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Zhang Z, Xie P, Guo Y, Zhou W, Liu E, Yu Y. Easy353: A Tool to Get Angiosperms353 Genes for Phylogenomic Research. Mol Biol Evol 2022; 39:6862883. [PMID: 36458838 PMCID: PMC9757696 DOI: 10.1093/molbev/msac261] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/28/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
The Angiosperms353 gene set (AGS) consists of a set of 353 universal low-copy nuclear genes that were selected by examining more than 600 angiosperm species. These genes can be used for phylogenetic studies and population genetics at multiple taxonomic scales. However, current pipelines are not able to recover Angiosperms353 genes efficiently and accurately from high-throughput sequences. Here, we developed Easy353, a reference-guided assembly tool to recover the AGS from high-throughput sequencing (HTS) data (including genome skimming, RNA-seq, and target enrichment). Easy353 is an open-source user-friendly assembler for diverse types of high-throughput data. It has a graphical user interface and a command-line interface that is compatible with all widely-used computer systems. Evaluations, based on both simulated and empirical data, suggest that Easy353 yields low rates of assembly errors.
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Affiliation(s)
- Zhen Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610065, P. R. China
| | - Pulin Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610065, P. R. China
| | - Yongling Guo
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610065, P. R. China
| | - Wenbin Zhou
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Enyan Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610065, P. R. China
| | - Yan Yu
- Corresponding author: E-mail:
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Testé E, Hernández-Rodríguez M, Veltjen E, Bécquer ER, Rodríguez-Meno A, Palmarola A, Samain MS, González-Torres LR, Robert T. Integrating morphological and genetic limits in the taxonomic delimitation of the Cuban taxa of Magnoliasubsect.Talauma (Magnoliaceae). PHYTOKEYS 2022; 213:35-66. [PMID: 36762245 PMCID: PMC9836609 DOI: 10.3897/phytokeys.213.82627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/30/2022] [Indexed: 06/18/2023]
Abstract
An accurate taxa delimitation, based on a full understanding of evolutionary processes involved in taxa differentiation, can be gained from a combination of ecological, morphological, and molecular approaches. The taxonomy of Magnoliasubsect.Talauma in Cuba has long been debated and exclusively based on traditional morphological study of a limited number of individuals. A more accurate description of leaf morphology variation using geometric morphometrics combined with genetic data could bring consistency to taxa delimitation in this group. Leaf samples for the morphological (243) and genetic (461) analyses were collected throughout the entire distribution range. The variability of each taxon was analyzed through multivariate and geometric morphometry, and 21 genetic markers (SSR). The observed leaf morphological variability was higher than previously described. Morphological and genetic classifications were highly congruent in two out of four taxa. Our data brought evidence that Magnoliaorbiculata can be considered a true species with very clear genetic and morphological limits. The main taxonomic issues concern the north-eastern Cuban populations of Magnoliasubsect.Talauma. The data supported the existence of two clear groups: corresponding mainly to M.minor-M.oblongifolia and T.ophiticola. However, these two groups cannot be considered fully delimited since genetic markers provided evidence of genetic admixture between them. Due to the likely absence of, at least strong, reproductive barriers between these three taxa, we propose therefore to consider them as a species complex.
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Affiliation(s)
- Ernesto Testé
- Jardín Botánico Nacional, Universidad de La Habana, Carretera “El Rocío” km 3½, 19230 Boyeros, La Habana, Cuba
- Ecologie Systématique et Evolution, Université Paris-Saclay, 360 Rue du Doyen André Guinier, 91405 Orsay, France
| | - Majela Hernández-Rodríguez
- Jardín Botánico Nacional, Universidad de La Habana, Carretera “El Rocío” km 3½, 19230 Boyeros, La Habana, Cuba
| | - Emily Veltjen
- Departamento de Biología Vegetal - Facultad de Biología, Universidad de La Habana, Calle 25 entre I y J, 10400 Vedado, La Habana, Cuba
| | - Eldis R. Bécquer
- Jardín Botánico Nacional, Universidad de La Habana, Carretera “El Rocío” km 3½, 19230 Boyeros, La Habana, Cuba
| | - Arlet Rodríguez-Meno
- Jardín Botánico Nacional, Universidad de La Habana, Carretera “El Rocío” km 3½, 19230 Boyeros, La Habana, Cuba
| | - Alejandro Palmarola
- Jardín Botánico Nacional, Universidad de La Habana, Carretera “El Rocío” km 3½, 19230 Boyeros, La Habana, Cuba
| | - Marie-Stephanie Samain
- Departamento de Biología Vegetal - Facultad de Biología, Universidad de La Habana, Calle 25 entre I y J, 10400 Vedado, La Habana, Cuba
- Ghent University Botanical Garden, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - Luis R. González-Torres
- Red de Diversidad Biológica del Occidente Mexicano, Instituto de Ecología, A.C., Avenida Lázaro Cárdenas 253, 61600 Pátzcuaro, Michoacán, México
| | - Thierry Robert
- Ecologie Systématique et Evolution, Université Paris-Saclay, 360 Rue du Doyen André Guinier, 91405 Orsay, France
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
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Guzmán-Díaz S, Núñez FAA, Veltjen E, Asselman P, Larridon I, Samain MS. Comparison of Magnoliaceae Plastomes: Adding Neotropical Magnolia to the Discussion. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030448. [PMID: 35161429 PMCID: PMC8838774 DOI: 10.3390/plants11030448] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/31/2022] [Accepted: 02/02/2022] [Indexed: 05/13/2023]
Abstract
Chloroplast genomes are considered to be highly conserved. Nevertheless, differences in their sequences are an important source of phylogenetically informative data. Chloroplast genomes are increasingly applied in evolutionary studies of angiosperms, including Magnoliaceae. Recent studies have focused on resolving the previously debated classification of the family using a phylogenomic approach and chloroplast genome data. However, most Neotropical clades and recently described species have not yet been included in molecular studies. We performed sequencing, assembly, and annotation of 15 chloroplast genomes from Neotropical Magnoliaceae species. We compared the newly assembled chloroplast genomes with 22 chloroplast genomes from across the family, including representatives from each genus and section. Family-wide, the chloroplast genomes presented a length of about 160 kb. The gene content in all species was constant, with 145 genes. The intergenic regions showed a higher level of nucleotide diversity than the coding regions. Differences were higher among genera than within genera. The phylogenetic analysis in Magnolia showed two main clades and corroborated that the current infrageneric classification does not represent natural groups. Although chloroplast genomes are highly conserved in Magnoliaceae, the high level of diversity of the intergenic regions still resulted in an important source of phylogenetically informative data, even for closely related taxa.
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Affiliation(s)
- Salvador Guzmán-Díaz
- Instituto de Ecología, A.C., Red de Diversidad Biológica del Occidente Mexicano, Pátzcuaro 61600, Mexico; (F.A.A.N.); (M.-S.S.)
- Correspondence:
| | - Fabián Augusto Aldaba Núñez
- Instituto de Ecología, A.C., Red de Diversidad Biológica del Occidente Mexicano, Pátzcuaro 61600, Mexico; (F.A.A.N.); (M.-S.S.)
| | - Emily Veltjen
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, 9000 Gent, Belgium; (E.V.); (P.A.); (I.L.)
- Ghent University Botanical Garden, Ghent University, 9000 Gent, Belgium
| | - Pieter Asselman
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, 9000 Gent, Belgium; (E.V.); (P.A.); (I.L.)
| | - Isabel Larridon
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, 9000 Gent, Belgium; (E.V.); (P.A.); (I.L.)
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Marie-Stéphanie Samain
- Instituto de Ecología, A.C., Red de Diversidad Biológica del Occidente Mexicano, Pátzcuaro 61600, Mexico; (F.A.A.N.); (M.-S.S.)
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, 9000 Gent, Belgium; (E.V.); (P.A.); (I.L.)
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