal.pbio.3002917

DO - 10.1371/journal.pbio.3002917

M3 - Article

C2 - 39585925

SN - 1544-9173

VL - 22

JO - PLOS BIOLOGY

JF - PLOS BIOLOGY

IS - 11

M1 - e3002917

ER -

Reconstructing the last common ancestor of all eukaryotes

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