251
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Wang WC, Chen SY, Zhang XZ. Chloroplast Genome Evolution in Actinidiaceae: clpP Loss, Heterogenous Divergence and Phylogenomic Practice. PLoS One 2016; 11:e0162324. [PMID: 27589600 PMCID: PMC5010200 DOI: 10.1371/journal.pone.0162324] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 08/19/2016] [Indexed: 12/13/2022] Open
Abstract
Actinidiaceae is a well-known economically important plant family in asterids. To elucidate the chloroplast (cp) genome evolution within this family, here we present complete genomes of three species from two sister genera (Clematoclethra and Actinidia) in the Actinidiaceae via genome skimming technique. Comparative analyses revealed that the genome structure and content were rather conservative in three cp genomes in spite of different inheritance pattern, i.e.paternal in Actinidia and maternal in Clematoclethra. The clpP gene was lacked in all the three sequenced cp genomes examined here indicating that the clpP gene loss is likely a conspicuous synapomorphic characteristic during the cp genome evolution of Actinidiaceae. Comprehensive sequence comparisons in Actinidiaceae cp genomes uncovered that there were apparently heterogenous divergence patterns among the cpDNA regions, suggesting a preferred data-partitioned analysis for cp phylogenomics. Twenty non-coding cpDNA loci with fast evolutionary rates are further identified as potential molecular markers for systematics studies of Actinidiaceae. Moreover, the cp phylogenomic analyses including 31 angiosperm plastomes strongly supported the monophyly of Actinidia, being sister to Clematoclethra in Actinidiaceae which locates in the basal asterids, Ericales.
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Affiliation(s)
- Wen-Cai Wang
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, United Kingdom
| | - Si-Yun Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xian-Zhi Zhang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
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252
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Lee J, Cho CH, Park SI, Choi JW, Song HS, West JA, Bhattacharya D, Yoon HS. Parallel evolution of highly conserved plastid genome architecture in red seaweeds and seed plants. BMC Biol 2016; 14:75. [PMID: 27589960 PMCID: PMC5010701 DOI: 10.1186/s12915-016-0299-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/17/2016] [Indexed: 11/10/2022] Open
Abstract
Background The red algae (Rhodophyta) diverged from the green algae and plants (Viridiplantae) over one billion years ago within the kingdom Archaeplastida. These photosynthetic lineages provide an ideal model to study plastid genome reduction in deep time. To this end, we assembled a large dataset of the plastid genomes that were available, including 48 from the red algae (17 complete and three partial genomes produced for this analysis) to elucidate the evolutionary history of these organelles. Results We found extreme conservation of plastid genome architecture in the major lineages of the multicellular Florideophyceae red algae. Only three minor structural types were detected in this group, which are explained by recombination events of the duplicated rDNA operons. A similar high level of structural conservation (although with different gene content) was found in seed plants. Three major plastid genome architectures were identified in representatives of 46 orders of angiosperms and three orders of gymnosperms. Conclusions Our results provide a comprehensive account of plastid gene loss and rearrangement events involving genome architecture within Archaeplastida and lead to one over-arching conclusion: from an ancestral pool of highly rearranged plastid genomes in red and green algae, the aquatic (Florideophyceae) and terrestrial (seed plants) multicellular lineages display high conservation in plastid genome architecture. This phenomenon correlates with, and could be explained by, the independent and widely divergent (separated by >400 million years) origins of complex sexual cycles and reproductive structures that led to the rapid diversification of these lineages. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0299-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- JunMo Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Seung In Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Ji Won Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hyun Suk Song
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - John A West
- School of Biosciences 2, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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253
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Barthlott W, Mail M, Neinhuis C. Superhydrophobic hierarchically structured surfaces in biology: evolution, structural principles and biomimetic applications. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:20160191. [PMID: 27354736 PMCID: PMC4928508 DOI: 10.1098/rsta.2016.0191] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/03/2016] [Indexed: 05/09/2023]
Abstract
A comprehensive survey of the construction principles and occurrences of superhydrophobic surfaces in plants, animals and other organisms is provided and is based on our own scanning electron microscopic examinations of almost 20 000 different species and the existing literature. Properties such as self-cleaning (lotus effect), fluid drag reduction (Salvinia effect) and the introduction of new functions (air layers as sensory systems) are described and biomimetic applications are discussed: self-cleaning is established, drag reduction becomes increasingly important, and novel air-retaining grid technology is introduced. Surprisingly, no evidence for lasting superhydrophobicity in non-biological surfaces exists (except technical materials). Phylogenetic trees indicate that superhydrophobicity evolved as a consequence of the conquest of land about 450 million years ago and may be a key innovation in the evolution of terrestrial life. The approximate 10 million extant species exhibit a stunning diversity of materials and structures, many of which are formed by self-assembly, and are solely based on a limited number of molecules. A short historical survey shows that bionics (today often called biomimetics) dates back more than 100 years. Statistical data illustrate that the interest in biomimetic surfaces is much younger still. Superhydrophobicity caught the attention of scientists only after the extreme superhydrophobicity of lotus leaves was published in 1997. Regrettably, parabionic products play an increasing role in marketing.This article is part of the themed issue 'Bioinspired hierarchically structured surfaces for green science'.
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Affiliation(s)
- W Barthlott
- Nees Institute for Biodiversity of Plants, University of Bonn, Venusbergweg 22, Bonn 53115, Germany
| | - M Mail
- Nees Institute for Biodiversity of Plants, University of Bonn, Venusbergweg 22, Bonn 53115, Germany Institute of Crop Science and Resource Conservation (INRES)-Horticultural Science, University of Bonn, Auf dem Hügel 6, Bonn 53121, Germany
| | - C Neinhuis
- Institute of Botany, Technische Universität Dresden, Zellescher Weg 20b, Dresden 01217, Germany B CUBE Innovation Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstrasse 18, Dresden 01217, Germany
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254
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Bellot S, Cusimano N, Luo S, Sun G, Zarre S, Gröger A, Temsch E, Renner SS. Assembled Plastid and Mitochondrial Genomes, as well as Nuclear Genes, Place the Parasite Family Cynomoriaceae in the Saxifragales. Genome Biol Evol 2016; 8:2214-30. [PMID: 27358425 PMCID: PMC4987112 DOI: 10.1093/gbe/evw147] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Cynomoriaceae, one of the last unplaced families of flowering plants, comprise one or two species or subspecies of root parasites that occur from the Mediterranean to the Gobi Desert. Using Illumina sequencing, we assembled the mitochondrial and plastid genomes as well as some nuclear genes of a
Cynomorium
specimen from Italy. Selected genes were also obtained by Sanger sequencing from individuals collected in China and Iran, resulting in matrices of 33 mitochondrial, 6 nuclear, and 14 plastid genes and rDNAs enlarged to include a representative angiosperm taxon sampling based on data available in GenBank. We also compiled a new geographic map to discern possible discontinuities in the parasites’ occurrence.
Cynomorium
has large genomes of 13.70–13.61 (Italy) to 13.95–13.76 pg (China). Its mitochondrial genome consists of up to 49 circular subgenomes and has an overall gene content similar to that of photosynthetic angiosperms, while its plastome retains only 27 of the normally 116 genes. Nuclear, plastid and mitochondrial phylogenies place Cynomoriaceae in Saxifragales, and we found evidence for several horizontal gene transfers from different hosts, as well as intracellular gene transfers.
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Affiliation(s)
- Sidonie Bellot
- Department of Plant Sciences, Plant Biodiversity Research, Technical University of Munich (TUM), Freising, Germany
| | - Natalie Cusimano
- Systematic Botany and Mycology, Faculty of Biology, University of Munich (LMU), Germany
| | - Shixiao Luo
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Guangzhou, China
| | - Guiling Sun
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, China
| | - Shahin Zarre
- Department of Plant Sciences, University of Tehran, Iran
| | | | - Eva Temsch
- Department of Systematic and Evolutionary Botany, University of Vienna, Austria
| | - Susanne S Renner
- Systematic Botany and Mycology, Faculty of Biology, University of Munich (LMU), Germany
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255
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Another look at the phylogenetic position of the grape order Vitales: Chloroplast phylogenomics with an expanded sampling of key lineages. Mol Phylogenet Evol 2016; 101:216-223. [DOI: 10.1016/j.ympev.2016.04.034] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 04/27/2016] [Accepted: 04/29/2016] [Indexed: 12/21/2022]
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256
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Cullen E, Rudall PJ. The remarkable stomata of horsetails (Equisetum): patterning, ultrastructure and development. ANNALS OF BOTANY 2016; 118:207-18. [PMID: 27268485 PMCID: PMC4970360 DOI: 10.1093/aob/mcw094] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 02/18/2016] [Accepted: 03/31/2016] [Indexed: 05/21/2023]
Abstract
BACKGROUND AND AIMS The stomata of Equisetum - the sole extant representative of an ancient group of land plants - are unique with respect to both structure and development, yet little is known about details of ultrastructure and patterning, and existing accounts of key developmental stages are conflicting. METHODS We used light and electron microscopy to examine mature stomata and stomatal development in Equisetum myriochaetum, and compared them with other land plants, including another putative fern relative, Psilotum We reviewed published reports of stomatal development to provide a comprehensive discussion of stomata in more distantly related taxa. KEY RESULTS Stomatal development in Equisetum is basipetal and sequential in strict linear cell files, in contrast with Psilotum, in which stomatal development occurs acropetally. In Equisetum, cell asymmetry occurs in the axial stomatal cell file, resulting in a meristemoidal mother cell that subsequently undergoes two successive asymmetric mitoses. Each stomatal cell complex is formed from a single precursor meristemoid, and consists of four cells: two guard cells and two mesogene subsidiary cells. Late periclinal divisions occur in the developing intervening cells. CONCLUSIONS In addition to the unique mature structure, several highly unusual developmental features include a well-defined series of asymmetric and symmetric mitoses in Equisetum, which differs markedly from Psilotum and other land plants. The results contribute to our understanding of the diverse patterns of stomatal development in land plants, including contrasting pathways to paracytic stomata. They add to a considerable catalogue of highly unusual traits of horsetails - one of the most evolutionarily isolated land-plant taxa.
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Affiliation(s)
- Erin Cullen
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Paula J Rudall
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
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257
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Beilby MJ. Multi-Scale Characean Experimental System: From Electrophysiology of Membrane Transporters to Cell-to-Cell Connectivity, Cytoplasmic Streaming and Auxin Metabolism. FRONTIERS IN PLANT SCIENCE 2016; 7:1052. [PMID: 27504112 PMCID: PMC4958633 DOI: 10.3389/fpls.2016.01052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/05/2016] [Indexed: 05/29/2023]
Abstract
The morphology of characean algae could be mistaken for a higher plant: stem-like axes with leaf-like branchlets anchored in the soil by root-like rhizoids. However, all of these structures are made up of giant multinucleate cells separated by multicellular nodal complexes. The excised internodal cells survive long enough for the nodes to give rise to new thallus. The size of the internodes and their thick cytoplasmic layer minimize impalement injury and allow specific micro-electrode placement. The cell structure can be manipulated by centrifugation, perfusion of cell contents or creation of cytoplasmic droplets, allowing access to both vacuolar and cytoplasmic compartments and both sides of the cell membranes. Thousands of electrical measurements on intact or altered cells and cytoplasmic droplets laid down basis to modern plant electrophysiology. Furthermore, the giant internodal cells and whole thalli facilitate research into many other plant properties. As nutrients have to be transported from rhizoids to growing parts of the thallus and hormonal signals need to pass from cell to cell, Characeae possess very fast cytoplasmic streaming. The mechanism was resolved in the characean model. Plasmodesmata between the internodal cells and nodal complexes facilitate transport of ions, nutrients and photosynthates across the nodes. The internal structure was found to be similar to those of higher plants. Recent experiments suggest a strong circadian influence on metabolic pathways producing indole-3-acetic acid (IAA) and serotonin/melatonin. The review will discuss the impact of the characean models arising from fragments of cells, single cells, cell-to-cell transport or whole thalli on understanding of plant evolution and physiology.
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Affiliation(s)
- Mary J. Beilby
- School of Physics, The University of New South Wales, SydneyNSW, Australia
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258
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Ni L, Zhao Z, Xu H, Chen S, Dorje G. Chloroplast genome structures in Gentiana (Gentianaceae), based on three medicinal alpine plants used in Tibetan herbal medicine. Curr Genet 2016; 63:241-252. [PMID: 27422574 DOI: 10.1007/s00294-016-0631-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 07/07/2016] [Accepted: 07/08/2016] [Indexed: 10/21/2022]
Abstract
The genus Gentiana is the largest in the Gentianaceae family with ca. 400 species. However, with most species growing on the Qinghai-Tibet plateau, the processes of adaptive evolution and speciation within the genus is not clear. Also, the genomic analyses could provide important information. So far, the complete chloroplast (cp) genome data of the genus are still deficient. As the second and third sequenced members within Gentianaceae, we report the construction of complete cp sequences of Gentiana robusta King ex Hook. f. and Gentiana crassicaulis Duthie ex Burk., and describe a comparative study of three Gentiana cp genomes, including the cp genome of Gentiana straminea Maxim. published previously. These cp genomes are highly conserved in gene size, gene content, and gene order and the rps16 pseudogene with exon2 missing was found common. Three repeat types and five SSR types were investigated, and the number and distribution are similar among the three genomes. Sixteen genome divergent hotspot regions were identified across these cp genomes that could provide potential molecular markers for further phylogenetic studies in Gentiana. The IR/SC boundary organizations in Gentianales cp genomes were compared and three different types of boundaries were observed. Six data partitions of cp genomes in Gentianales were used for phylogenetic analyses and different data partitions were largely congruent with each other. The ML phylogenetic tree was constructed based on the fragments in cp genomes commonly available in 33 species from Lamiids, including 12 species in Gentianales, 1 in Boraginaceae, 10 in Solanales, and 10 in Lamiales. The result strongly supports the position of Boraginaceae (Ehretia acuminata) as the sister of Solanales, with the bootstrap values of 97 %. This study provides a platform for further research into the molecular phylogenetics of species in the order Gentianales (family Gentianaceae) notably in respect of speciation and species identification.
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Affiliation(s)
- Lianghong Ni
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Zhili Zhao
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Hongxi Xu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Gaawe Dorje
- Tibetan Traditional Medical College, Lhasa, 850000, China
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259
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Emms DM, Covshoff S, Hibberd JM, Kelly S. Independent and Parallel Evolution of New Genes by Gene Duplication in Two Origins of C4 Photosynthesis Provides New Insight into the Mechanism of Phloem Loading in C4 Species. Mol Biol Evol 2016; 33:1796-806. [PMID: 27016024 PMCID: PMC4915358 DOI: 10.1093/molbev/msw057] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
UNLABELLED C4 photosynthesis is considered one of the most remarkable examples of evolutionary convergence in eukaryotes. However, it is unknown whether the evolution of C4 photosynthesis required the evolution of new genes. Genome-wide gene-tree species-tree reconciliation of seven monocot species that span two origins of C4 photosynthesis revealed that there was significant parallelism in the duplication and retention of genes coincident with the evolution of C4 photosynthesis in these lineages. Specifically, 21 orthologous genes were duplicated and retained independently in parallel at both C4 origins. Analysis of this gene cohort revealed that the set of parallel duplicated and retained genes is enriched for genes that are preferentially expressed in bundle sheath cells, the cell type in which photosynthesis was activated during C4 evolution. Furthermore, functional analysis of the cohort of parallel duplicated genes identified SWEET-13 as a potential key transporter in the evolution of C4 photosynthesis in grasses, and provides new insight into the mechanism of phloem loading in these C4 species. KEY WORDS C4 photosynthesis, gene duplication, gene families, parallel evolution.
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Affiliation(s)
- David M Emms
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Sarah Covshoff
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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260
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Simmons MP, Gatesy J. Biases of tree-independent-character-subsampling methods. Mol Phylogenet Evol 2016; 100:424-443. [DOI: 10.1016/j.ympev.2016.04.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/16/2016] [Accepted: 04/15/2016] [Indexed: 12/21/2022]
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261
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Horst NA, Reski R. Alternation of generations - unravelling the underlying molecular mechanism of a 165-year-old botanical observation. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:549-51. [PMID: 27094475 DOI: 10.1111/plb.12468] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/15/2016] [Indexed: 05/02/2023]
Abstract
Characteristically, land plants exhibit a life cycle with an 'alternation of generations' and thus alternate between a haploid gametophyte and a diploid sporophyte. At meiosis and fertilisation the transitions between these two ontogenies take place in distinct single stem cells. The evolutionary invention of an embryo, and thus an upright multicellular sporophyte, in the ancestor of land plants formed the basis for the evolution of increasingly complex plant morphologies shaping Earth's ecosystems. Recent research employing the moss Physcomitrella patens revealed the homeotic gene BELL1 as a master regulator of the gametophyte-to-sporophyte transition. Here, we discuss these findings in the context of classical botanical observations.
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Affiliation(s)
- N A Horst
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - R Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- BIOSS - Centre for Biological Signalling Studies, Freiburg, Germany
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262
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Liu TJ, Zhang CY, Yan HF, Zhang L, Ge XJ, Hao G. Complete plastid genome sequence of Primula sinensis (Primulaceae): structure comparison, sequence variation and evidence for accD transfer to nucleus. PeerJ 2016; 4:e2101. [PMID: 27375965 PMCID: PMC4928469 DOI: 10.7717/peerj.2101] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/10/2016] [Indexed: 11/22/2022] Open
Abstract
Species-rich genus Primula L. is a typical plant group with which to understand genetic variance between species in different levels of relationships. Chloroplast genome sequences are used to be the information resource for quantifying this difference and reconstructing evolutionary history. In this study, we reported the complete chloroplast genome sequence of Primula sinensis and compared it with other related species. This genome of chloroplast showed a typical circular quadripartite structure with 150,859 bp in sequence length consisting of 37.2% GC base. Two inverted repeated regions (25,535 bp) were separated by a large single-copy region (82,064 bp) and a small single-copy region (17,725 bp). The genome consists of 112 genes, including 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Among them, seven coding genes, seven tRNA genes and four rRNA genes have two copies due to their locations in the IR regions. The accD and infA genes lacking intact open reading frames (ORF) were identified as pseudogenes. SSR and sequence variation analyses were also performed on the plastome of Primula sinensis, comparing with another available plastome of P. poissonii. The four most variable regions, rpl36–rps8, rps16–trnQ, trnH–psbA and ndhC–trnV, were identified. Phylogenetic relationship estimates using three sub-datasets extracted from a matrix of 57 protein-coding gene sequences showed the identical result that was consistent with previous studies. A transcript found from P. sinensis transcriptome showed a high similarity to plastid accD functional region and was identified as a putative plastid transit peptide at the N-terminal region. The result strongly suggested that plastid accD has been functionally transferred to the nucleus in P. sinensis.
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Affiliation(s)
- Tong-Jian Liu
- College of Life Sciences, South China Agricultural University , Guangzhou , China
| | - Cai-Yun Zhang
- College of Life Sciences, South China Agricultural University , Guangzhou , China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou , China
| | - Lu Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou , China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou , China
| | - Gang Hao
- College of Life Sciences, South China Agricultural University , Guangzhou , China
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263
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Sudianto E, Wu CS, Lin CP, Chaw SM. Revisiting the Plastid Phylogenomics of Pinaceae with Two Complete Plastomes of Pseudolarix and Tsuga. Genome Biol Evol 2016; 8:1804-11. [PMID: 27352945 PMCID: PMC4943178 DOI: 10.1093/gbe/evw106] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2016] [Indexed: 11/30/2022] Open
Abstract
Phylogeny of the ten Pinaceous genera has long been contentious. Plastid genomes (plastomes) provide an opportunity to resolve this problem because they contain rich evolutionary information. To comprehend the plastid phylogenomics of all ten Pinaceous genera, we sequenced the plastomes of two previously unavailable genera, Pseudolarix amabilis (122,234 bp) and Tsuga chinensis (120,859 bp). Both plastomes share similar gene repertoire and order. Here for the first time we report a unique insertion of tandem repeats in accD of T. chinensis From the 65 plastid protein-coding genes common to all Pinaceous genera, we re-examined the phylogenetic relationship among all Pinaceous genera. Our two phylogenetic trees are congruent in an identical tree topology, with the five genera of the Abietoideae subfamily constituting a monophyletic clade separate from the other three subfamilies: Pinoideae, Piceoideae, and Laricoideae. The five genera of Abietoideae were grouped into two sister clades consisting of (1) Cedrus alone and (2) two sister subclades of Pseudolarix-Tsuga and Abies-Keteleeria, with the former uniquely losing the gene psaM and the latter specifically excluding the 3 psbA from the residual inverted repeat.
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Affiliation(s)
- Edi Sudianto
- Biodiversity Program, Taiwan International Graduate Program, Biodiversity Research Center, Academia Sinica and National Taiwan Normal University, Nankang District, Taipei 11529, Taiwan Department of Life Science, National Taiwan Normal University, Wenshan District, Taipei 11677, Taiwan Biodiversity Research Center, Academia Sinica, Nankang District, Taipei 11529, Taiwan
| | - Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Nankang District, Taipei 11529, Taiwan
| | - Ching-Ping Lin
- Biodiversity Research Center, Academia Sinica, Nankang District, Taipei 11529, Taiwan Present Address: Institute of Plant and Microbial Biology, Academia Sinica, Nankang District, Taipei 11529, Taiwan
| | - Shu-Miaw Chaw
- Biodiversity Program, Taiwan International Graduate Program, Biodiversity Research Center, Academia Sinica and National Taiwan Normal University, Nankang District, Taipei 11529, Taiwan Biodiversity Research Center, Academia Sinica, Nankang District, Taipei 11529, Taiwan
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264
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Bardon L, Sothers C, Prance GT, Malé PJG, Xi Z, Davis CC, Murienne J, García-Villacorta R, Coissac E, Lavergne S, Chave J. Unraveling the biogeographical history of Chrysobalanaceae from plastid genomes. AMERICAN JOURNAL OF BOTANY 2016; 103:1089-1102. [PMID: 27329943 DOI: 10.3732/ajb.1500463] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 05/04/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY The complex geological and climatic history of the Neotropics has had major implications on the diversification of plant lineages. Chrysobalanaceae is a pantropical family of trees and shrubs with 75% of its 531 species found in the Neotropics, and a time-calibrated phylogeny of this family should shed light on the tempo of diversification in the Neotropical flora. Previously published phylogenetic hypotheses of this family were poorly supported, and its biogeography remains unclear. METHODS We assembled the complete plastid genome of 51 Chrysobalanaceae species, and increased taxon sampling by Sanger-sequencing of five plastid regions for an additional 88 species. We generated a time-calibrated tree including all 139 Chrsyobalanaceae species and 23 outgroups. We then conducted an ancestral area reconstruction analysis and estimated diversification rates in the family. KEY RESULTS The tree generated with the plastid genome alignment was almost fully resolved. It supports the polyphyly of Licania and Hirtella. The family has diversified starting around the Eocene-Oligocene transition. An ancestral area reconstruction confirms a Paleotropical origin for Chrysobalanaceae with several transoceanic dispersal events. The main Neotropical clade likely resulted from a single migration event from Africa around 28 mya ago, which subsequently underwent rapid diversification. CONCLUSIONS Given the diverse ecologies exhibited by extant species, we hypothesize that the rapid diversification of Chrysobalanaceae following the colonization of the Neotropics was triggered by habitat specialization during the complex geological and paleoclimatic history of the Neotropics.
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Affiliation(s)
- Léa Bardon
- Laboratoire Evolution et Diversité Biologique UMR 5174 CNRS, ENFA, Université Paul Sabatier 31062 Toulouse, France
| | - Cynthia Sothers
- Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom
| | - Ghillean T Prance
- Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom
| | - Pierre-Jean G Malé
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
| | - Zhenxiang Xi
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts 02138, USA
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts 02138, USA
| | - Jerome Murienne
- Laboratoire Evolution et Diversité Biologique UMR 5174 CNRS, ENFA, Université Paul Sabatier 31062 Toulouse, France
| | | | - Eric Coissac
- Université Grenoble Alpes, CNRS, UMR 5553 LECA, F-38000 Grenoble, France
| | - Sébastien Lavergne
- Université Grenoble Alpes, CNRS, UMR 5553 LECA, F-38000 Grenoble, France
| | - Jérôme Chave
- Laboratoire Evolution et Diversité Biologique UMR 5174 CNRS, ENFA, Université Paul Sabatier 31062 Toulouse, France
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265
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de Vries J, Stanton A, Archibald JM, Gould SB. Streptophyte Terrestrialization in Light of Plastid Evolution. TRENDS IN PLANT SCIENCE 2016; 21:467-476. [PMID: 26895731 DOI: 10.1016/j.tplants.2016.01.021] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/19/2016] [Accepted: 01/28/2016] [Indexed: 05/21/2023]
Abstract
Key steps in evolution are often singularities. The emergence of land plants is one such case and it is not immediately apparent why. A recent analysis found that the zygnematophycean algae represent the closest relative to embryophytes. Intriguingly, many exaptations thought essential to conquer land are common among various streptophytes, but zygnematophycean algae share with land plants the transfer of a few plastid genes to the nucleus. Considering the contribution of the chloroplast to terrestrialization highlights potentially novel exaptations that currently remain unexplored. We discuss how the streptophyte chloroplast evolved into what we refer to as the embryoplast, and argue this was as important for terrestrialization by freshwater algae as the host cell-associated exaptations that are usually focused upon.
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Affiliation(s)
- Jan de Vries
- Institute for Molecular Evolution, Heinrich-Heine-University (HHU) Düsseldorf, 40225 Düsseldorf, Germany
| | - Amanda Stanton
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Sven B Gould
- Institute for Molecular Evolution, Heinrich-Heine-University (HHU) Düsseldorf, 40225 Düsseldorf, Germany.
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266
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Chloroplast phylogenomic data from the green algal order Sphaeropleales (Chlorophyceae, Chlorophyta) reveal complex patterns of sequence evolution. Mol Phylogenet Evol 2016; 98:176-83. [DOI: 10.1016/j.ympev.2016.01.022] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 12/08/2015] [Accepted: 01/19/2016] [Indexed: 01/16/2023]
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267
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Tiley GP, Ané C, Burleigh JG. Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data. Genome Biol Evol 2016; 8:1023-37. [PMID: 26988251 PMCID: PMC4860690 DOI: 10.1093/gbe/evw058] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Whole-genome duplications (WGDs) have helped shape the genomes of land plants, and recent evidence suggests that the genomes of all angiosperms have experienced at least two ancient WGDs. In plants, WGDs often are followed by rapid fractionation, in which many homeologous gene copies are lost. Thus, it can be extremely difficult to identify, let alone characterize, ancient WGDs. In this study, we use a new maximum likelihood estimator to test for evidence of ancient WGDs in land plants and estimate the fraction of new genes copies that are retained following a WGD using gene count data, the number of gene copies in gene families. We identified evidence of many putative ancient WGDs in land plants and found that the genome fractionation rates vary tremendously among ancient WGDs. Analyses of WGDs within Brassicales also indicate that background gene duplication and loss rates vary across land plants, and different gene families have different probabilities of being retained following a WGD. Although our analyses are largely robust to errors in duplication and loss rates and the choice of priors, simulations indicate that this method can have trouble detecting multiple WGDs that occur on the same branch, especially when the gene retention rates for ancient WGDs are very low. They also suggest that we should carefully evaluate evidence for some ancient plant WGD hypotheses.
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Affiliation(s)
| | - Cécile Ané
- Department of Statistics, University of Wisconsin-Madison Department of Botany, University of Wisconsin-Madison
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268
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Luo Y, Ma PF, Li HT, Yang JB, Wang H, Li DZ. Plastid Phylogenomic Analyses Resolve Tofieldiaceae as the Root of the Early Diverging Monocot Order Alismatales. Genome Biol Evol 2016; 8:932-45. [PMID: 26957030 PMCID: PMC4823975 DOI: 10.1093/gbe/evv260] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2015] [Indexed: 01/03/2023] Open
Abstract
The predominantly aquatic order Alismatales, which includes approximately 4,500 species within Araceae, Tofieldiaceae, and the core alismatid families, is a key group in investigating the origin and early diversification of monocots. Despite their importance, phylogenetic ambiguity regarding the root of the Alismatales tree precludes answering questions about the early evolution of the order. Here, we sequenced the first complete plastid genomes from three key families in this order:Potamogeton perfoliatus(Potamogetonaceae),Sagittaria lichuanensis(Alismataceae), andTofieldia thibetica(Tofieldiaceae). Each family possesses the typical quadripartite structure, with plastid genome sizes of 156,226, 179,007, and 155,512 bp, respectively. Among them, the plastid genome ofS. lichuanensisis the largest in monocots and the second largest in angiosperms. Like other sequenced Alismatales plastid genomes, all three families generally encode the same 113 genes with similar structure and arrangement. However, we detected 2.4 and 6 kb inversions in the plastid genomes ofSagittariaandPotamogeton, respectively. Further, we assembled a 79 plastid protein-coding gene sequence data matrix of 22 taxa that included the three newly generated plastid genomes plus 19 previously reported ones, which together represent all primary lineages of monocots and outgroups. In plastid phylogenomic analyses using maximum likelihood and Bayesian inference, we show both strong support for Acorales as sister to the remaining monocots and monophyly of Alismatales. More importantly, Tofieldiaceae was resolved as the most basal lineage within Alismatales. These results provide new insights into the evolution of Alismatales as well as the early-diverging monocots as a whole.
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Affiliation(s)
- Yang Luo
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, China
| | - Peng-Fei Ma
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hong Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - De-Zhu Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
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269
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Lam VKY, Merckx VSFT, Graham SW. A few-gene plastid phylogenetic framework for mycoheterotrophic monocots. AMERICAN JOURNAL OF BOTANY 2016; 103:692-708. [PMID: 27056932 DOI: 10.3732/ajb.1500412] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 02/08/2016] [Indexed: 05/03/2023]
Abstract
PREMISE OF THE STUDY Few-gene studies with broad taxon sampling have provided major insights into phylogeny and underpin plant classification. However, they have typically excluded heterotrophic plants because of loss, pseudogenization, or rapid evolution of plastid genes. Here we performed a phylogenetic survey of three commonly retained plastid genes to assess their utility in placing mycoheterotrophs. METHODS We surveyed accD, clpP, and matK for 34 taxa from seven monocot families that include full mycoheterotrophs and a broad sampling of photosynthetic taxa. After screening for weak contaminants, we conducted phylogenetic analyses and characterized among-lineage rate variation. KEY RESULTS Likelihood analyses strongly supported local placements of fully mycoheterotrophic taxa for Corsiaceae, Iridaceae, Orchidaceae, and Petrosaviaceae, in positions consistent with other studies. Depression of likelihood bootstrap support values near mycoheterotrophic clades was alleviated when each mycoheterotrophic family was considered separately. Triuridaceae (Sciaphila) monophyly was recovered in a partitioned likelihood analysis, and the family then placed as sister to Cyclanthaceae-Pandanaceae. Burmanniaceae placed in Dioscoreales with weak to strong support depending on analysis details, and we inferred a plastid-based phylogeny for the family. Thismiaceae species may retain a plastid genome, based on accD retention. The inferred position of Thismiaceae is unstable, but was close to Taccaceae (Dioscoreales) in some analyses. CONCLUSIONS Long branches/elevated substitution rates, missing genes, and occasional contaminants are challenges for plastid-based phylogenetic inference with full mycoheterotrophs. However, most mycoheterotrophs can be readily integrated into the broad picture of plant phylogeny using several plastid genes and broad taxonomic sampling.
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Affiliation(s)
- Vivienne K Y Lam
- Department of Botany, 6270 University Boulevard, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada UBC Botanical Garden & Centre for Plant Research, 6804 Marine Drive SW, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | | | - Sean W Graham
- Department of Botany, 6270 University Boulevard, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada UBC Botanical Garden & Centre for Plant Research, 6804 Marine Drive SW, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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270
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Cusimano N, Wicke S. Massive intracellular gene transfer during plastid genome reduction in nongreen Orobanchaceae. THE NEW PHYTOLOGIST 2016; 210:680-93. [PMID: 26671255 DOI: 10.1111/nph.13784] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 10/28/2015] [Indexed: 05/10/2023]
Abstract
Plastid genomes (plastomes) of nonphotosynthetic plants experience extensive gene losses and an acceleration of molecular evolutionary rates. Here, we inferred the mechanisms and timing of reductive genome evolution under relaxed selection in the broomrape family (Orobanchaceae). We analyzed the plastomes of several parasites with a major focus on the genus Orobanche using genome-descriptive and Bayesian phylogenetic-comparative methods. Besides this, we scanned the parasites' other cellular genomes to trace the fate of all genes that were purged from their plastomes. Our analyses indicate that the first functional gene losses occurred within 10 Myr of the transition to obligate parasitism in Orobanchaceae, and that the physical plastome reduction proceeds by small deletions that accumulate over time. Evolutionary rate shifts coincide with the genomic reduction process in broomrapes, suggesting that the shift of selectional constraints away from photosynthesis to other molecular processes alters the plastid rate equilibrium. Most of the photosynthesis-related genes or fragments of genes lost from the plastomes of broomrapes have survived in their nuclear or mitochondrial genomes as the results of multiple intracellular transfers and subsequent fragmentation. Our findings indicate that nonessential DNA is eliminated much faster in the plastomes of nonphotosynthetic parasites than in their other cellular genomes.
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Affiliation(s)
- Natalie Cusimano
- Department of Biology, Ludwig Maximilian University of Munich, Menzinger Street 67, Munich, 80638, Germany
| | - Susann Wicke
- Institute for Evolution and Biodiversity, University of Muenster, Huefferstr. 1, Muenster, 48149, Germany
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271
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Rose JP, Kriebel R, Sytsma KJ. Shape analysis of moss (Bryophyta) sporophytes: Insights into land plant evolution. AMERICAN JOURNAL OF BOTANY 2016; 103:652-62. [PMID: 26944353 DOI: 10.3732/ajb.1500394] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 01/08/2016] [Indexed: 05/05/2023]
Abstract
PREMISE OF THE STUDY The alternation of generations life cycle represents a key feature of land-plant evolution and has resulted in a diverse array of sporophyte forms and modifications in all groups of land plants. We test the hypothesis that evolution of sporangium (capsule) shape of the mosses-the second most diverse land-plant lineage-has been driven by differing physiological demands of life in diverse habitats. This study provides an important conceptual framework for analyzing the evolution of a single, homologous character in a continuous framework across a deep expanse of time, across all branches of the tree of life. METHODS We reconstruct ancestral sporangium shape and ancestral habitat on the largest phylogeny of mosses to date, and use phylogenetic generalized least squares regression to test the association between habitat and sporangium shape. In addition, we examine the association between shifts in sporangium shape and species diversification. RESULTS We demonstrate that sporangium shape is convergent, under natural selection, and associated with habitat type, and that many shifts in speciation rate are associated with shifts in sporangium shape. CONCLUSIONS Our results suggest that natural selection in different microhabitats results in the diversity of sporangium shape found in mosses, and that many increasing shifts in speciation rate result in changes in sporangium shape across their 480 million year history. Our framework provides a way to examine if diversification shifts in other land plants are also associated with massive changes in sporophyte form, among other morphological traits.
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Affiliation(s)
- Jeffrey P Rose
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, Wisconsin 53706.
| | - Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, Wisconsin 53706
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, Wisconsin 53706
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272
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Condamine FL, Leslie AB, Antonelli A. Ancient islands acted as refugia and pumps for conifer diversity. Cladistics 2016; 33:69-92. [DOI: 10.1111/cla.12155] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2016] [Indexed: 01/19/2023] Open
Affiliation(s)
- Fabien L. Condamine
- Department of Biological and Environmental Sciences; University of Gothenburg; Box 461 SE-405 30 Göteborg Sweden
- Department of Biological Sciences; University of Alberta; Edmonton T6G 2E9 AB Canada
- CNRS, UMR 5554 Institut des Sciences de l'Evolution, Université de Montpellier; Place Eugène Bataillon 34095 Montpellier France
| | - Andrew B. Leslie
- Department of Ecology and Evolutionary Biology; Brown University; Providence RI 02912 USA
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences; University of Gothenburg; Box 461 SE-405 30 Göteborg Sweden
- Gothenburg Botanical Garden; Carl Skottsbergs gata 22A 413 19 Gothenburg Sweden
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273
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Sun Y, Moore MJ, Zhang S, Soltis PS, Soltis DE, Zhao T, Meng A, Li X, Li J, Wang H. Phylogenomic and structural analyses of 18 complete plastomes across nearly all families of early-diverging eudicots, including an angiosperm-wide analysis of IR gene content evolution. Mol Phylogenet Evol 2016; 96:93-101. [DOI: 10.1016/j.ympev.2015.12.006] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 12/01/2015] [Accepted: 12/09/2015] [Indexed: 11/27/2022]
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274
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Zhu A, Guo W, Gupta S, Fan W, Mower JP. Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates. THE NEW PHYTOLOGIST 2016; 209:1747-56. [PMID: 26574731 DOI: 10.1111/nph.13743] [Citation(s) in RCA: 277] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/01/2015] [Indexed: 05/20/2023]
Abstract
Rates of nucleotide substitution were previously shown to be several times slower in the plastid inverted repeat (IR) compared with single-copy (SC) regions, suggesting that the IR provides enhanced copy-correction activity. To examine the generality of this synonymous rate dependence on the IR, we compared plastomes from 69 pairs of closely related species representing 52 families of angiosperms, gymnosperms, and ferns. We explored the breadth of IR boundary shifts in land plants and demonstrate that synonymous substitution rates are, on average, 3.7 times slower in IR genes than in SC genes. In addition, genes moved from the SC into the IR exhibit lower synonymous rates consistent with other IR genes, while genes moved from the IR into the SC exhibit higher rates consistent with other SC genes. Surprisingly, however, several plastid genes from Pelargonium, Plantago, and Silene have highly accelerated synonymous rates despite their IR localization. Together, these results provide strong evidence that the duplicative nature of the IR reduces the substitution rate within this region. The anomalously fast-evolving genes in Pelargonium, Plantago, and Silene indicate localized hypermutation, potentially induced by a higher level of error-prone double-strand break repair in these regions, which generates substitutional rate variation.
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Affiliation(s)
- Andan Zhu
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Wenhu Guo
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA
| | - Sakshi Gupta
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
| | - Weishu Fan
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - 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
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275
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Schierwater B, Holland PWH, Miller DJ, Stadler PF, Wiegmann BM, Wörheide G, Wray GA, DeSalle R. Never Ending Analysis of a Century Old Evolutionary Debate: “Unringing” the Urmetazoon Bell. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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276
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Uribe-Convers S, Settles ML, Tank DC. A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae). PLoS One 2016; 11:e0148203. [PMID: 26828929 PMCID: PMC4734709 DOI: 10.1371/journal.pone.0148203] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 01/14/2016] [Indexed: 11/30/2022] Open
Abstract
Advances in high-throughput sequencing (HTS) have allowed researchers to obtain large amounts of biological sequence information at speeds and costs unimaginable only a decade ago. Phylogenetics, and the study of evolution in general, is quickly migrating towards using HTS to generate larger and more complex molecular datasets. In this paper, we present a method that utilizes microfluidic PCR and HTS to generate large amounts of sequence data suitable for phylogenetic analyses. The approach uses the Fluidigm Access Array System (Fluidigm, San Francisco, CA, USA) and two sets of PCR primers to simultaneously amplify 48 target regions across 48 samples, incorporating sample-specific barcodes and HTS adapters (2,304 unique amplicons per Access Array). The final product is a pooled set of amplicons ready to be sequenced, and thus, there is no need to construct separate, costly genomic libraries for each sample. Further, we present a bioinformatics pipeline to process the raw HTS reads to either generate consensus sequences (with or without ambiguities) for every locus in every sample or—more importantly—recover the separate alleles from heterozygous target regions in each sample. This is important because it adds allelic information that is well suited for coalescent-based phylogenetic analyses that are becoming very common in conservation and evolutionary biology. To test our approach and bioinformatics pipeline, we sequenced 576 samples across 96 target regions belonging to the South American clade of the genus Bartsia L. in the plant family Orobanchaceae. After sequencing cleanup and alignment, the experiment resulted in ~25,300bp across 486 samples for a set of 48 primer pairs targeting the plastome, and ~13,500bp for 363 samples for a set of primers targeting regions in the nuclear genome. Finally, we constructed a combined concatenated matrix from all 96 primer combinations, resulting in a combined aligned length of ~40,500bp for 349 samples.
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Affiliation(s)
- Simon Uribe-Convers
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- Stillinger Herbarium, University of Idaho, Moscow, Idaho, United States of America
- * E-mail:
| | - Matthew L. Settles
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
| | - David C. Tank
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- Stillinger Herbarium, University of Idaho, Moscow, Idaho, United States of America
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277
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Simmons MP, Sloan DB, Gatesy J. The effects of subsampling gene trees on coalescent methods applied to ancient divergences. Mol Phylogenet Evol 2016; 97:76-89. [PMID: 26768112 DOI: 10.1016/j.ympev.2015.12.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 12/03/2015] [Accepted: 12/20/2015] [Indexed: 10/22/2022]
Abstract
Gene-tree-estimation error is a major concern for coalescent methods of phylogenetic inference. We sampled eight empirical studies of ancient lineages with diverse numbers of taxa and genes for which the original authors applied one or more coalescent methods. We found that the average pairwise congruence among gene trees varied greatly both between studies and also often within a study. We recommend that presenting plots of pairwise congruence among gene trees in a dataset be treated as a standard practice for empirical coalescent studies so that readers can readily assess the extent and distribution of incongruence among gene trees. ASTRAL-based coalescent analyses generally outperformed MP-EST and STAR with respect to both internal consistency (congruence between analyses of subsamples of genes with the complete dataset of all genes) and congruence with the concatenation-based topology. We evaluated the approach of subsampling gene trees that are, on average, more congruent with other gene trees as a method to reduce artifacts caused by gene-tree-estimation errors on coalescent analyses. We suggest that this method is well suited to testing whether gene-tree-estimation error is a primary cause of incongruence between concatenation- and coalescent-based results, to reconciling conflicting phylogenetic results based on different coalescent methods, and to identifying genes affected by artifacts that may then be targeted for reciprocal illumination. We provide scripts that automate the process of calculating pairwise gene-tree incongruence and subsampling trees while accounting for differential taxon sampling among genes. Finally, we assert that multiple tree-search replicates should be implemented as a standard practice for empirical coalescent studies that apply MP-EST.
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Affiliation(s)
- Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA.
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - John Gatesy
- Department of Biology, University of California, Riverside, CA 92521, USA
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278
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Barrett CF, Baker WJ, Comer JR, Conran JG, Lahmeyer SC, Leebens-Mack JH, Li J, Lim GS, Mayfield-Jones DR, Perez L, Medina J, Pires JC, Santos C, Wm Stevenson D, Zomlefer WB, Davis JI. Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots. THE NEW PHYTOLOGIST 2016; 209:855-70. [PMID: 26350789 DOI: 10.1111/nph.13617] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 07/23/2015] [Indexed: 05/03/2023]
Abstract
Despite progress based on multilocus, phylogenetic studies of the palms (order Arecales, family Arecaceae), uncertainty remains in resolution/support among major clades and for the placement of the palms among the commelinid monocots. Palms and related commelinids represent a classic case of substitution rate heterogeneity that has not been investigated in the genomic era. To address questions of relationships, support and rate variation among palms and commelinid relatives, 39 plastomes representing the palms and related family Dasypogonaceae were generated via genome skimming and integrated within a monocot-wide matrix for phylogenetic and molecular evolutionary analyses. Support was strong for 'deep' relationships among the commelinid orders, among the five palm subfamilies, and among tribes of the subfamily Coryphoideae. Additionally, there was extreme heterogeneity in the plastid substitution rates across the commelinid orders indicated by model based analyses, with c. 22 rate shifts, and significant departure from a global clock. To date, this study represents the most comprehensively sampled matrix of plastomes assembled for monocot angiosperms, providing genome-scale support for phylogenetic relationships of monocot angiosperms, and lays the phylogenetic groundwork for comparative analyses of the drivers and correlates of such drastic differences in substitution rates across a diverse and significant clade.
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Affiliation(s)
- Craig F Barrett
- Department of Biological Sciences, California State University, Los Angeles, CA, 90032, USA
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | | | - Jason R Comer
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - John G Conran
- Department of Genetics and Evolution, School of Biological Sciences, University of Adelaide, Adelaide, 5005, Australia
| | - Sean C Lahmeyer
- Herbarium, The Huntington Library, Art Collection, and Botanical Gardens, San Marino, CA, 91108, USA
| | | | - Jeff Li
- Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, CA, 92521, USA
| | - Gwynne S Lim
- L. H. Bailey Hortorium and Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
| | - Dustin R Mayfield-Jones
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
- Division of Biological Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Leticia Perez
- Department of Biological Sciences, California State University, Los Angeles, CA, 90032, USA
| | - Jesus Medina
- Department of Biological Sciences, California State University, Los Angeles, CA, 90032, USA
| | - J Chris Pires
- Division of Biological Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Cristian Santos
- Department of Biological Sciences, California State University, Los Angeles, CA, 90032, USA
| | - Dennis Wm Stevenson
- Pfizer Laboratory of Molecular Systematics, New York Botanical Garden, Bronx, NY, 10458, USA
| | - Wendy B Zomlefer
- Herbarium, The Huntington Library, Art Collection, and Botanical Gardens, San Marino, CA, 91108, USA
| | - Jerrold I Davis
- L. H. Bailey Hortorium and Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
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Ross TG, Barrett CF, Soto Gomez M, Lam VK, Henriquez CL, Les DH, Davis JI, Cuenca A, Petersen G, Seberg O, Thadeo M, Givnish TJ, Conran J, Stevenson DW, Graham SW. Plastid phylogenomics and molecular evolution of Alismatales. Cladistics 2015; 32:160-178. [DOI: 10.1111/cla.12133] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2015] [Indexed: 11/27/2022] Open
Affiliation(s)
- T. Gregory Ross
- Department of Botany 6270 University Boulevard University of British Columbia Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research 6804 Marine Drive SW University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Craig F. Barrett
- Department of Biological Sciences 5151 State University Dr. California State University Los Angeles CA 90032‐8201 USA
| | - Marybel Soto Gomez
- Department of Botany 6270 University Boulevard University of British Columbia Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research 6804 Marine Drive SW University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Vivienne K.Y. Lam
- Department of Botany 6270 University Boulevard University of British Columbia Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research 6804 Marine Drive SW University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Claudia L. Henriquez
- Evolution, Ecology & Population Biology Division of Biology Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
| | - Donald H. Les
- Department of Ecology and Evolutionary Biology University of Connecticut Storrs CT 06269‐3043 USA
| | - Jerrold I. Davis
- L. H. Bailey Hortorium and Section of Plant Biology Cornell University Ithaca NY 14853 USA
| | - Argelia Cuenca
- Natural History Museum of Denmark University of Copenhagen Sølvgade 83 Opg. S DK‐1307 Copenhagen Denmark
| | - Gitte Petersen
- Natural History Museum of Denmark University of Copenhagen Sølvgade 83 Opg. S DK‐1307 Copenhagen Denmark
| | - Ole Seberg
- Natural History Museum of Denmark University of Copenhagen Sølvgade 83 Opg. S DK‐1307 Copenhagen Denmark
| | | | | | - John Conran
- Australian Centre for Evolutionary Biology and Biodiversity & Sprigg Geobiology Centre School of Biological Sciences Benham Bldg DX 650 312 The University of Adelaide Adelaide SA 5005 Australia
| | | | - Sean W. Graham
- Department of Botany 6270 University Boulevard University of British Columbia Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research 6804 Marine Drive SW University of British Columbia Vancouver BC V6T 1Z4 Canada
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280
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Berger BA, Kriebel R, Spalink D, Sytsma KJ. Divergence times, historical biogeography, and shifts in speciation rates of Myrtales. Mol Phylogenet Evol 2015; 95:116-36. [PMID: 26585030 DOI: 10.1016/j.ympev.2015.10.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 09/03/2015] [Accepted: 10/04/2015] [Indexed: 01/22/2023]
Abstract
We examine the eudicot order Myrtales, a clade with strong Gondwanan representation for most of its families. Although previous phylogenetic studies greatly improved our understanding of intergeneric and interspecific relationships within the order, our understanding of inter-familial relationships still remains unresolved; hence, we also lack a robust time-calibrated chronogram to address hypotheses (e.g., biogeography and diversification rates) that have implicit time assumptions. Six loci (rbcL, ndhF, matK, matR, 18S, and 26S) were amplified and sequenced for 102 taxa across Myrtales for phylogenetic reconstruction and ten fossil priors were utilized to produce a chronogram in BEAST. Combretaceae is identified as the sister clade to all remaining families with moderate support, and within the latter clade, two strongly supported groups are seen: (1) Onagraceae+Lythraceae, and (2) Melastomataceae+the Crypteroniaceae, Alzateaceae, Penaeaceae clade along with Myrtaceae+Vochysiaceae. Divergence time estimates suggest Myrtales diverged from Geraniales ∼124Mya during the Aptian of the Early Cretaceous. The crown date for Myrtales is estimated at ∼116Mya (Albian-Aptian). BioGeoBEARS showed significant improvement in the likelihood score when the "jump dispersal" parameter was added. South America and/or Africa are implicated as important ancestral areas in all deeper nodes. BAMM analyses indicate that the best configuration included three significant shifts in diversification rates within Myrtales: near the crown of Melastomataceae (∼67-64Mya), along the stem of subfamily Myrtoideae (Myrtaceae; ∼75Mya), and along the stem of tribe Combreteae (Combretaceae; ∼50-45Mya). Issues with conducting diversification analyses more generally are examined in the context of scale, taxon sampling, and larger sets of phylogenetic trees.
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Affiliation(s)
- Brent A Berger
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11432, USA; Department of Botany, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, USA.
| | - Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, USA
| | - Daniel Spalink
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, USA
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, USA
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281
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Uddenberg D, Akhter S, Ramachandran P, Sundström JF, Carlsbecker A. Sequenced genomes and rapidly emerging technologies pave the way for conifer evolutionary developmental biology. FRONTIERS IN PLANT SCIENCE 2015; 6:970. [PMID: 26579190 PMCID: PMC4630563 DOI: 10.3389/fpls.2015.00970] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/22/2015] [Indexed: 05/20/2023]
Abstract
Conifers, Ginkgo, cycads and gnetophytes comprise the four groups of extant gymnosperms holding a unique position of sharing common ancestry with the angiosperms. Comparative studies of gymnosperms and angiosperms are the key to a better understanding of ancient seed plant morphologies, how they have shifted over evolution to shape modern day species, and how the genes governing these morphologies have evolved. However, conifers and other gymnosperms have been notoriously difficult to study due to their long generation times, inaccessibility to genetic experimentation and unavailable genome sequences. Now, with three draft genomes from spruces and pines, rapid advances in next generation sequencing methods for genome wide expression analyses, and enhanced methods for genetic transformation, we are much better equipped to address a number of key evolutionary questions relating to seed plant evolution. In this mini-review we highlight recent progress in conifer developmental biology relevant to evo-devo questions. We discuss how genome sequence data and novel techniques might allow us to explore genetic variation and naturally occurring conifer mutants, approaches to reduce long generation times to allow for genetic studies in conifers, and other potential upcoming research avenues utilizing current and emergent techniques. Results from developmental studies of conifers and other gymnosperms in comparison to those in angiosperms will provide information to trace core molecular developmental control tool kits of ancestral seed plants, but foremost they will greatly improve our understanding of the biology of conifers and other gymnosperms in their own right.
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Affiliation(s)
- Daniel Uddenberg
- Physiological Botany, Department of Organismal Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Uppsala University, Uppsala, Sweden
| | - Shirin Akhter
- Department of Plant Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Prashanth Ramachandran
- Physiological Botany, Department of Organismal Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Uppsala University, Uppsala, Sweden
| | - Jens F. Sundström
- Department of Plant Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Annelie Carlsbecker
- Physiological Botany, Department of Organismal Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Uppsala University, Uppsala, Sweden
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282
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Stull GW, Duno de Stefano R, Soltis DE, Soltis PS. Resolving basal lamiid phylogeny and the circumscription of Icacinaceae with a plastome-scale data set. AMERICAN JOURNAL OF BOTANY 2015; 102:1794-813. [PMID: 26507112 DOI: 10.3732/ajb.1500298] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/16/2015] [Indexed: 05/08/2023]
Abstract
PREMISE OF THE STUDY Major relationships within Lamiidae, an asterid clade with ∼40000 species, have largely eluded resolution despite two decades of intensive study. The phylogenetic positions of Icacinaceae and other early-diverging lamiid clades (Garryales, Metteniusaceae, and Oncothecaceae) have been particularly problematic, hindering classification and impeding our understanding of early lamiid (and euasterid) character evolution. METHODS To resolve basal lamiid phylogeny, we sequenced 50 plastid genomes using the Illumina sequencing platform and combined these with available asterid plastome sequence data for more comprehensive phylogenetic analyses. KEY RESULTS Our analyses resolved basal lamiid relationships with strong support, including the circumscription and phylogenetic position of the enigmatic Icacinaceae. This greatly improved basal lamiid phylogeny offers insight into character evolution and facilitates an updated classification for this clade, which we present here, including phylogenetic definitions for 10 new or converted clade names. We also offer recommendations for applying this classification to the Angiosperm Phylogeny Group (APG) system, including the recognition of a reduced Icacinaceae, an expanded Metteniusaceae, and two orders new to APG: Icacinales (Icacinaceae + Oncothecaceae) and Metteniusales (Metteniusaceae). CONCLUSIONS The lamiids possibly radiated from an ancestry of tropical trees with inconspicuous flowers and large, drupaceous fruits, given that these morphological characters are distributed across a grade of lineages (Icacinaceae, Oncothecaceae, Metteniusaceae) subtending the core lamiid clade (Boraginales, Gentianales, Lamiales, Solanales, Vahlia). Furthermore, the presence of similar morphological features among members of Aquifoliales suggests these characters might be ancestral for the Gentianidae (euasterids) as a whole.
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Affiliation(s)
- Gregory W Stull
- Department of Biology, University of Florida, Gainesville, Florida 32611-8525 USA Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611-7800 USA
| | - Rodrigo Duno de Stefano
- Herbario CICY, Centro de Investigación Científicas de Yucatán A. C., Mérida, Yucatán 97200 Mexico
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, Florida 32611-8525 USA Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611-7800 USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611-7800 USA
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283
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Srivastava D, Shanker A. Identification of Simple Sequence Repeats in Chloroplast Genomes of Magnoliids Through Bioinformatics Approach. Interdiscip Sci 2015; 8:327-336. [PMID: 26471998 DOI: 10.1007/s12539-015-0129-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 06/11/2015] [Accepted: 09/30/2015] [Indexed: 10/22/2022]
Abstract
Basal angiosperms or Magnoliids is an important clade of commercially important plants which mainly include spices and edible fruits. In this study, 17 chloroplast genome sequences belonging to clade Magnoliids were screened for the identification of chloroplast simple sequence repeats (cpSSRs). Simple sequence repeats or microsatellites are short stretches of DNA up to 1-6 base pair in length. These repeats are ubiquitous and play important role in the development of molecular markers and to study the mapping of traits of economic, medical or ecological interest. A total of 479 SSRs were detected, showing average density of 1 SSR/6.91 kb. Depending on the repeat units, the length of SSRs ranged from 12 to 24 bp for mono-, 12 to 18 bp for di-, 12 to 26 bp for tri-, 12 to 24 bp for tetra-, 15 bp for penta- and 18 bp for hexanucleotide repeats. Mononucleotide repeats were the most frequent (207, 43.21 %) followed by tetranucleotide repeats (130, 27.13 %). Penta- and hexanucleotide repeats were least frequent or absent in these chloroplast genomes.
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Affiliation(s)
- Deepika Srivastava
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Banasthali, Rajasthan, 304022, India
| | - Asheesh Shanker
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Banasthali, Rajasthan, 304022, India.
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284
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Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants. BMC Genomics 2015; 16:781. [PMID: 26463180 PMCID: PMC4603344 DOI: 10.1186/s12864-015-2031-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 10/09/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Simple Sequence Repeats (SSRs) are widely used in population genetic studies but their classical development is costly and time-consuming. The ever-increasing available DNA datasets generated by high-throughput techniques offer an inexpensive alternative for SSRs discovery. Expressed Sequence Tags (ESTs) have been widely used as SSR source for plants of economic relevance but their application to non-model species is still modest. METHODS Here, we explored the use of publicly available ESTs (GenBank at the National Center for Biotechnology Information-NCBI) for SSRs development in non-model plants, focusing on genera listed by the International Union for the Conservation of Nature (IUCN). We also search two model genera with fully annotated genomes for EST-SSRs, Arabidopsis and Oryza, and used them as controls for genome distribution analyses. Overall, we downloaded 16 031 555 sequences for 258 plant genera which were mined for SSRsand their primers with the help of QDD1. Genome distribution analyses in Oryza and Arabidopsis were done by blasting the sequences with SSR against the Oryza sativa and Arabidopsis thaliana reference genomes implemented in the Basal Local Alignment Tool (BLAST) of the NCBI website. Finally, we performed an empirical test to determine the performance of our EST-SSRs in a few individuals from four species of two eudicot genera, Trifolium and Centaurea. RESULTS We explored a total of 14 498 726 EST sequences from the dbEST database (NCBI) in 257 plant genera from the IUCN Red List. We identify a very large number (17 102) of ready-to-test EST-SSRs in most plant genera (193) at no cost. Overall, dinucleotide and trinucleotide repeats were the prevalent types but the abundance of the various types of repeat differed between taxonomic groups. Control genomes revealed that trinucleotide repeats were mostly located in coding regions while dinucleotide repeats were largely associated with untranslated regions. Our results from the empirical test revealed considerable amplification success and transferability between congenerics. CONCLUSIONS The present work represents the first large-scale study developing SSRs by utilizing publicly accessible EST databases in threatened plants. Here we provide a very large number of ready-to-test EST-SSR (17 102) for 193 genera. The cross-species transferability suggests that the number of possible target species would be large. Since trinucleotide repeats are abundant and mainly linked to exons they might be useful in evolutionary and conservation studies. Altogether, our study highly supports the use of EST databases as an extremely affordable and fast alternative for SSR developing in threatened plants.
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285
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Pérez-Escobar OA, Balbuena JA, Gottschling M. Rumbling Orchids: How To Assess Divergent Evolution Between Chloroplast Endosymbionts and the Nuclear Host. Syst Biol 2015; 65:51-65. [DOI: 10.1093/sysbio/syv070] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 09/15/2015] [Indexed: 01/17/2023] Open
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286
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Hohmann N, Wolf EM, Lysak MA, Koch MA. A Time-Calibrated Road Map of Brassicaceae Species Radiation and Evolutionary History. THE PLANT CELL 2015; 27:2770-84. [PMID: 26410304 PMCID: PMC4682323 DOI: 10.1105/tpc.15.00482] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 08/13/2015] [Accepted: 09/05/2015] [Indexed: 05/18/2023]
Abstract
The Brassicaceae include several major crop plants and numerous important model species in comparative evolutionary research such as Arabidopsis, Brassica, Boechera, Thellungiella, and Arabis species. As any evolutionary hypothesis needs to be placed in a temporal context, reliably dated major splits within the evolution of Brassicaceae are essential. We present a comprehensive time-calibrated framework with important divergence time estimates based on whole-chloroplast sequence data for 29 Brassicaceae species. Diversification of the Brassicaceae crown group started at the Eocene-to-Oligocene transition. Subsequent major evolutionary splits are dated to ∼20 million years ago, coinciding with the Oligocene-to-Miocene transition, with increasing drought and aridity and transient glaciation events. The age of the Arabidopsis thaliana crown group is 6 million years ago, at the Miocene and Pliocene border. The overall species richness of the family is well explained by high levels of neopolyploidy (43% in total), but this trend is neither directly associated with an increase in genome size nor is there a general lineage-specific constraint. Our results highlight polyploidization as an important source for generating new evolutionary lineages adapted to changing environments. We conclude that species radiation, paralleled by high levels of neopolyploidization, follows genome size decrease, stabilization, and genetic diploidization.
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Affiliation(s)
- Nora Hohmann
- Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Eva M Wolf
- Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Martin A Lysak
- Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Marcus A Koch
- Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
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287
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Simmons MP, Gatesy J. Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms. Mol Phylogenet Evol 2015; 91:98-122. [DOI: 10.1016/j.ympev.2015.05.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/01/2015] [Accepted: 05/14/2015] [Indexed: 11/24/2022]
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288
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Les DH. Water from the rock: Ancient aquatic angiosperms flow from the fossil record. Proc Natl Acad Sci U S A 2015; 112:10825-6. [PMID: 26290578 PMCID: PMC4568265 DOI: 10.1073/pnas.1514280112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Donald H Les
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269
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289
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Horsetails are the sister group to all other monilophytes and Marattiales are sister to leptosporangiate ferns. Mol Phylogenet Evol 2015; 90:140-9. [DOI: 10.1016/j.ympev.2015.05.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 05/09/2015] [Accepted: 05/11/2015] [Indexed: 11/23/2022]
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290
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Gomez B, Daviero-Gomez V, Coiffard C, Martín-Closas C, Dilcher DL. Montsechia, an ancient aquatic angiosperm. Proc Natl Acad Sci U S A 2015; 112:10985-8. [PMID: 26283347 PMCID: PMC4568254 DOI: 10.1073/pnas.1509241112] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The early diversification of angiosperms in diverse ecological niches is poorly understood. Some have proposed an origin in a darkened forest habitat and others an open aquatic or near aquatic habitat. The research presented here centers on Montsechia vidalii, first recovered from lithographic limestone deposits in the Pyrenees of Spain more than 100 y ago. This fossil material has been poorly understood and misinterpreted in the past. Now, based upon the study of more than 1,000 carefully prepared specimens, a detailed analysis of Montsechia is presented. The morphology and anatomy of the plant, including aspects of its reproduction, suggest that Montsechia is sister to Ceratophyllum (whenever cladistic analyses are made with or without a backbone). Montsechia was an aquatic angiosperm living and reproducing below the surface of the water, similar to Ceratophyllum. Montsechia is Barremian in age, raising questions about the very early divergence of the Ceratophyllum clade compared with its position as sister to eudicots in many cladistic analyses. Lower Cretaceous aquatic angiosperms, such as Archaefructus and Montsechia, open the possibility that aquatic plants were locally common at a very early stage of angiosperm evolution and that aquatic habitats may have played a major role in the diversification of some early angiosperm lineages.
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Affiliation(s)
- Bernard Gomez
- CNRS-UMR 5276 Laboratoire de Géologie de Lyon-Terre, Planètes, Environnement, Université Lyon 1 (Claude Bernard), 69622 Villeurbanne, France;
| | - Véronique Daviero-Gomez
- CNRS-UMR 5276 Laboratoire de Géologie de Lyon-Terre, Planètes, Environnement, Université Lyon 1 (Claude Bernard), 69622 Villeurbanne, France
| | - Clément Coiffard
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, 10115 Berlin, Germany
| | - Carles Martín-Closas
- Departament d'Estratigrafia, Paleontologia i Geociències marines, Facultat de Geologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
| | - David L Dilcher
- Department of Geological Sciences, Indiana University, Bloomington, IN 47405
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291
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Bonavita S, Regina TMR. The evolutionary conservation of rps3 introns and rps19-rps3-rpl16 gene cluster in Adiantum capillus-veneris mitochondria. Curr Genet 2015; 62:173-84. [PMID: 26281979 DOI: 10.1007/s00294-015-0512-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 07/29/2015] [Accepted: 08/03/2015] [Indexed: 11/26/2022]
Abstract
Ferns are a large and evolutionarily critical group of vascular land plants for which quite limited mitochondrial gene content and genome organization data are, currently, available. This study reports that the gene for the ribosomal protein S3 (rps3) is preserved and physically clustered to an upstream rps19 and a downstream overlapping rpl16 locus in the mitochondrial DNA of the true fern Adiantum capillus-veneris L. Sequence analysis also revealed that the rps3 gene is interrupted by two cis-splicing group II introns, like the counterpart in lycopod and gymnosperm representatives. A preliminary polymerase chain reaction (PCR) survey confirmed a scattered distribution pattern of both the rps3 introns also in other fern lineages. Northern blot and reverse transcription (RT)-PCR analyses demonstrated that the three ribosomal protein genes are co-transcribed as a polycistronic mRNA and modified by RNA editing. Particularly, the U-to-C type editing amends numerous genomic stop codons in the A. capillus-veneris rps19, rps3 and rpl16 sequences, thus, assuring the synthesis of complete and functional polypeptides. Collectively, the findings from this study further expand our knowledge of the mitochondrial rps3 architecture and evolution, also, bridging the significant molecular data gaps across the so far underrepresented ferns and all land plants.
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Affiliation(s)
- Savino Bonavita
- Dipartimento di Biologia, Ecologia e Scienze della Terra (DiBEST), Università della Calabria, via Ponte P. Bucci, 87036, Arcavacata di Rende, Cosenza, Italy
| | - Teresa Maria Rosaria Regina
- Dipartimento di Biologia, Ecologia e Scienze della Terra (DiBEST), Università della Calabria, via Ponte P. Bucci, 87036, Arcavacata di Rende, Cosenza, Italy.
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292
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Folk RA, Mandel JR, Freudenstein JV. A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: A phylogenomic example from Heuchera (Saxifragaceae). APPLICATIONS IN PLANT SCIENCES 2015; 3:apps1500039. [PMID: 26312196 PMCID: PMC4542943 DOI: 10.3732/apps.1500039] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 07/09/2015] [Indexed: 05/18/2023]
Abstract
PREMISE OF THE STUDY Phylogenetic inference is moving to large multilocus data sets, yet there remains uncertainty in the choice of marker and sequencing method at low taxonomic levels. To address this gap, we present a method for enriching long loci spanning intron-exon boundaries in the genus Heuchera. METHODS Two hundred seventy-eight loci were designed using a splice-site prediction method combining transcriptomic and genomic data. Biotinylated probes were designed for enrichment of these loci. Reference-based assembly was performed using genomic references; additionally, chloroplast and mitochondrial genomes were used as references for off-target reads. The data were aligned and subjected to coalescent and concatenated phylogenetic analyses to demonstrate support for major relationships. RESULTS Complete or nearly complete (>99%) sequences were assembled from essentially all loci from all taxa. Aligned introns showed a fourfold increase in divergence as opposed to exons. Concatenated analysis gave decisive support to all nodes, and support was also high and relationships mostly similar in the coalescent analysis. Organellar phylogenies were also well-supported and conflicted with the nuclear signal. DISCUSSION Our approach shows promise for resolving a recent radiation. Enrichment for introns is highly successful with little or no sequencing dropout at low taxonomic levels despite higher substitution and indel frequencies, and should be exploited in studies of species complexes.
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Affiliation(s)
- Ryan A. Folk
- Herbarium, The Ohio State University, Columbus, Ohio 43212 USA
- Author for correspondence:
| | - Jennifer R. Mandel
- Department of Biology, University of Memphis, Memphis, Tennessee 38152 USA
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293
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Folk RA, Mandel JR, Freudenstein JV. A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: A phylogenomic example from Heuchera (Saxifragaceae). APPLICATIONS IN PLANT SCIENCES 2015. [PMID: 26312196 DOI: 10.5061/dryad.4cn66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
PREMISE OF THE STUDY Phylogenetic inference is moving to large multilocus data sets, yet there remains uncertainty in the choice of marker and sequencing method at low taxonomic levels. To address this gap, we present a method for enriching long loci spanning intron-exon boundaries in the genus Heuchera. METHODS Two hundred seventy-eight loci were designed using a splice-site prediction method combining transcriptomic and genomic data. Biotinylated probes were designed for enrichment of these loci. Reference-based assembly was performed using genomic references; additionally, chloroplast and mitochondrial genomes were used as references for off-target reads. The data were aligned and subjected to coalescent and concatenated phylogenetic analyses to demonstrate support for major relationships. RESULTS Complete or nearly complete (>99%) sequences were assembled from essentially all loci from all taxa. Aligned introns showed a fourfold increase in divergence as opposed to exons. Concatenated analysis gave decisive support to all nodes, and support was also high and relationships mostly similar in the coalescent analysis. Organellar phylogenies were also well-supported and conflicted with the nuclear signal. DISCUSSION Our approach shows promise for resolving a recent radiation. Enrichment for introns is highly successful with little or no sequencing dropout at low taxonomic levels despite higher substitution and indel frequencies, and should be exploited in studies of species complexes.
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Affiliation(s)
- Ryan A Folk
- Herbarium, The Ohio State University, Columbus, Ohio 43212 USA
| | - Jennifer R Mandel
- Department of Biology, University of Memphis, Memphis, Tennessee 38152 USA
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294
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Lam VKY, Soto Gomez M, Graham SW. The Highly Reduced Plastome of Mycoheterotrophic Sciaphila (Triuridaceae) Is Colinear with Its Green Relatives and Is under Strong Purifying Selection. Genome Biol Evol 2015; 105:480-494. [PMID: 26170229 DOI: 10.1002/ajb2.1070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/02/2018] [Indexed: 05/03/2023] Open
Abstract
The enigmatic monocot family Triuridaceae provides a potentially useful model system for studying the effects of an ancient loss of photosynthesis on the plant plastid genome, as all of its members are mycoheterotrophic and achlorophyllous. However, few studies have placed the family in a comparative context, and its phylogenetic placement is only partly resolved. It was also unclear whether any taxa in this family have retained a plastid genome. Here, we used genome survey sequencing to retrieve plastid genome data for Sciaphila densiflora (Triuridaceae) and ten autotrophic relatives in the orders Dioscoreales and Pandanales. We recovered a highly reduced plastome for Sciaphila that is nearly colinear with Carludovica palmata, a photosynthetic relative that belongs to its sister group in Pandanales, Cyclanthaceae-Pandanaceae. This phylogenetic placement is well supported and robust to a broad range of analytical assumptions in maximum-likelihood inference, and is congruent with recent findings based on nuclear and mitochondrial evidence. The 28 genes retained in the S. densiflora plastid genome are involved in translation and other nonphotosynthetic functions, and we demonstrate that nearly all of the 18 protein-coding genes are under strong purifying selection. Our study confirms the utility of whole plastid genome data in phylogenetic studies of highly modified heterotrophic plants, even when they have substantially elevated rates of substitution.
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Affiliation(s)
- Vivienne K Y Lam
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marybel Soto Gomez
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
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295
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Rothfels CJ, Li FW, Sigel EM, Huiet L, Larsson A, Burge DO, Ruhsam M, Deyholos M, Soltis DE, Stewart CN, Shaw SW, Pokorny L, Chen T, dePamphilis C, DeGironimo L, Chen L, Wei X, Sun X, Korall P, Stevenson DW, Graham SW, Wong GKS, Pryer KM. The evolutionary history of ferns inferred from 25 low-copy nuclear genes. AMERICAN JOURNAL OF BOTANY 2015. [PMID: 26199366 DOI: 10.3732/ajb.1500089] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
UNLABELLED • PREMISE OF THE STUDY Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data.• METHODS Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35877 bp), along with rigorous alignment, orthology inference and model selection.• KEY RESULTS Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to ∼200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data.• CONCLUSIONS Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies.
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Affiliation(s)
- Carl J Rothfels
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6J 3S7, Canada
| | - Fay-Wei Li
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
| | - Erin M Sigel
- Department of Botany (MRC 166), National Museum of Natural History, Smithsonian Institution, P.O. Box 37012 Washington, District of Columbia 20013-7012 USA
| | - Layne Huiet
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
| | - Anders Larsson
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-752 36 Uppsala, Sweden
| | - Dylan O Burge
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, California 94118 USA
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, UK
| | - Michael Deyholos
- Department of Biology, University of British Columbia, Okanagan Campus, 1177 Research Road, Kelowna, British Columbia V1V 1V7, Canada
| | - Douglas E Soltis
- Florida Museum of Natural History, Department of Biology, and the Genetics Institute. University of Florida. Gainesville, Florida 32611 USA
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996, USA
| | | | - Lisa Pokorny
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico-Consejo Superior de Investigaciones Científicas, 28014 Madrid, Spain
| | - Tao Chen
- Shenzhen Fairy Lake Botanical Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China
| | - Claude dePamphilis
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 USA
| | - Lisa DeGironimo
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458 USA
| | - Li Chen
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Xiaofeng Wei
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Xiao Sun
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Petra Korall
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-752 36 Uppsala, Sweden
| | - Dennis W Stevenson
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458 USA
| | - Sean W Graham
- Department of Botany & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6J 3S7, Canada
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Kathleen M Pryer
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
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296
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Ševčíková T, Horák A, Klimeš V, Zbránková V, Demir-Hilton E, Sudek S, Jenkins J, Schmutz J, Přibyl P, Fousek J, Vlček Č, Lang BF, Oborník M, Worden AZ, Eliáš M. Updating algal evolutionary relationships through plastid genome sequencing: did alveolate plastids emerge through endosymbiosis of an ochrophyte? Sci Rep 2015; 5:10134. [PMID: 26017773 PMCID: PMC4603697 DOI: 10.1038/srep10134] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/31/2015] [Indexed: 01/15/2023] Open
Abstract
Algae with secondary plastids of a red algal origin, such as ochrophytes (photosynthetic stramenopiles), are diverse and ecologically important, yet their evolutionary history remains controversial. We sequenced plastid genomes of two ochrophytes, Ochromonas sp. CCMP1393 (Chrysophyceae) and Trachydiscus minutus (Eustigmatophyceae). A shared split of the clpC gene as well as phylogenomic analyses of concatenated protein sequences demonstrated that chrysophytes and eustigmatophytes form a clade, the Limnista, exhibiting an unexpectedly elevated rate of plastid gene evolution. Our analyses also indicate that the root of the ochrophyte phylogeny falls between the recently redefined Khakista and Phaeista assemblages. Taking advantage of the expanded sampling of plastid genome sequences, we revisited the phylogenetic position of the plastid of Vitrella brassicaformis, a member of Alveolata with the least derived plastid genome known for the whole group. The results varied depending on the dataset and phylogenetic method employed, but suggested that the Vitrella plastids emerged from a deep ochrophyte lineage rather than being derived vertically from a hypothetical plastid-bearing common ancestor of alveolates and stramenopiles. Thus, we hypothesize that the plastid in Vitrella, and potentially in other alveolates, may have been acquired by an endosymbiosis of an early ochrophyte.
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Affiliation(s)
- Tereza Ševčíková
- University of Ostrava, Faculty of Science, Department of Biology and Ecology, Life Science Research Centre, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic.,University of South Bohemia, Faculty of Science, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Vladimír Klimeš
- University of Ostrava, Faculty of Science, Department of Biology and Ecology, Life Science Research Centre, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Veronika Zbránková
- University of Ostrava, Faculty of Science, Department of Biology and Ecology, Life Science Research Centre, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Elif Demir-Hilton
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA 95039, USA
| | - Sebastian Sudek
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA 95039, USA
| | - Jerry Jenkins
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, Alabama 35806, USA
| | - Pavel Přibyl
- Centre for Algology and Biorefinery Research Centre of Competence, Institute of Botany, Czech Academy of Sciences, Dukelská 135, 379 82 Třeboň, Czech Republic
| | - Jan Fousek
- Institute of Molecular Genetics, Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Čestmír Vlček
- Institute of Molecular Genetics, Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - B Franz Lang
- Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, 2900 Boulevard Edouard Montpetit, Montréal, Québec, H3C 3J7, Canada
| | - Miroslav Oborník
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic.,University of South Bohemia, Faculty of Science, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA 95039, USA.,Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, M5G 1Z8, Canada
| | - Marek Eliáš
- University of Ostrava, Faculty of Science, Department of Biology and Ecology, Life Science Research Centre, Chittussiho 10, 710 00 Ostrava, Czech Republic
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Saarela JM, Wysocki WP, Barrett CF, Soreng RJ, Davis JI, Clark LG, Kelchner SA, Pires JC, Edger PP, Mayfield DR, Duvall MR. Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes. AOB PLANTS 2015; 7:plv046. [PMID: 25940204 PMCID: PMC4480051 DOI: 10.1093/aobpla/plv046] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/21/2015] [Indexed: 05/08/2023]
Abstract
Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single- and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some 'early-diverging' tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with protein-coding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae-Meliceae and Ampelodesmeae-Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae-Triticeae clade and Poeae. Within Poeae, a novel sister group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae-Brizinae clade, are discordant between MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a Dactylidinae-Loliinae clade.
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Affiliation(s)
- Jeffery M Saarela
- Botany Section, Research and Collections, Canadian Museum of Nature, PO Box 3443 Stn. D, Ottawa, ON, Canada K1P 3P4
| | - William P Wysocki
- Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA
| | - Craig F Barrett
- Department of Biological Sciences, California State University, 5151 State University Dr., Los Angeles, CA 90032-8201, USA
| | - Robert J Soreng
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Jerrold I Davis
- Section of Plant Biology, Cornell University, 412 Mann Library, Ithaca, NY 14853, USA
| | - Lynn G Clark
- Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011-1020, USA
| | - Scot A Kelchner
- Biological Sciences, Idaho State University, 921 S. 8th Ave, Pocatello, ID 83209, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, 1201 Rollins St, Columbia, MO 65211, USA
| | - Patrick P Edger
- Department of Plant and Microbial Biology, University of California - Berkeley, Berkeley, CA 94720, USA
| | - Dustin R Mayfield
- Division of Biological Sciences, University of Missouri, 1201 Rollins St, Columbia, MO 65211, USA
| | - Melvin R Duvall
- Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA
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298
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Sinn BT, Kelly LM, Freudenstein JV. Phylogenetic relationships in Asarum: Effect of data partitioning and a revised classification. AMERICAN JOURNAL OF BOTANY 2015; 102:765-79. [PMID: 26022490 DOI: 10.3732/ajb.1400316] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 03/27/2015] [Indexed: 05/23/2023]
Abstract
PREMISE OF THE STUDY Generic boundaries and infrageneric relationships among the charismatic temperate magnoliid Asarum sensu lato (Aristolochiaceae) have long been uncertain. Previous molecular phylogenetic analyses used either plastid or nuclear loci alone and varied greatly in their taxonomic implications for the genus. We analyzed additional molecular markers from the nuclear and plastid genomes, reevaluated the possibility of a derived loss of autonomous self-pollination, and investigated the topological effects of matrix-partitioning-scheme choice. METHODS We sequenced seven plastid regions and the nuclear ITS1-ITS2 region of 58 individuals representing all previously recognized Asarum s.l. segregate genera and the monotypic genus Saruma. Matrices were partitioned using common a priori partitioning schemes and PartitionFinder. KEY RESULTS Topologies that were recovered using a priori partitioning of matrices differed from those recovered using a PartitionFinder-selected scheme, and by analysis method. We recovered six monophyletic groups that we circumscribed into three subgenera and six sections. Putative fungal mimic characters served as synapomorphies only for subgenus Heterotropa. Subgenus Geotaenium, a new subgenus, was recovered as sister to the remainder of Asarum by ML analyses of highly partitioned datasets. Section Longistylis, also newly named, is sister to section Hexastylis. CONCLUSIONS Our analyses do not unambiguously support a single origin for all fungal-mimicry characters. Topologies recovered through the analysis of PartitionFinder-optimized matrices can differ drastically from those inferred from a priori partitioned matrices, and by analytical method. We recommend that investigators evaluate the topological effects of matrix partitioning using multiple methods of phylogenetic reconstruction.
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Affiliation(s)
- Brandon T Sinn
- The Ohio State University Museum of Biological Diversity, Department of Evolution, Ecology, and Organismal Biology, 1315 Kinnear Road, Columbus, Ohio 43212 USA
| | - Lawrence M Kelly
- The New York Botanical Garden, 2900 Southern Boulevard, Bronx, New York 10458-5126 USA
| | - John V Freudenstein
- The Ohio State University Museum of Biological Diversity, Department of Evolution, Ecology, and Organismal Biology, 1315 Kinnear Road, Columbus, Ohio 43212 USA
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299
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Ruhlman TA, Chang WJ, Chen JJW, Huang YT, Chan MT, Zhang J, Liao DC, Blazier JC, Jin X, Shih MC, Jansen RK, Lin CS. NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss. BMC PLANT BIOLOGY 2015; 15:100. [PMID: 25886915 PMCID: PMC4404220 DOI: 10.1186/s12870-015-0484-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/30/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Key innovations have facilitated novel niche utilization, such as the movement of the algal predecessors of land plants into terrestrial habitats where drastic fluctuations in light intensity, ultraviolet radiation and water limitation required a number of adaptations. The NDH (NADH dehydrogenase-like) complex of Viridiplantae plastids participates in adapting the photosynthetic response to environmental stress, suggesting its involvement in the transition to terrestrial habitats. Although relatively rare, the loss or pseudogenization of plastid NDH genes is widely distributed across diverse lineages of photoautotrophic seed plants and mutants/transgenics lacking NDH function demonstrate little difference from wild type under non-stressed conditions. This study analyzes large transcriptomic and genomic datasets to evaluate the persistence and loss of NDH expression across plants. RESULTS Nuclear expression profiles showed accretion of the NDH gene complement at key transitions in land plant evolution, such as the transition to land and at the base of the angiosperm lineage. While detection of transcripts for a selection of non-NDH, photosynthesis related proteins was independent of the state of NDH, coordinate, lineage-specific loss of plastid NDH genes and expression of nuclear-encoded NDH subunits was documented in Pinaceae, gnetophytes, Orchidaceae and Geraniales confirming the independent and complete loss of NDH in these diverse seed plant taxa. CONCLUSION The broad phylogenetic distribution of NDH loss and the subtle phenotypes of mutants suggest that the NDH complex is of limited biological significance in contemporary plants. While NDH activity appears dispensable under favorable conditions, there were likely sufficiently frequent episodes of abiotic stress affecting terrestrial habitats to allow the retention of NDH activity. These findings reveal genetic factors influencing plant/environment interactions in a changing climate through 450 million years of land plant evolution.
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Affiliation(s)
- Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - Wan-Jung Chang
- Agricultural Biotechnology Research Center of Academia Sinica, Agricultural Technology Building, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan.
| | - Jeremy J W Chen
- Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan.
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan.
| | - Ming-Tsair Chan
- Agricultural Biotechnology Research Center of Academia Sinica, Agricultural Technology Building, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan.
| | - Jin Zhang
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - De-Chih Liao
- Agricultural Biotechnology Research Center of Academia Sinica, Agricultural Technology Building, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan.
| | - John C Blazier
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - Xiaohua Jin
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Ming-Che Shih
- Agricultural Biotechnology Research Center of Academia Sinica, Agricultural Technology Building, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan.
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
- Department of Biological Science, Biotechnology Research Group, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center of Academia Sinica, Agricultural Technology Building, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan.
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300
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Melton JT, Leliaert F, Tronholm A, Lopez-Bautista JM. The complete chloroplast and mitochondrial genomes of the green macroalga Ulva sp. UNA00071828 (Ulvophyceae, Chlorophyta). PLoS One 2015; 10:e0121020. [PMID: 25849557 PMCID: PMC4388391 DOI: 10.1371/journal.pone.0121020] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/09/2015] [Indexed: 11/18/2022] Open
Abstract
Sequencing mitochondrial and chloroplast genomes has become an integral part in understanding the genomic machinery and the phylogenetic histories of green algae. Previously, only three chloroplast genomes (Oltmannsiellopsis viridis, Pseudendoclonium akinetum, and Bryopsis hypnoides) and two mitochondrial genomes (O. viridis and P. akinetum) from the class Ulvophyceae have been published. Here, we present the first chloroplast and mitochondrial genomes from the ecologically and economically important marine, green algal genus Ulva. The chloroplast genome of Ulva sp. was 99,983 bp in a circular-mapping molecule that lacked inverted repeats, and thus far, was the smallest ulvophycean plastid genome. This cpDNA was a highly compact, AT-rich genome that contained a total of 102 identified genes (71 protein-coding genes, 28 tRNA genes, and three ribosomal RNA genes). Additionally, five introns were annotated in four genes: atpA (1), petB (1), psbB (2), and rrl (1). The circular-mapping mitochondrial genome of Ulva sp. was 73,493 bp and follows the expanded pattern also seen in other ulvophyceans and trebouxiophyceans. The Ulva sp. mtDNA contained 29 protein-coding genes, 25 tRNA genes, and two rRNA genes for a total of 56 identifiable genes. Ten introns were annotated in this mtDNA: cox1 (4), atp1 (1), nad3 (1), nad5 (1), and rrs (3). Double-cut-and-join (DCJ) values showed that organellar genomes across Chlorophyta are highly rearranged, in contrast to the highly conserved organellar genomes of the red algae (Rhodophyta). A phylogenomic investigation of 51 plastid protein-coding genes showed that Ulvophyceae is not monophyletic, and also placed Oltmannsiellopsis (Oltmannsiellopsidales) and Tetraselmis (Chlorodendrophyceae) closely to Ulva (Ulvales) and Pseudendoclonium (Ulothrichales).
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Affiliation(s)
- James T. Melton
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama 35487-0345, United States of America
- * E-mail:
| | - Frederik Leliaert
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama 35487-0345, United States of America
- Marine Biology Research Group, Department of Biology, Ghent University, Krijgslaan 281-S8, 9000 Ghent, Belgium
| | - Ana Tronholm
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama 35487-0345, United States of America
- Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, Florida 34949, United States of America
| | - Juan M. Lopez-Bautista
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama 35487-0345, United States of America
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