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Barreto de Jesus P, de Mattos Lyra G, Zhang H, Toyota Fujii M, Nauer F, Marcos de Castro Nunes J, Davis CC, Cabral Oliveira M. Phylogenomics and taxon-rich phylogenies of new and historical specimens shed light on the systematics of Hypnea (Cystocloniaceae, Rhodophyta). Mol Phylogenet Evol 2023; 183:107752. [PMID: 36893930 DOI: 10.1016/j.ympev.2023.107752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 02/17/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
Cystocloniacae is a highly diverse family of Rhodophyta, including species of ecological and economic importance, whose phylogeny remains largely unresolved. Species delimitation is unclear, particularly in the most speciose genus, Hypnea, and cryptic diversity has been revealed by recent molecular assessments, especially in the tropics. Here, we carried out the first phylogenomic investigation of Cystocloniaceae, focused on the genus Hypnea, inferred from chloroplast and mitochondrial genomes including taxa sampled from new and historical collections. In this work, molecular synapomorphies (gene losses, InDels and gene inversions) were identified to better characterize clades in our congruent organellar phylogenies. We also present taxon-rich phylogenies based on plastid and mitochondrial markers. Molecular and morphological comparisons of historic collections with contemporary specimens revealed the need for taxonomic updates in Hypnea, the synonymization of H. marchantae to a later heterotypic synonym of H. cervicornis and the description of three new species: H. davisiana sp. nov., H. djamilae sp. nov. and H. evaristoae sp. nov.
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Affiliation(s)
- Priscila Barreto de Jesus
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (CCNH - UFABC), Rua Arcturus 03, São Bernardo do Campo, São Paulo, 09606-070, Brazil; Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo, São Paulo, 05508-090, Brazil.
| | - Goia de Mattos Lyra
- Programa de Pós-Graduação em Biodiversidade e Evolução, Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, s/n, Salvador, Bahia, 40170-115, Brasil; Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge Massachusetts 02138, USA; Laboratório de Algas Marinhas, Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, s/n, Salvador Bahia 40170-115, Brasil
| | - Hongrui Zhang
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge Massachusetts 02138, USA
| | - Mutue Toyota Fujii
- Núcleo de Conservação da Biodiversidade, Instituto de Pesquisas Ambientais, Av. Miguel Estefano 3687, 04301-902, São Paulo, Brazil
| | - Fabio Nauer
- Núcleo de Conservação da Biodiversidade, Instituto de Pesquisas Ambientais, Av. Miguel Estefano 3687, 04301-902, São Paulo, Brazil; Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo, São Paulo, 05508-090, Brazil
| | - José Marcos de Castro Nunes
- Programa de Pós-Graduação em Biodiversidade e Evolução, Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, s/n, Salvador, Bahia, 40170-115, Brasil; Laboratório de Algas Marinhas, Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, s/n, Salvador Bahia 40170-115, Brasil
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge Massachusetts 02138, USA
| | - Mariana Cabral Oliveira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo, São Paulo, 05508-090, Brazil
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Fan W, Liu F, Jia Q, Du H, Chen W, Ruan J, Lei J, Li DZ, Mower JP, Zhu A. Fragaria mitogenomes evolve rapidly in structure but slowly in sequence and incur frequent multinucleotide mutations mediated by microinversions. THE NEW PHYTOLOGIST 2022; 236:745-759. [PMID: 35731093 DOI: 10.1111/nph.18334] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Plant mitochondrial DNA has been described as evolving rapidly in structure but slowly in sequence. However, many of the noncoding portions of plant mitogenomes are not homologous among species, raising questions about the rate and spectrum of mutations in noncoding regions. Recent studies have suggested that the lack of homology in noncoding regions could be due to increased sequence divergence. We compared 30 kb of coding and 200 kb of noncoding DNA from 13 sequenced Fragaria mitogenomes, followed by analysis of the rate of sequence divergence, microinversion events and structural variations. Substitution rates in synonymous sites and nongenic sites are nearly identical, suggesting that the genome-wide point mutation rate is generally consistent. A surprisingly high number of large multinucleotide substitutions were detected in Fragaria mitogenomes, which may have resulted from microinversion events and could affect phylogenetic signal and local rate estimates. Fragaria mitogenomes preferentially accumulate deletions relative to insertions and substantial genomic arrangements, whereas mutation rates could positively associate with these sequence and structural changes among species. Together, these observations suggest that plant mitogenomes exhibit low point mutations genome-wide but exceptionally high structural variations, and our results favour a gain-and-loss model for the rapid loss of homology among plant mitogenomes.
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Affiliation(s)
- Weishu Fan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Fang Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiaoya Jia
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, China
| | - Haiyuan Du
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wu Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiwei Ruan
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Jiajun Lei
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Andan Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
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