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2. Duplication and sub‐functionalization of flavonoid biosynthesis genes plays important role in Leguminosae root nodule symbiosis evolution.

Author

Liu, Tengfei, Liu, Haiyue, Xian, Wenfei, Liu, Zhi, Yuan, Yaqin, Fan, Jingwei, Xiang, Shuaiying, Yang, Xia, Liu, Yucheng, Liu, Shulin, Zhang, Min, Shen, Yanting, Jiao, Yuannian, Cheng, Shifeng, Doyle, Jeff J., Xie, Fang, Li, Jiayang, and Tian, Zhixi

Subjects
CHALCONE synthase, AGRICULTURE, CHROMOSOME duplication, ROOT-tubercles, SOYBEAN, MEDICAGO
Abstract

Gene innovation plays an essential role in trait evolution. Rhizobial symbioses, the most important N2‐fixing agent in agricultural systems that exists mainly in Leguminosae, is one of the most attractive evolution events. However, the gene innovations underlying Leguminosae root nodule symbiosis (RNS) remain largely unknown. Here, we investigated the gene gain event in Leguminosae RNS evolution through comprehensive phylogenomic analyses. We revealed that Leguminosae‐gain genes were acquired by gene duplication and underwent a strong purifying selection. Kyoto Encyclopedia of Genes and Genomes analyses showed that the innovated genes were enriched in flavonoid biosynthesis pathways, particular downstream of chalcone synthase (CHS). Among them, Leguminosae‐gain type Ⅱ chalcone isomerase (CHI) could be further divided into CHI1A and CHI1B clades, which resulted from the products of tandem duplication. Furthermore, the duplicated CHI genes exhibited exon–intron structural divergences evolved through exon/intron gain/loss and insertion/deletion. Knocking down CHI1B significantly reduced nodulation in Glycine max (soybean) and Medicago truncatula; whereas, knocking down its duplication gene CHI1A had no effect on nodulation. Therefore, Leguminosae‐gain type Ⅱ CHI participated in RNS and the duplicated CHI1A and CHI1B genes exhibited RNS functional divergence. This study provides functional insights into Leguminosae‐gain genetic innovation and sub‐functionalization after gene duplication that contribute to the evolution and adaptation of RNS in Leguminosae. [ABSTRACT FROM AUTHOR]

Published
2024
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3. nQuack: An R package for predicting ploidal level from sequence data using site‐based heterozygosity.

Author

Gaynor, Michelle L., Landis, Jacob B., O'Connor, Timothy K., Laport, Robert G., Doyle, Jeff J., Soltis, Douglas E., Ponciano, José Miguel, and Soltis, Pamela S.

Subjects
PLOIDY, HETEROZYGOSITY, NUCLEOTIDE sequence, DISTRIBUTION (Probability theory), DNA sequencing
Abstract

Premise: Traditional methods of ploidal‐level estimation are tedious; using DNA sequence data for cytotype estimation is an ideal alternative. Multiple statistical approaches to leverage sequence data for ploidy inference based on site‐based heterozygosity have been developed. However, these approaches may require high‐coverage sequence data, use inappropriate probability distributions, or have additional statistical shortcomings that limit inference abilities. We introduce nQuack, an open‐source R package that addresses the main shortcomings of current methods. Methods and Results: nQuack performs model selection for improved ploidy predictions. Here, we implement expectation maximization algorithms with normal, beta, and beta‐binomial distributions. Using extensive computer simulations that account for variability in sequencing depth, as well as real data sets, we demonstrate the utility and limitations of nQuack. Conclusions: Inferring ploidy based on site‐based heterozygosity alone is difficult. Even though nQuack is more accurate than similar methods, we suggest caution when relying on any site‐based heterozygosity method to infer ploidy. [ABSTRACT FROM AUTHOR]

Published
2024
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8. Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis

Author

Griesmann, Maximilian, Chang, Yue, Liu, Xin, Song, Yue, Haberer, Georg, Crook, Matthew B., Billault-Penneteau, Benjamin, Lauressergues, Dominique, Keller, Jean, Imanishi, Leandro, Roswanjaya, Yuda Purwana, Kohlen, Wouter, Pujic, Petar, Battenberg, Kai, Alloisio, Nicole, Liang, Yuhu, Hilhorst, Henk, Salgado, Marco G., Hocher, Valerie, Gherbi, Hassen, Svistoonoff, Sergio, Doyle, Jeff J., He, Shixu, Xu, Yan, Xu, Shanyun, Qu, Jing, Gao, Qiang, Fang, Xiaodong, Fu, Yuan, Normand, Philippe, Berry, Alison M., Wall, Luis G., Ané, Jean-Michel, Pawlowski, Katharina, Xu, Xun, Yang, Huanming, Spannagl, Manuel, Mayer, Klaus F. X., Wong, Gane Ka-Shu, Parniske, Martin, Delaux, Pierre-Marc, and Cheng, Shifeng

Published
2018

12. A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny

Author

Azani, Nasim, Babineau, Marielle, Bailey, C. Donovan, Banks, Hannah, Barbosa, Ariane R., Pinto, Rafael Barbosa, Boatwright, James S., Borges, Leonardo M., Brown, Gillian K., Bruneau, Anne, Candido, Elisa, Cardoso, Domingos, Chung, Kuo-Fang, Clark, Ruth P., Conceição, Adilva de S., Crisp, Michael, Cubas, Paloma, Delgado-Salinas, Alfonso, Dexter, Kyle G., Doyle, Jeff J., Duminil, Jérôme, Egan, Ashley N., Estrella, Manuel de la, Falcão, Marcus J., Filatov, Dmitry A., Fortuna-Perez, Ana Paula, Fortunato, Renée H., Gagnon, Edeline, Gasson, Peter, Rando, Juliana Gastaldello, de Azevedo Tozzi, Ana Maria Goulart, Gunn, Bee, Harris, David, Haston, Elspeth, Hawkins, Julie A., Herendeen, Patrick S., Hughes, Colin E., Iganci, João R.V., Javadi, Firouzeh, Kanu, Sheku Alfred, Kazempour-Osaloo, Shahrokh, Kite, Geoffrey C., Klitgaard, Bente B., Kochanovski, Fábio J., Koenen, Erik J.M., Kovar, Lynsey, Lavin, Matt, Roux, Marianne le, Lewis, Gwilym P., Lima, Haroldo C. de, López-Roberts, Maria Cristina, Mackinder, Barbara, Maia, Vitor Hugo, Malécot, Valéry, Mansano, Vidal F., Marazzi, Brigitte, Mattapha, Sawai, Miller, Joseph T., Mitsuyuki, Chika, Moura, Tania, Murphy, Daniel J., Nageswara-Rao, Madhugiri, Nevado, Bruno, Neves, Danilo, Ojeda, Dario I., Pennington, R. Toby, Prado, Darién E., Prenner, Gerhard, de Queiroz, Luciano Paganucci, Ramos, Gustavo, Filardi, Fabiana L. Ranzato, Ribeiro, Pétala G., Rico-Arce, María de Lourdes, Sanderson, Michael J., Santos-Silva, Juliana, São-Mateus, Wallace M.B., Silva, Marcos J.S., Simon, Marcelo F., Sinou, Carole, Snak, Cristiane, de Souza, Élvia R., Sprent, Janet, Steele, Kelly P., Steier, Julia E., Steeves, Royce, Stirton, Charles H., Tagane, Shuichiro, Torke, Benjamin M., Toyama, Hironori, da Cruz, Daiane Trabuco, Vatanparast, Mohammad, Wieringa, Jan J., Wink, Michael, Wojciechowski, Martin F., Yahara, Tetsukazu, Yi, Tingshuang, and Zimmerman, Erin

Published
2017

21. Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)

Author

Leebens-Mack, Jim, Vision, Todd, Brenner, Eric, Bowers, John E, Cannon, Steven, Clement, Mark J, Cunningham, Clifford W, DePamphilis, Claude, DeSalle, Rob, Doyle, Jeff J, Eisen, Jonathan A, Gu, Xun, Harshman, John, Jansen, Robert K, Kellogg, Elizabeth A, Koonin, Eugene V, Mishler, Brent D, Philippe, Herv, Pires, J Chris, Qiu, Yin-Long, Rhee, Seung Y, Sjlander, Kimmen, Soltis, Douglas E, Soltis, Pamela S, Stevenson, Dennis W, Wall, Kerr, Warnow, Tandy, and Zmasek, Christian

Subjects
Biological Sciences, Genetics, Human Genome, Biotechnology, Genomics, Phylogeny, Reference Standards, Bioinformatics, Biological sciences
Abstract

In the eight years since phylogenomics was introduced as the intersection of genomics and phylogenetics, the field has provided fundamental insights into gene function, genome history and organismal relationships. The utility of phylogenomics is growing with the increase in the number and diversity of taxa for which whole genome and large transcriptome sequence sets are being generated. We assert that the synergy between genomic and phylogenetic perspectives in comparative biology would be enhanced by the development and refinement of minimal reporting standards for phylogenetic analyses. Encouraged by the development of the Minimum Information About a Microarray Experiment (MIAME) standard, we propose a similar roadmap for the development of a Minimal Information About a Phylogenetic Analysis (MIAPA) standard. Key in the successful development and implementation of such a standard will be broad participation by developers of phylogenetic analysis software, phylogenetic database developers, practitioners of phylogenomics, and journal editors.

Published
2006

45. Cell types as species: Exploring a metaphor

Author

Doyle, Jeff J.

Subjects
Plant Science
Abstract

The concept of “cell type,” though fundamental to cell biology, is controversial. Cells have historically been classified into types based on morphology, physiology, or location. More recently, single cell transcriptomic studies have revealed fine-scale differences among cells with similar gross phenotypes. Transcriptomic snapshots of cells at various stages of differentiation, and of cells under different physiological conditions, have shown that in many cases variation is more continuous than discrete, raising questions about the relationship between cell type and cell state. Some researchers have rejected the notion of fixed types altogether. Throughout the history of discussions on cell type, cell biologists have compared the problem of defining cell type with the interminable and often contentious debate over the definition of arguably the most important concept in systematics and evolutionary biology, “species.” In the last decades, systematics, like cell biology, has been transformed by the increasing availability of molecular data, and the fine-grained resolution of genetic relationships have generated new ideas about how that variation should be classified. There are numerous parallels between the two fields that make exploration of the “cell types as species” metaphor timely. These parallels begin with philosophy, with discussion of both cell types and species as being either individuals, groups, or something in between (e.g., homeostatic property clusters). In each field there are various different types of lineages that form trees or networks that can (and in some cases do) provide criteria for grouping. Developing and refining models for evolutionary divergence of species and for cell type differentiation are parallel goals of the two fields. The goal of this essay is to highlight such parallels with the hope of inspiring biologists in both fields to look for new solutions to similar problems outside of their own field.

Published
2022

50. Legume phylogeny and classification in the 21st century: Progress, prospects and lessons for other species-rich clades

Author

The Legume Phylogeny Working Group, Bruneau, Anne, Doyle, Jeff J., Herendeen, Patrick, Hughes, Colin, Kenicer, Greg, Lewis, Gwilym, Mackinder, Barbara, Pennington, R. Toby, Sanderson, Michael J., Wojciechowski, Martin F., Boatwright, Stephen, Brown, Gillian, Cardoso, Domingos, Crisp, Michael, Egan, Ashley, Fortunato, Renée H., Hawkins, Julie, Kajita, Tadashi, Klitgaard, Bente, Koenen, Erik, Lavin, Matt, Luckow, Melissa, Marazzi, Brigitte, McMahon, Michelle M., Miller, Joseph T., Murphy, Daniel J., Ohashi, Hiroyoshi, de Queiroz, Luciano P., Rico, Lourdes, Särkinen, Tiina, Schrire, Brian, Simon, Marcelo F., Souza, Elvia R., Steele, Kelly, Torke, Benjamin M., Wieringa, Jan J., and van Wyk, Ben-Erik

Published
2013

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