Month: January 2021

New publication on mosses: Fontinalis genome

Posted on January 30, 2021 by Bernard Goffinet

Yu J., L. Li, S. Wang, S. Dong, Z. Chen, N. Patel, B. Goffinet, H. Chen, H. Liu & Y. Liu. 2021. Draft genome of the aquatic moss Fontinalis antipyretica (Fontinalaceae, Bryophyta). Gigabyte (online November 2020). pdf

Abstract read: Mosses comprise one of three lineages forming a sister group to extant vascular plants. Having emerged from an early split in the diversification of embryophytes, mosses may offer complementary insights into the evolution of traits following the transition to, and colonization of, land. Here, we report the draft nuclear genome of Fontinalis antipyretica (Fontinalaceae, Hypnales), a charismatic aquatic moss that is widespread in temperate regions of the Northern Hemisphere. We sequenced and de novo-assembled its genome using the 10X Genomics method. The genome comprises 385.2 Mbp, with a scaffold N50 of 45.8 Kbp. The assembly captured 87.2% of the 430 genes in the BUSCO Viridiplantae odb10 dataset. The newly generated F. antipyretica genome is the third moss genome, and the second seedless aquatic plant genome, to be sequenced and assembled to date.

New publications: “first” exploration of Diego Ramirez (subantarctic Chile)

Posted on January 28, 2021January 28, 2021 by Bernard Goffinet

Outcomes of our expedition of 2018 to the subantarctic Chilean island of Diego Ramirez have now been published in this issue of Anales del Instituto de la Patagonia.

Mackenzie R., O. Vidal, S. Rosenfeld, T. Contador, O. Barroso, B. Goffinet, F. Massardo, P. Arce-Johnson & R. Rozzi. 2020. Flora vascular y ausencia de especies exóticas en el archipiélago Diego Ramírez (56°31’S), Chile. Anales del Instituto de la Patagonia 48(3): 138–148. pdf

Goffinet B., J.J. Engel, M. von Konrat, R. MacKenzie, T. Contador, S. Rosenfeld, O. Barroso & R. Rozzi. 2020. Bryophyte records from Isla Gonzalo, Diego Ramirez Islands, Americas’ deep southern ocean archipelago. Anales del Instituto de la Patagonia 48(3): 127–138. pdf

Marambio J., S. Rosenfeld, J. P. Rodríguez, F. Méndez, T. Contador, R. Mackenzie, B. Goffinet, R. Rozzi & A. Mansilla. 2020. Siete nuevos registros de macroalgas para el archipiélago Diego Ramírez (56°31’S): el valor del nuevo parque marino como sumidero de carbono y conservación de la biodiversidad subantártica. Anales del Instituto de la Patagonia 48(3): 99–111. pdf

Contador T., J. Rendoll, R. Mackenzie, S. Rosenfeld, O. Barroso, R. Rozzi, B. Goffinet, J. Kennedy & P. Convey, P. 2020. Comunidades de Invertebrados Terrestres en el Archipiélago Diego Ramírez (56°, 31’s) y sus Afinidades con las Islas Sub-Antárticas del Océano Austral. Anales del Instituto de la Patagonia 48(3): 83–98. pdf

Rozzi R., R.D. Credo, T. Contador, E. Schüttler, S. Rosenfeld, R. MacKenzie, O. Barroso, E.A. Silva-Rodríguez, X. Álvarez Bustos, A. Silva, I. Ramírez, J. Mella, J. Herreros, J. Rendoll-Cárcamo, J. Marambio, J. Ojeda, F. Méndez, K.P. Moses, J. Kennedy, S. Russell, B. Goffinet, F. Aguirre, L. Sánchez-Jardón, E. Barros, R.A. Vásquez, E. Poulin, F. Squeo, J.J. Armesto, A. Mansilla & F. Massardo. 2020. Extensión de la Red de Estudios Socio-Ecológicos a Largo Plazo (LTSER-Chile) en la Reserva de la Biosfera Cabo de Hornos y el Nuevo Parque Marino Islas Diego Ramírez-Paso Drake (Extension of the long term socio-ecological research network (LTSER-Chile) in the Cape Horn Biosphere Reserve and the new marine park Diego Ramirez Islands Drake passage). Anales del Instituto de la Patagonia 48(3): 45–81. pdf

New publication on bryophytes

Posted on January 27, 2021January 27, 2021 by Bernard Goffinet

Dong S., H.-L. Li, B. Goffinet & Y. Liu. 2021. Exploring the impact of RNA editing on mitochondrial phylogenetic analyses in liverworts, an early land plant lineage. Journal of Systematics and Evolution in press.

Abstract: Plant mitochondrial protein-coding genes are slow evolving, and therefore are less subject to substitution saturation, and therefore perhaps more suitable for resolving deep relationships of high taxonomic categories. Plant mitochondrial genes hold, however, hundreds of RNA editing sites, involving mostly non-synonymous substitutions in the first and second codon positions, which has been reported to affect phylogenetic reconstructions. We have previously identified ca. 4700 mitochondrial RNA editing sites within a group of liverworts representing the ordinal diversity of liverworts, allowing us to critically evaluate the impacts of RNA editing sites on phylogenetic reconstructions in liverworts. Our phylogenetic inferences are mostly congruent on topology inferred from the original mitochondrial gene dataset, dataset with RNA editing sites corrected, and dataset with RNA editing sites excluded. The RNA editing site excluded dataset recovered a topology identical to that of the RNA editing site corrected dataset, supporting the sister relationship of Ptilidium and Jungermanniales, whereas the original dataset supported the sister relationship of Ptilidium and Jungermanniidae. The controversial placements of Ptilidium could be explained by site-wise log-likelihood analysis, as the majority of liverwort RNA editing sites supported the sister relationship of Ptilidium and Jungermanniidae, hence the correction or exclusion of the RNA editing sites changed the tree topology and supported the sister relationship of Ptilidium and Jungermanniales. Our study shows that RNA editing sites potentially impact phylogenetic analyses, suggesting that both genome and transcriptome derived data should be used with caution for phylogenetic reconstruction with genes hosting vast numbers of RNA editing sites such as plant organellar genes.