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Zwonitzer KD, Tressel LG, Wu Z, Kan S, Broz AK, Mower JP, Ruhlman TA, Jansen RK, Sloan DB, Havird JC. Genome copy number predicts extreme evolutionary rate variation in plant mitochondrial DNA. Proc Natl Acad Sci U S A 2024; 121:e2317240121. [PMID: 38427600 DOI: 10.1073/pnas.2317240121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/22/2024] [Indexed: 03/03/2024] Open
Abstract
Nuclear and organellar genomes can evolve at vastly different rates despite occupying the same cell. In most bilaterian animals, mitochondrial DNA (mtDNA) evolves faster than nuclear DNA, whereas this trend is generally reversed in plants. However, in some exceptional angiosperm clades, mtDNA substitution rates have increased up to 5,000-fold compared with closely related lineages. The mechanisms responsible for this acceleration are generally unknown. Because plants rely on homologous recombination to repair mtDNA damage, we hypothesized that mtDNA copy numbers may predict evolutionary rates, as lower copy numbers may provide fewer templates for such repair mechanisms. In support of this hypothesis, we found that copy number explains 47% of the variation in synonymous substitution rates of mtDNA across 60 diverse seed plant species representing ~300 million years of evolution. Copy number was also negatively correlated with mitogenome size, which may be a cause or consequence of mutation rate variation. Both relationships were unique to mtDNA and not observed in plastid DNA. These results suggest that homologous recombinational repair plays a role in driving mtDNA substitution rates in plants and may explain variation in mtDNA evolution more broadly across eukaryotes. Our findings also contribute to broader questions about the relationships between mutation rates, genome size, selection efficiency, and the drift-barrier hypothesis.
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Affiliation(s)
- Kendra D Zwonitzer
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - Lydia G Tressel
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
- Marine College, Shandong University, Weihai 264209, China
| | - Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, CO 80523
| | - Jeffrey P Mower
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588
| | - Tracey A Ruhlman
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - Robert K Jansen
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523
| | - Justin C Havird
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
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Lee C, Ruhlman TA, Jansen RK. Rate accelerations in plastid and mitochondrial genomes of Cyperaceae occur in the same clades. Mol Phylogenet Evol 2023; 182:107760. [PMID: 36921696 DOI: 10.1016/j.ympev.2023.107760] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 01/28/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
Cyperaceae, the second largest family in the monocot order Poales, comprises >5500 species and includes the genus Eleocharis with ∼ 250 species. A previous study of complete plastomes of two Eleocharis species documented extensive structural heteroplasmy, gene order changes, high frequency of dispersed repeats along with gene losses and duplications. To better understand the phylogenetic distribution of gene and intron content as well as rates and patterns of sequence evolution within and between mitochondrial and plastid genomes of Eleocharis and Cyperaceae, an additional 29 Eleocharis organelle genomes were sequenced and analyzed. Eleocharis experienced extensive gene loss in both genomes while loss of introns was mitochondria-specific. Eleocharis has higher rates of synonymous (dS) and nonsynonymous (dN) substitutions in the plastid and mitochondrion than most sampled angiosperms, and the pattern was distinct from other eudicot lineages with accelerated rates. Several clades showed higher dS and dN in mitochondrial genes than in plastid genes. Furthermore, nucleotide substitution rates of mitochondrial genes were significantly accelerated on the branch leading to Cyperaceae compared to most angiosperms. Mitochondrial genes of Cyperaceae exhibited dramatic loss of RNA editing sites and a negative correlation between RNA editing and dS values was detected among angiosperms. Mutagenic retroprocessing and dysfunction of DNA replication, repair and recombination genes are the most likely cause of striking rate accelerations and loss of edit sites and introns in Eleocharis and Cyperaceae organelle genomes.
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Affiliation(s)
- Chaehee Lee
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA; Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA.
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
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3
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Zhou W, Armijos CE, Lee C, Lu R, Wang J, Ruhlman TA, Jansen RK, Jones AM, Jones CD. Plastid Genome Assembly Using Long-read Data (ptGAUL). Mol Ecol Resour 2023. [PMID: 36939021 PMCID: PMC10354735 DOI: 10.1111/1755-0998.13787] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/23/2023] [Accepted: 03/16/2023] [Indexed: 03/21/2023]
Abstract
Although plastid genome (plastome) structure is highly conserved across most seed plants, investigations during the past two decades revealed several disparately related lineages that experienced substantial rearrangements. Most plastomes contain a large inverted repeat and two single-copy regions, and few dispersed repeats; however, the plastomes of some taxa harbor long repeat sequences (>300 bp). These long repeats make it challenging to assemble complete plastomes using short-read data leading to misassemblies and consensus sequences with spurious rearrangements. Single-molecule, long-read sequencing has the potential to overcome these challenges, yet there is no consensus on the most effective method for accurately assembling plastomes using long-read data. We generated a pipeline, plastid Genome Assembly Using Long-read data (ptGAUL), to address the problem of plastome assembly using long-read data from Oxford Nanopore Technologies (ONT) or Pacific Biosciences platforms. We demonstrated the efficacy of the ptGAUL pipeline using 16 published long-read datasets. We showed that ptGAUL quickly produces accurate and unbiased assemblies using only ~50✕ coverage of plastome data. Additionally, we deployed ptGAUL to assemble four new Juncus (Juncaceae) plastomes using ONT long reads. Our results revealed many long repeats and rearrangements in Juncus plastomes compared with basal lineages of Poales.
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Affiliation(s)
- Wenbin Zhou
- Departments of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Carolina E Armijos
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito USFQ, Diego de Robles s/n y Vía Interocéanica, Quito, 170901, Ecuador
| | - Chaehee Lee
- Department of Plant Sciences, University of California, Davis, Davis, CA, 95616, USA
| | - Ruisen Lu
- Institute of Botany, Jiangsu, Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Jeremy Wang
- Departments of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, TX, 78712, USA
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, TX, 78712, USA
| | - Alan M Jones
- Departments of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Departments of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Corbin D Jones
- Departments of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Departments of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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Choi IS, Wojciechowski MF, Steele KP, Hopkins A, Ruhlman TA, Jansen RK. Plastid phylogenomics uncovers multiple species in Medicago truncatula (Fabaceae) germplasm accessions. Sci Rep 2022; 12:21172. [PMID: 36477422 PMCID: PMC9729603 DOI: 10.1038/s41598-022-25381-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Medicago truncatula is a model legume that has been extensively investigated in diverse subdisciplines of plant science. Medicago littoralis can interbreed with M. truncatula and M. italica; these three closely related species form a clade, i.e. TLI clade. Genetic studies have indicated that M. truncatula accessions are heterogeneous but their taxonomic identities have not been verified. To elucidate the phylogenetic position of diverse M. truncatula accessions within the genus, we assembled 54 plastid genomes (plastomes) using publicly available next-generation sequencing data and conducted phylogenetic analyses using maximum likelihood. Five accessions showed high levels of plastid DNA polymorphism. Three of these highly polymorphic accessions contained sequences from both M. truncatula and M. littoralis. Phylogenetic analyses of sequences placed some accessions closer to distantly related species suggesting misidentification of source material. Most accessions were placed within the TLI clade and maximally supported the interrelationships of three subclades. Two Medicago accessions were placed within a M. italica subclade of the TLI clade. Plastomes with a 45-kb (rpl20-ycf1) inversion were placed within the M. littoralis subclade. Our results suggest that the M. truncatula accession genome pool represents more than one species due to possible mistaken identities and gene flow among closely related species.
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Affiliation(s)
- In-Su Choi
- grid.89336.370000 0004 1936 9924Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712 USA ,grid.215654.10000 0001 2151 2636School of Life Sciences, Arizona State University, Tempe, AZ 85287 USA ,grid.411970.a0000 0004 0532 6499Department of Biological Sciences and Biotechnology, Hannam University, Daejeon, 34054 Korea
| | - Martin F. Wojciechowski
- grid.215654.10000 0001 2151 2636School of Life Sciences, Arizona State University, Tempe, AZ 85287 USA
| | - Kelly P. Steele
- grid.215654.10000 0001 2151 2636Division of Applied Science and Mathematics, Arizona State University, Mesa, AZ 85212 USA
| | - Andrew Hopkins
- grid.215654.10000 0001 2151 2636School of Life Sciences, Arizona State University, Tempe, AZ 85287 USA
| | - Tracey A. Ruhlman
- grid.89336.370000 0004 1936 9924Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712 USA
| | - Robert K. Jansen
- grid.89336.370000 0004 1936 9924Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712 USA
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Nefissi Ouertani R, Arasappan D, Ruhlman TA, Ben Chikha M, Abid G, Mejri S, Ghorbel A, Jansen RK. Effects of Salt Stress on Transcriptional and Physiological Responses in Barley Leaves with Contrasting Salt Tolerance. Int J Mol Sci 2022; 23:5006. [PMID: 35563398 PMCID: PMC9103072 DOI: 10.3390/ijms23095006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/22/2022] [Accepted: 04/28/2022] [Indexed: 01/27/2023] Open
Abstract
Salt stress negatively impacts crop production worldwide. Genetic diversity among barley (Hordeum vulgare) landraces adapted to adverse conditions should provide a valuable reservoir of tolerance genes for breeding programs. To identify molecular and biochemical differences between barley genotypes, transcriptomic and antioxidant enzyme profiles along with several morpho-physiological features were compared between salt-tolerant (Boulifa) and salt-sensitive (Testour) genotypes subjected to salt stress. Decreases in biomass, photosynthetic parameters, and relative water content were low in Boulifa compared to Testour. Boulifa had better antioxidant protection against salt stress than Testour, with greater antioxidant enzymes activities including catalase, superoxide dismutase, and guaiacol peroxidase. Transcriptome assembly for both genotypes revealed greater accumulation of differentially expressed transcripts in Testour compared to Boulifa, emphasizing the elevated transcriptional response in Testour following salt exposure. Various salt-responsive genes, including the antioxidant catalase 3, the osmoprotectant betaine aldehyde dehydrogenase 2, and the transcription factors MYB20 and MYB41, were induced only in Boulifa. By contrast, several genes associated with photosystems I and II, and light receptor chlorophylls A and B, were more repressed in Testour. Co-expression network analysis identified specific gene modules correlating with differences in genotypes and morpho-physiological traits. Overall, salinity-induced differential transcript accumulation underlies the differential morpho-physiological response in both genotypes and could be important for breeding salt tolerance in barley.
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Affiliation(s)
- Rim Nefissi Ouertani
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, BP 901, Hammam-Lif 2050, Tunisia; (M.B.C.); (S.M.); (A.G.)
| | - Dhivya Arasappan
- Center for Biomedical Research Support, University of Texas at Austin, Austin, TX 78712, USA;
| | - Tracey A. Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA;
| | - Mariem Ben Chikha
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, BP 901, Hammam-Lif 2050, Tunisia; (M.B.C.); (S.M.); (A.G.)
| | - Ghassen Abid
- Laboratory of Legumes and Sustainable Agrosystems, Center of Biotechnology of Borj Cedria, BP 901, Hammam-Lif 2050, Tunisia;
| | - Samiha Mejri
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, BP 901, Hammam-Lif 2050, Tunisia; (M.B.C.); (S.M.); (A.G.)
| | - Abdelwahed Ghorbel
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, BP 901, Hammam-Lif 2050, Tunisia; (M.B.C.); (S.M.); (A.G.)
| | - Robert K. Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA;
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia
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Choi IS, Wojciechowski MF, Steele KP, Hunter SG, Ruhlman TA, Jansen RK. Born in the mitochondrion and raised in the nucleus: evolution of a novel tandem repeat family in Medicago polymorpha (Fabaceae). Plant J 2022; 110:389-406. [PMID: 35061308 DOI: 10.1111/tpj.15676] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
Plant nuclear genomes harbor sequence elements derived from the organelles (mitochondrion and plastid) through intracellular gene transfer (IGT). Nuclear genomes also show a dramatic range of repeat content, suggesting that any sequence can be readily amplified. These two aspects of plant nuclear genomes are well recognized but have rarely been linked. Through investigation of 31 Medicago taxa we detected exceptionally high post-IGT amplification of mitochondrial (mt) DNA sequences containing rps10 in the nuclear genome of Medicago polymorpha and closely related species. The amplified sequences were characterized as tandem arrays of five distinct repeat motifs (2157, 1064, 987, 971, and 587 bp) that have diverged from the mt genome (mitogenome) in the M. polymorpha nuclear genome. The mt rps10-like arrays were identified in seven loci (six intergenic and one telomeric) of the nuclear chromosome assemblies and were the most abundant tandem repeat family, representing 1.6-3.0% of total genomic DNA, a value approximately three-fold greater than the entire mitogenome in M. polymorpha. Compared to a typical mt gene, the mt rps10-like sequence coverage level was 691.5-7198-fold higher in M. polymorpha and closely related species. In addition to the post-IGT amplification, our analysis identified the canonical telomeric repeat and the species-specific satellite arrays that are likely attributable to an ancestral chromosomal fusion in M. polymorpha. A possible relationship between chromosomal instability and the mt rps10-like tandem repeat family in the M. polymorpha clade is discussed.
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Affiliation(s)
- In-Su Choi
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | | | - Kelly P Steele
- Division of Science and Mathematics, Arizona State University, Mesa, AZ, 85212, USA
| | - Sarah G Hunter
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
- Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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Choi IS, Cardoso D, de Queiroz LP, de Lima HC, Lee C, Ruhlman TA, Jansen RK, Wojciechowski MF. Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics. Front Plant Sci 2022; 13:823190. [PMID: 35283880 PMCID: PMC8905342 DOI: 10.3389/fpls.2022.823190] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/31/2022] [Indexed: 05/31/2023]
Abstract
Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one of the most extraordinarily diverse clades among angiosperms. Papilionoids are a major source of food and forage, are ecologically successful in all major biomes, and display dramatic variation in both floral architecture and plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding of relationships among the major groups of Papilionoideae, yet the backbone of the subfamily phylogeny remains unresolved. In this study, we sequenced and assembled 39 new plastomes that are covering key genera representing the morphological diversity in the subfamily. From 244 total taxa, we produced eight datasets for maximum likelihood (ML) analyses based on entire plastomes and/or concatenated sequences of 77 protein-coding sequences (CDS) and two datasets for multispecies coalescent (MSC) analyses based on individual gene trees. We additionally produced a combined nucleotide dataset comprising CDS plus matK gene sequences only, in which most papilionoid genera were sampled. A ML tree based on the entire plastome maximally supported all of the deep and most recent divergences of papilionoids (223 out of 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, and Amburaneae), Cladrastis, Andira, and Exostyleae clades formed a grade to the remainder of the Papilionoideae, concordant with nine ML and two MSC trees. Phylogenetic relationships among the remaining five papilionoid lineages (Vataireoid, Dermatophyllum, Genistoid s.l., Dalbergioid s.l., and Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because of insufficient support and/or conflicting relationships among trees. Our study fully resolved most of the deep nodes of Papilionoideae, however, some relationships require further exploration. More genome-scale data and rigorous analyses are needed to disentangle phylogenetic relationships among the five remaining lineages.
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Affiliation(s)
- In-Su Choi
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Domingos Cardoso
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, Salvador, Brazil
| | - Luciano P. de Queiroz
- Department of Biological Sciences, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Haroldo C. de Lima
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Chaehee Lee
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
| | - Tracey A. Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
| | - Robert K. Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
- Center of Excellence for Bionanoscience Research, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
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Lee C, Choi IS, Cardoso D, de Lima HC, de Queiroz LP, Wojciechowski MF, Jansen RK, Ruhlman TA. The chicken or the egg? Plastome evolution and an independent loss of the inverted repeat in papilionoid legumes. Plant J 2021; 107:861-875. [PMID: 34021942 DOI: 10.1111/tpj.15351] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/22/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
The plastid genome (plastome), while surprisingly constant in gene order and content across most photosynthetic angiosperms, exhibits variability in several unrelated lineages. During the diversification history of the legume family Fabaceae, plastomes have undergone many rearrangements, including inversions, expansion, contraction and loss of the typical inverted repeat (IR), gene loss and repeat accumulation in both shared and independent events. While legume plastomes have been the subject of study for some time, most work has focused on agricultural species in the IR-lacking clade (IRLC) and the plant model Medicago truncatula. The subfamily Papilionoideae, which contains virtually all of the agricultural legume species, also comprises most of the plastome variation detected thus far in the family. In this study three non-papilioniods were included among 34 newly sequenced legume plastomes, along with 33 publicly available sequences, to assess plastome structural evolution in the subfamily. In an effort to examine plastome variation across the subfamily, approximately 20% of the sampling represents the IRLC with the remainder selected to represent the early-branching papilionoid clades. A number of IR-related and repeat-mediated changes were identified and examined in a phylogenetic context. Recombination between direct repeats associated with ycf2 resulted in intraindividual plastome heteroplasmy. Although loss of the IR has not been reported in legumes outside of the IRLC, one genistoid taxon was found to completely lack the typical plastome IR. The role of the IR and non-IR repeats in the progression of plastome change is discussed.
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Affiliation(s)
- Chaehee Lee
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - In-Su Choi
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-4501, USA
| | - Domingos Cardoso
- Instituto de Biologia, Universidade Federal de Bahia (UFBA), Rua Barão de Jeremoabo, s.n., Ondina, Salvador, Bahia, 40170-115, Brazil
| | - Haroldo C de Lima
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rua Pacheco Leão, Rio de Janeiro, 915 22460-030, Brazil
| | - Luciano P de Queiroz
- Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Novo Horizonte, Feira de Santana, Bahia, 44036-900, Brazil
| | | | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
- Center of Excellence for Bionanoscience Research, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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Nefissi Ouertani R, Arasappan D, Abid G, Ben Chikha M, Jardak R, Mahmoudi H, Mejri S, Ghorbel A, Ruhlman TA, Jansen RK. Transcriptomic Analysis of Salt-Stress-Responsive Genes in Barley Roots and Leaves. Int J Mol Sci 2021; 22:8155. [PMID: 34360920 PMCID: PMC8348758 DOI: 10.3390/ijms22158155] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 12/03/2022] Open
Abstract
Barley is characterized by a rich genetic diversity, making it an important model for studies of salinity response with great potential for crop improvement. Moreover, salt stress severely affects barley growth and development, leading to substantial yield loss. Leaf and root transcriptomes of a salt-tolerant Tunisian landrace (Boulifa) exposed to 2, 8, and 24 h salt stress were compared with pre-exposure plants to identify candidate genes and pathways underlying barley's response. Expression of 3585 genes was upregulated and 5586 downregulated in leaves, while expression of 13,200 genes was upregulated and 10,575 downregulated in roots. Regulation of gene expression was severely impacted in roots, highlighting the complexity of salt stress response mechanisms in this tissue. Functional analyses in both tissues indicated that response to salt stress is mainly achieved through sensing and signaling pathways, strong transcriptional reprograming, hormone osmolyte and ion homeostasis stabilization, increased reactive oxygen scavenging, and activation of transport and photosynthesis systems. A number of candidate genes involved in hormone and kinase signaling pathways, as well as several transcription factor families and transporters, were identified. This study provides valuable information on early salt-stress-responsive genes in roots and leaves of barley and identifies several important players in salt tolerance.
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Affiliation(s)
- Rim Nefissi Ouertani
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia; (R.N.O.); (M.B.C.); (R.J.); (S.M.); (A.G.)
| | - Dhivya Arasappan
- Center for Biomedical Research Support, University of Texas at Austin, Austin, TX 78712, USA;
| | - Ghassen Abid
- Laboratory of Legumes and Sustainable Agrosystems, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia;
| | - Mariem Ben Chikha
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia; (R.N.O.); (M.B.C.); (R.J.); (S.M.); (A.G.)
| | - Rahma Jardak
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia; (R.N.O.); (M.B.C.); (R.J.); (S.M.); (A.G.)
| | - Henda Mahmoudi
- International Center for Biosaline Agriculture, Dubai 00000, United Arab Emirates;
| | - Samiha Mejri
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia; (R.N.O.); (M.B.C.); (R.J.); (S.M.); (A.G.)
| | - Abdelwahed Ghorbel
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia; (R.N.O.); (M.B.C.); (R.J.); (S.M.); (A.G.)
| | - Tracey A. Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA;
| | - Robert K. Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA;
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia
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10
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Shrestha B, Gilbert LE, Ruhlman TA, Jansen RK. Rampant Nuclear Transfer and Substitutions of Plastid Genes in Passiflora. Genome Biol Evol 2021; 12:1313-1329. [PMID: 32539116 PMCID: PMC7488351 DOI: 10.1093/gbe/evaa123] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2020] [Indexed: 12/15/2022] Open
Abstract
Gene losses in plastid genomes (plastomes) are often accompanied by functional transfer to the nucleus or substitution of an alternative nuclear-encoded gene. Despite the highly conserved gene content in plastomes of photosynthetic land plants, recent gene loss events have been documented in several disparate angiosperm clades. Among these lineages, Passiflora lacks several essential ribosomal genes, rps7, rps16, rpl20, rpl22, and rpl32, the two largest plastid genes, ycf1 and ycf2, and has a highly divergent rpoA. Comparative transcriptome analyses were performed to determine the fate of the missing genes in Passiflora. Putative functional transfers of rps7, rpl22, and rpl32 to nucleus were detected, with the nuclear transfer of rps7, representing a novel event in angiosperms. Plastid-encoded rps7 was transferred into the intron of a nuclear-encoded plastid-targeted thioredoxin m-type gene, acquiring its plastid transit peptide (TP). Plastid rpl20 likely experienced a novel substitution by a duplicated, nuclear-encoded mitochondrial-targeted rpl20 that has a similar gene structure. Additionally, among rosids, evidence for a third independent transfer of rpl22 in Passiflora was detected that gained a TP from a nuclear gene containing an organelle RNA recognition motif. Nuclear transcripts representing rpoA, ycf1, and ycf2 were not detected. Further analyses suggest that the divergent rpoA remains functional and that the gene is under positive or purifying selection in different clades. Comparative analyses indicate that alternative translocon and motor protein complexes may have substituted for the loss of ycf1 and ycf2 in Passiflora.
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Affiliation(s)
- Bikash Shrestha
- Department of Integrative Biology, University of Texas, Austin
| | - Lawrence E Gilbert
- Faculty of Science, Department of Biological Sciences, Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Robert K Jansen
- Department of Integrative Biology, University of Texas, Austin.,Faculty of Science, Department of Biological Sciences, Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
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11
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Lee C, Ruhlman TA, Jansen RK. Unprecedented Intraindividual Structural Heteroplasmy in Eleocharis (Cyperaceae, Poales) Plastomes. Genome Biol Evol 2021; 12:641-655. [PMID: 32282915 PMCID: PMC7426004 DOI: 10.1093/gbe/evaa076] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2020] [Indexed: 12/13/2022] Open
Abstract
Plastid genomes (plastomes) of land plants have a conserved quadripartite structure in a gene-dense unit genome consisting of a large inverted repeat that separates two single copy regions. Recently, alternative plastome structures were suggested in Geraniaceae and in some conifers and Medicago the coexistence of inversion isomers has been noted. In this study, plastome sequences of two Cyperaceae, Eleocharis dulcis (water chestnut) and Eleocharis cellulosa (gulf coast spikerush), were completed. Unlike the conserved plastomes in basal groups of Poales, these Eleocharis plastomes have remarkably divergent features, including large plastome sizes, high rates of sequence rearrangements, low GC content and gene density, gene duplications and losses, and increased repetitive DNA sequences. A novel finding among these features was the unprecedented level of heteroplasmy with the presence of multiple plastome structural types within a single individual. Illumina paired-end assemblies combined with PacBio single-molecule real-time sequencing, long-range polymerase chain reaction, and Sanger sequencing data identified at least four different plastome structural types in both Eleocharis species. PacBio long read data suggested that one of the four E. dulcis plastome types predominates.
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Affiliation(s)
- Chaehee Lee
- Department of Integrative Biology, University of Texas at Austin
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin.,Center of Excellence for Bionanoscience Research, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
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12
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Choi IS, Wojciechowski MF, Ruhlman TA, Jansen RK. In and out: Evolution of viral sequences in the mitochondrial genomes of legumes (Fabaceae). Mol Phylogenet Evol 2021; 163:107236. [PMID: 34147655 DOI: 10.1016/j.ympev.2021.107236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 10/21/2022]
Abstract
Plant specific mitoviruses in the 'genus' Mitovirus (Narnaviridae) and their integrated sequences (non-retroviral endogenous RNA viral elements or NERVEs) have been recently identified in various plant lineages. However, the sparse phylogenetic coverage of complete plant mitochondrial genome (mitogenome) sequences and the non-conserved nature of mitochondrial intergenic regions have hindered comparative studies on mitovirus NERVEs in plants. In this study, 10 new mitogenomes were sequenced from legumes (Fabaceae). Based on comparative genomic analysis of 27 total mitogenomes, we identified mitovirus NERVEs and transposable elements across the family. All legume mitogenomes included NERVEs and total NERVE length varied from ca. 2 kb in the papilionoid Trifolium to 35 kb in the mimosoid Acacia. Most of the NERVE integration sites were in highly variable intergenic regions, however, some were positioned in six cis-spliced mitochondrial introns. In the Acacia mitogenome, there were L1-like transposon sequences including an almost full-length copy with target site duplications (TSDs). The integration sites of NERVEs in four introns showed evidence of L1-like retrotransposition events. Phylogenetic analysis revealed that there were multiple instances of precise deletion of NERVEs between TSDs. This study provides clear evidence that a L1-like retrotransposition mechanism has a long history of contributing to the integration of viral RNA into plant mitogenomes while microhomology-mediated deletion can restore the integration site.
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Affiliation(s)
- In-Su Choi
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | | | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA; Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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13
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Abstract
The interest in producing pharmaceutical proteins in a nontoxic plant host has led to the development of an approach to express such proteins in transplastomic lettuce (Lactuca sativa). A number of therapeutic proteins and vaccine antigen candidates have been stably integrated into the lettuce plastid genome using biolistic DNA delivery. High levels of accumulation and retention of biological activity suggest that lettuce may provide and ideal platform for the production of biopharmaceuticals.
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Affiliation(s)
- Tracey A Ruhlman
- Integrative Biology, University of Texas at Austin, Austin, TX, USA.
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14
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Abstract
The plastid genome (plastome ) has proved a valuable source of data for evaluating evolutionary relationships among angiosperms. Through basic and applied approaches, plastid transformation technology offers the potential to understand and improve plant productivity, providing food, fiber, energy, and medicines to meet the needs of a burgeoning global population. The growing genomic resources available to both phylogenetic and biotechnological investigations is allowing novel insights and expanding the scope of plastome research to encompass new species. In this chapter, we present an overview of some of the seminal and contemporary research that has contributed to our current understanding of plastome evolution and attempt to highlight the relationship between evolutionary mechanisms and the tools of plastid genetic engineering.
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Affiliation(s)
- Tracey A Ruhlman
- Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - Robert K Jansen
- Integrative Biology, University of Texas at Austin, Austin, TX, USA
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15
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Choi K, Weng ML, Ruhlman TA, Jansen RK. Extensive variation in nucleotide substitution rate and gene/intron loss in mitochondrial genomes of Pelargonium. Mol Phylogenet Evol 2020; 155:106986. [PMID: 33059063 DOI: 10.1016/j.ympev.2020.106986] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 07/16/2020] [Accepted: 10/07/2020] [Indexed: 12/30/2022]
Abstract
Geraniaceae organelle genomes have been shown to exhibit several highly unusual features compared to most other photosynthetic angiosperms. This includes massively rearranged plastomes with considerable size variation, extensive gene and intron loss, accelerated rates of nucleotide substitutions in both mitogenomes and plastomes, and biparental inheritance and cytonuclear incompatibility of the plastome. Most previous studies have focused on plastome evolution with mitogenome comparisons limited to only a few taxa or genes. In this study, mitogenomes and transcriptomes were examined for 27 species of Geraniales, including 13 species of Pelargonium. Extensive gene and intron losses were detected across the Geraniales with Pelargonium representing the most gene depauperate lineage in the family. Plotting these events on the Geraniaceae phylogenetic tree showed that gene losses occurred multiple times, whereas intron losses more closely reflected the relationships among taxa. In addition, P. australe acquired an intron by horizontal transfer. Comparisons of nucleotide substitution rates in Pelargonium showed that synonymous changes in nuclear genes were much lower than in mitochondrial genes. This is in contrast to the previously published studies that indicated that nuclear genes have 16 fold higher rates than mitochondrial genes across angiosperms. Elevated synonymous substitutions occurred for each mitochondrial gene in Pelargonium with the highest values 783 and 324 times higher than outgroups and other Geraniaceae, respectively. Pelargonium is one of four unrelated genera of angiosperms (Ajuga, Plantago and Silene) that have experienced highly accelerated nucleotide substitutions in mitogenomes. It is distinct from most angiosperms in also having elevated substitution rates in plastid genes but the cause of rate accelerations in Pelargonium plastomes and mitogenomes may be different.
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Affiliation(s)
- KyoungSu Choi
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Mao-Lun Weng
- Department of Biology, Westfield State University, Westfield, MA, USA
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA; Center for Excellence for Bionanoscience Research, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia.
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16
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Gonçalves DJP, Jansen RK, Ruhlman TA, Mandel JR. Under the rug: Abandoning persistent misconceptions that obfuscate organelle evolution. Mol Phylogenet Evol 2020; 151:106903. [PMID: 32628998 DOI: 10.1016/j.ympev.2020.106903] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 06/29/2020] [Indexed: 02/01/2023]
Abstract
The advent and advance of next generation sequencing over the past two decades made it possible to accumulate large quantities of sequence reads that could be used to assemble complete or nearly complete organelle genomes (plastome or mitogenome). The result has been an explosive increase in the availability of organelle genome sequences with over 4000 different species of green plants currently available on GenBank. During the same time period, plant molecular biologists greatly enhanced the understanding of the structure, repair, replication, recombination, transcription and translation, and inheritance of organelle DNA. Unfortunately many plant evolutionary biologists are unaware of or have overlooked this knowledge, resulting in misrepresentation of several phenomena that are critical for phylogenetic and evolutionary studies using organelle genomes. We believe that confronting these misconceptions about organelle genome organization, composition, and inheritance will improve our understanding of the evolutionary processes that underly organelle evolution. Here we discuss four misconceptions that can limit evolutionary biology studies and lead to inaccurate phylogenies and incorrect structure of the organellar DNA used to infer organelle evolution.
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Affiliation(s)
- Deise J P Gonçalves
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78713, USA.
| | - Robert K Jansen
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78713, USA; Center of Excellence for Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Tracey A Ruhlman
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78713, USA
| | - Jennifer R Mandel
- Department of Biological Sciences, Center for Biodiversity Research, University of Memphis, Memphis, TN 38152, USA
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17
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Choi IS, Ruhlman TA, Jansen RK. Comparative Mitogenome Analysis of the Genus Trifolium Reveals Independent Gene Fission of ccmFn and Intracellular Gene Transfers in Fabaceae. Int J Mol Sci 2020; 21:E1959. [PMID: 32183014 PMCID: PMC7139807 DOI: 10.3390/ijms21061959] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 02/15/2020] [Accepted: 02/17/2020] [Indexed: 01/30/2023] Open
Abstract
The genus Trifolium is the largest of the tribe Trifolieae in the subfamily Papilionoideae (Fabaceae). The paucity of mitochondrial genome (mitogenome) sequences has hindered comparative analyses among the three genomic compartments of the plant cell (nucleus, mitochondrion and plastid). We assembled four mitogenomes from the two subgenera (Chronosemium and Trifolium) of the genus. The four Trifolium mitogenomes were compact (294,911-348,724 bp in length) and contained limited repetitive (6.6-8.6%) DNA. Comparison of organelle repeat content highlighted the distinct evolutionary trajectory of plastid genomes in a subset of Trifolium species. Intracellular gene transfer (IGT) was analyzed among the three genomic compartments revealing functional transfer of mitochondrial rps1 to nuclear genome along with other IGT events. Phylogenetic analysis based on mitochondrial and nuclear rps1 sequences revealed that the functional transfer in Trifolieae was independent from the event that occurred in robinioid clade that includes genus Lotus. A novel, independent fission event of ccmFn in Trifolium was identified, caused by a 59 bp deletion. Fissions of this gene reported previously in land plants were reassessed and compared with Trifolium.
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Affiliation(s)
- In-Su Choi
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA; (T.A.R.); (R.K.J.)
| | - Tracey A. Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA; (T.A.R.); (R.K.J.)
| | - Robert K. Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA; (T.A.R.); (R.K.J.)
- Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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18
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Choi IS, Schwarz EN, Ruhlman TA, Khiyami MA, Sabir JSM, Hajarah NH, Sabir MJ, Rabah SO, Jansen RK. Fluctuations in Fabaceae mitochondrial genome size and content are both ancient and recent. BMC Plant Biol 2019; 19:448. [PMID: 31653201 PMCID: PMC6814987 DOI: 10.1186/s12870-019-2064-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/02/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Organelle genome studies of Fabaceae, an economically and ecologically important plant family, have been biased towards the plastid genome (plastome). Thus far, less than 15 mitochondrial genome (mitogenome) sequences of Fabaceae have been published, all but four of which belong to the subfamily Papilionoideae, limiting the understanding of size variation and content across the family. To address this, four mitogenomes were sequenced and assembled from three different subfamilies (Cercidoideae, Detarioideae and Caesalpinioideae). RESULTS Phylogenetic analysis based on shared mitochondrial protein coding regions produced a fully resolved and well-supported phylogeny that was completely congruent with the plastome tree. Comparative analyses suggest that two kinds of mitogenome expansions have occurred in Fabaceae. Size expansion of four genera (Tamarindus, Libidibia, Haematoxylum, and Leucaena) in two subfamilies (Detarioideae and Caesalpinioideae) occurred in relatively deep nodes, and was mainly caused by intercellular gene transfer and/or interspecific horizontal gene transfer (HGT). The second, more recent expansion occurred in the Papilionoideae as a result of duplication of native mitochondrial sequences. Family-wide gene content analysis revealed 11 gene losses, four (rps2, 7, 11 and 13) of which occurred in the ancestor of Fabaceae. Losses of the remaining seven genes (cox2, rpl2, rpl10, rps1, rps19, sdh3, sdh4) were restricted to specific lineages or occurred independently in different clades. Introns of three genes (cox2, ccmFc and rps10) showed extensive lineage-specific length variation due to large sequence insertions and deletions. Shared DNA analysis among Fabaceae mitogenomes demonstrated a substantial decay of intergenic spacers and provided further insight into HGT between the mimosoid clade of Caesalpinioideae and the holoparasitic Lophophytum (Balanophoraceae). CONCLUSION This study represents the most exhaustive analysis of Fabaceae mitogenomes so far, and extends the understanding the dynamic variation in size and gene/intron content. The four newly sequenced mitogenomes reported here expands the phylogenetic coverage to four subfamilies. The family has experienced multiple mitogenome size fluctuations in both ancient and recent times. The causes of these size variations are distinct in different lineages. Fabaceae mitogenomes experienced extensive size fluctuation by recruitment of exogenous DNA and duplication of native mitochondrial DNA.
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Affiliation(s)
- In-Su Choi
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712 USA
| | - Erika N. Schwarz
- Department of Biological Sciences, St. Edward’s University, Austin, TX 78704 USA
| | - Tracey A. Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712 USA
| | - Mohammad A. Khiyami
- King Abdulaziz City for Science and Technology (KACST), Riyadh, 11442 Saudi Arabia
| | - Jamal S. M. Sabir
- Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Nahid H. Hajarah
- Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Mernan J. Sabir
- Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Samar O. Rabah
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Robert K. Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712 USA
- Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
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19
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Shrestha B, Weng ML, Theriot EC, Gilbert LE, Ruhlman TA, Krosnick SE, Jansen RK. Highly accelerated rates of genomic rearrangements and nucleotide substitutions in plastid genomes of Passiflora subgenus Decaloba. Mol Phylogenet Evol 2019; 138:53-64. [PMID: 31129347 DOI: 10.1016/j.ympev.2019.05.030] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 05/22/2019] [Accepted: 05/22/2019] [Indexed: 12/26/2022]
Abstract
Plastid genomes (plastomes) of photosynthetic angiosperms are for the most part highly conserved in their organization, mode of inheritance and rates of nucleotide substitution. A small number of distantly related lineages share a syndrome of features that deviate from this general pattern, including extensive genomic rearrangements, accelerated rates of nucleotide substitution, biparental inheritance and plastome-genome incompatibility. Previous studies of plastomes in Passiflora with limited taxon sampling suggested that the genus exhibits this syndrome. To examine this phenomenon further, 15 new plastomes from Passiflora were sequenced and combined with previously published data to examine the phylogenetic relationships, genome organization and evolutionary rates across all five subgenera and the sister genus Adenia. Phylogenomic analyses using 68 protein-coding genes shared by Passiflora generated a fully resolved and strongly supported tree that is congruent with previous phylogenies based on a few plastid and nuclear loci. This phylogeny was used to examine the distribution of plastome rearrangements across Passiflora. Multiple gene and intron losses and inversions were identified in Passiflora with some occurring in parallel and others that extended across the Passifloraceae. Furthermore, extensive expansions and contractions of the inverted repeat (IR) were uncovered and in some cases this resulted in exclusion of all ribosomal RNA genes from the IR. The most highly rearranged lineage was subgenus Decaloba, which experienced extensive IR expansion that incorporated up to 25 protein-coding genes usually located in large single copy region. Nucleotide substitution rate analyses of 68 protein-coding genes across the genus showed lineage- and locus-specific acceleration. Significant increase in dS, dN and dN/dS was detected for clpP across the genus and for ycf4 in certain lineages. Significant increases in dN and dN/dS for ribosomal subunits and plastid-encoded RNA polymerase genes were detected in the branch leading to the expanded IR-clade in subgenus Decaloba. This subgenus displays the syndrome of unusual features, making it an ideal system to investigate the dynamic evolution of angiosperm plastomes.
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Affiliation(s)
- Bikash Shrestha
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - Mao-Lun Weng
- Department of Biology, Westfield State University, Westfield, MA, USA
| | - Edward C Theriot
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Lawrence E Gilbert
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Shawn E Krosnick
- Department of Biology, Tennessee Tech University, Cookeville, TN, USA
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA; Center of Excellence for Bionanoscience Research, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia
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20
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Rabah SO, Lee C, Hajrah NH, Makki RM, Alharby HF, Alhebshi AM, Sabir JSM, Jansen RK, Ruhlman TA. Plastome Sequencing of Ten Nonmodel Crop Species Uncovers a Large Insertion of Mitochondrial DNA in Cashew. Plant Genome 2017; 10. [PMID: 29293812 DOI: 10.3835/plantgenome2017.03.0020] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In plant evolution, intracellular gene transfer (IGT) is a prevalent, ongoing process. While nuclear and mitochondrial genomes are known to integrate foreign DNA via IGT and horizontal gene transfer (HGT), plastid genomes (plastomes) have resisted foreign DNA incorporation and only recently has IGT been uncovered in the plastomes of a few land plants. In this study, we completed plastome sequences for l0 crop species and describe a number of structural features including variation in gene and intron content, inversions, and expansion and contraction of the inverted repeat (IR). We identified a putative in cinnamon ( J. Presl) and other sequenced Lauraceae and an apparent functional transfer of to the nucleus of quinoa ( Willd.). In the orchard tree cashew ( L.), we report the insertion of an ∼6.7-kb fragment of mitochondrial DNA into the plastome IR. BLASTn analyses returned high identity hits to mitogenome sequences including an intact open reading frame. Using three plastome markers for five species of , we generated a phylogeny to investigate the distribution and timing of the insertion. Four species share the insertion, suggesting that this event occurred <20 million yr ago in a single clade in the genus. Our study extends the observation of mitochondrial to plastome IGT to include long-lived tree species. While previous studies have suggested possible mechanisms facilitating IGT to the plastome, more examples of this phenomenon, along with more complete mitogenome sequences, will be required before a common, or variable, mechanism can be elucidated.
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Park S, Ruhlman TA, Weng ML, Hajrah NH, Sabir JS, Jansen RK. Contrasting Patterns of Nucleotide Substitution Rates Provide Insight into Dynamic Evolution of Plastid and Mitochondrial Genomes of Geranium. Genome Biol Evol 2017; 9:1766-1780. [PMID: 28854633 PMCID: PMC5570028 DOI: 10.1093/gbe/evx124] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2017] [Indexed: 12/25/2022] Open
Abstract
Geraniaceae have emerged as a model system for investigating the causes and consequences of variation in plastid and mitochondrial genomes. Incredible structural variation in plastid genomes (plastomes) and highly accelerated evolutionary rates have been reported in selected lineages and functional groups of genes in both plastomes and mitochondrial genomes (mitogenomes), and these phenomena have been implicated in cytonuclear incompatibility. Previous organelle genome studies have included limited sampling of Geranium, the largest genus in the family with over 400 species. This study reports on rates and patterns of nucleotide substitutions in plastomes and mitogenomes of 17 species of Geranium and representatives of other Geraniaceae. As detected across other angiosperms, substitution rates in the plastome are 3.5 times higher than the mitogenome in most Geranium. However, in the branch leading to Geranium brycei/Geranium incanum mitochondrial genes experienced significantly higher dN and dS than plastid genes, a pattern that has only been detected in one other angiosperm. Furthermore, rate accelerations differ in the two organelle genomes with plastomes having increased dN and mitogenomes with increased dS. In the Geranium phaeum/Geranium reflexum clade, duplicate copies of clpP and rpoA genes that experienced asymmetric rate divergence were detected in the single copy region of the plastome. In the case of rpoA, the branch leading to G. phaeum/G. reflexum experienced positive selection or relaxation of purifying selection. Finally, the evolution of acetyl-CoA carboxylase is unusual in Geraniaceae because it is only the second angiosperm family where both prokaryotic and eukaryotic ACCases functionally coexist in the plastid.
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Affiliation(s)
- Seongjun Park
- Department of Integrative Biology, University of Texas at Austin
| | | | - Mao-Lun Weng
- Department of Integrative Biology, University of Texas at Austin
- Department of Biology and Microbiology, South Dakota State University
| | - Nahid H. Hajrah
- Genomic and Biotechnology Research Group, Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jamal S.M. Sabir
- Genomic and Biotechnology Research Group, Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Robert K. Jansen
- Department of Integrative Biology, University of Texas at Austin
- Genomic and Biotechnology Research Group, Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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Ruhlman TA, Zhang J, Blazier JC, Sabir JSM, Jansen RK. Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure. Am J Bot 2017; 104:559-572. [PMID: 28400415 DOI: 10.3732/ajb.1600453] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 02/23/2017] [Indexed: 05/21/2023]
Abstract
PREMISE OF THE STUDY There is a misinterpretation in the literature regarding the variable orientation of the small single copy region of plastid genomes (plastomes). The common phenomenon of small and large single copy inversion, hypothesized to occur through intramolecular recombination between inverted repeats (IR) in a circular, single unit-genome, in fact, more likely occurs through recombination-dependent replication (RDR) of linear plastome templates. If RDR can be primed through both intra- and intermolecular recombination, then this mechanism could not only create inversion isomers of so-called single copy regions, but also an array of alternative sequence arrangements. METHODS We used Illumina paired-end and PacBio single-molecule real-time (SMRT) sequences to characterize repeat structure in the plastome of Monsonia emarginata (Geraniaceae). We used OrgConv and inspected nucleotide alignments to infer ancestral nucleotides and identify gene conversion among repeats and mapped long (>1 kb) SMRT reads against the unit-genome assembly to identify alternative sequence arrangements. RESULTS Although M. emarginata lacks the canonical IR, we found that large repeats (>1 kilobase; kb) represent ∼22% of the plastome nucleotide content. Among the largest repeats (>2 kb), we identified GC-biased gene conversion and mapping filtered, long SMRT reads to the M. emarginata unit-genome assembly revealed alternative, substoichiometric sequence arrangements. CONCLUSION We offer a model based on RDR and gene conversion between long repeated sequences in the M. emarginata plastome and provide support that both intra-and intermolecular recombination between large repeats, particularly in repeat-rich plastomes, varies unit-genome structure while homogenizing the nucleotide sequence of repeats.
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Affiliation(s)
- Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712 USA
| | - Jin Zhang
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712 USA
| | - John C Blazier
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712 USA
| | - Jamal S M Sabir
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589 Saudi Arabia
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712 USA
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589 Saudi Arabia
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Weng ML, Ruhlman TA, Jansen RK. Expansion of inverted repeat does not decrease substitution rates in Pelargonium plastid genomes. New Phytol 2017; 214:842-851. [PMID: 27991660 DOI: 10.1111/nph.14375] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/04/2016] [Indexed: 05/23/2023]
Abstract
For species with minor inverted repeat (IR) boundary changes in the plastid genome (plastome), nucleotide substitution rates were previously shown to be lower in the IR than the single copy regions (SC). However, the impact of large-scale IR expansion/contraction on plastid nucleotide substitution rates among closely related species remains unclear. We included plastomes from 22 Pelargonium species, including eight newly sequenced genomes, and used both pairwise and model-based comparisons to investigate the impact of the IR on sequence evolution in plastids. Ten types of plastome organization with different inversions or IR boundary changes were identified in Pelargonium. Inclusion in the IR was not sufficient to explain the variation of nucleotide substitution rates. Instead, the rate heterogeneity in Pelargonium plastomes was a mixture of locus-specific, lineage-specific and IR-dependent effects. Our study of Pelargonium plastomes that vary in IR length and gene content demonstrates that the evolutionary consequences of retaining these repeats are more complicated than previously suggested.
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Affiliation(s)
- Mao-Lun Weng
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57006, USA
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas, Austin, TX, 78712, USA
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas, Austin, TX, 78712, USA
- Department of Biological Sciences, Biotechnology Research Group, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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Sabir JSM, Jansen RK, Arasappan D, Calderon V, Noutahi E, Zheng C, Park S, Sabir MJ, Baeshen MN, Hajrah NH, Khiyami MA, Baeshen NA, Obaid AY, Al-Malki AL, Sankoff D, El-Mabrouk N, Ruhlman TA. The nuclear genome of Rhazya stricta and the evolution of alkaloid diversity in a medically relevant clade of Apocynaceae. Sci Rep 2016; 6:33782. [PMID: 27653669 PMCID: PMC5031960 DOI: 10.1038/srep33782] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 09/02/2016] [Indexed: 12/31/2022] Open
Abstract
Alkaloid accumulation in plants is activated in response to stress, is limited in distribution and specific alkaloid repertoires are variable across taxa. Rauvolfioideae (Apocynaceae, Gentianales) represents a major center of structural expansion in the monoterpenoid indole alkaloids (MIAs) yielding thousands of unique molecules including highly valuable chemotherapeutics. The paucity of genome-level data for Apocynaceae precludes a deeper understanding of MIA pathway evolution hindering the elucidation of remaining pathway enzymes and the improvement of MIA availability in planta or in vitro. We sequenced the nuclear genome of Rhazya stricta (Apocynaceae, Rauvolfioideae) and present this high quality assembly in comparison with that of coffee (Rubiaceae, Coffea canephora, Gentianales) and others to investigate the evolution of genome-scale features. The annotated Rhazya genome was used to develop the community resource, RhaCyc, a metabolic pathway database. Gene family trees were constructed to identify homologs of MIA pathway genes and to examine their evolutionary history. We found that, unlike Coffea, the Rhazya lineage has experienced many structural rearrangements. Gene tree analyses suggest recent, lineage-specific expansion and diversification among homologs encoding MIA pathway genes in Gentianales and provide candidate sequences with the potential to close gaps in characterized pathways and support prospecting for new MIA production avenues.
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Affiliation(s)
- Jamal S. M. Sabir
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Robert K. Jansen
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Integrative Biology, University of Texas at Austin, Austin, 78712 Texas, USA
| | - Dhivya Arasappan
- Department of Integrative Biology, University of Texas at Austin, Austin, 78712 Texas, USA
| | - Virginie Calderon
- Département d’informatique et de recherche opérationnelle, Université de Montréal, CP 6128 succ Centre-Ville, Montréal, H3C 3J7 Québec, Canada
| | - Emmanuel Noutahi
- Département d’informatique et de recherche opérationnelle, Université de Montréal, CP 6128 succ Centre-Ville, Montréal, H3C 3J7 Québec, Canada
| | - Chunfang Zheng
- Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Ave., Ottawa, K1N 6N5 Ontario Canada
| | - Seongjun Park
- Department of Integrative Biology, University of Texas at Austin, Austin, 78712 Texas, USA
| | - Meshaal J. Sabir
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mohammed N. Baeshen
- Department of Biological Sciences, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Nahid H. Hajrah
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | | | - Nabih A. Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Abdullah Y. Obaid
- Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Abdulrahman L. Al-Malki
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - David Sankoff
- Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Ave., Ottawa, K1N 6N5 Ontario Canada
| | - Nadia El-Mabrouk
- Département d’informatique et de recherche opérationnelle, Université de Montréal, CP 6128 succ Centre-Ville, Montréal, H3C 3J7 Québec, Canada
| | - Tracey A. Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, 78712 Texas, USA
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Abstract
Plastids and mitochondria have many protein complexes that include subunits encoded by organelle and nuclear genomes. In animal cells, compensatory evolution between mitochondrial and nuclear-encoded subunits was identified and the high mitochondrial mutation rates were hypothesized to drive compensatory evolution in nuclear genomes. In plant cells, compensatory evolution between plastid and nucleus has rarely been investigated in a phylogenetic framework. To investigate plastid–nuclear coevolution, we focused on plastid ribosomal protein genes that are encoded by plastid and nuclear genomes from 27 Geraniales species. Substitution rates were compared for five sets of genes representing plastid- and nuclear-encoded ribosomal subunit proteins targeted to the cytosol or the plastid as well as nonribosomal protein controls. We found that nonsynonymous substitution rates (dN) and the ratios of nonsynonymous to synonymous substitution rates (ω) were accelerated in both plastid- (CpRP) and nuclear-encoded subunits (NuCpRP) of the plastid ribosome relative to control sequences. Our analyses revealed strong signals of cytonuclear coevolution between plastid- and nuclear-encoded subunits, in which nonsynonymous substitutions in CpRP and NuCpRP tend to occur along the same branches in the Geraniaceae phylogeny. This coevolution pattern cannot be explained by physical interaction between amino acid residues. The forces driving accelerated coevolution varied with cellular compartment of the sequence. Increased ω in CpRP was mainly due to intensified positive selection whereas increased ω in NuCpRP was caused by relaxed purifying selection. In addition, the many indels identified in plastid rRNA genes in Geraniaceae may have contributed to changes in plastid subunits.
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Affiliation(s)
- Mao-Lun Weng
- Department of Biology, University of Maryland, College Park Department of Integrative Biology, University of Texas, Austin
| | | | - Robert K Jansen
- Department of Integrative Biology, University of Texas, Austin Department of Biological Sciences, Biotechnology Research Group, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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Blazier JC, Jansen RK, Mower JP, Govindu M, Zhang J, Weng ML, Ruhlman TA. Variable presence of the inverted repeat and plastome stability in Erodium. Ann Bot 2016; 117:1209-20. [PMID: 27192713 PMCID: PMC4904181 DOI: 10.1093/aob/mcw065] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/05/2016] [Accepted: 02/22/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Several unrelated lineages such as plastids, viruses and plasmids, have converged on quadripartite genomes of similar size with large and small single copy regions and a large inverted repeat (IR). Except for Erodium (Geraniaceae), saguaro cactus and some legumes, the plastomes of all photosynthetic angiosperms display this structure. The functional significance of the IR is not understood and Erodium provides a system to examine the role of the IR in the long-term stability of these genomes. We compared the degree of genomic rearrangement in plastomes of Erodium that differ in the presence and absence of the IR. METHODS We sequenced 17 new Erodium plastomes. Using 454, Illumina, PacBio and Sanger sequences, 16 genomes were assembled and categorized along with one incomplete and two previously published Erodium plastomes. We conducted phylogenetic analyses among these species using a dataset of 19 protein-coding genes and determined if significantly higher evolutionary rates had caused the long branch seen previously in phylogenetic reconstructions within the genus. Bioinformatic comparisons were also performed to evaluate plastome evolution across the genus. KEY RESULTS Erodium plastomes fell into four types (Type 1-4) that differ in their substitution rates, short dispersed repeat content and degree of genomic rearrangement, gene and intron content and GC content. Type 4 plastomes had significantly higher rates of synonymous substitutions (dS) for all genes and for 14 of the 19 genes non-synonymous substitutions (dN) were significantly accelerated. We evaluated the evidence for a single IR loss in Erodium and in doing so discovered that Type 4 plastomes contain a novel IR. CONCLUSIONS The presence or absence of the IR does not affect plastome stability in Erodium. Rather, the overall repeat content shows a negative correlation with genome stability, a pattern in agreement with other angiosperm groups and recent findings on genome stability in bacterial endosymbionts.
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Affiliation(s)
- John C Blazier
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Madhu Govindu
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Jin Zhang
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Mao-Lun Weng
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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27
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Blazier JC, Ruhlman TA, Weng ML, Rehman SK, Sabir JSM, Jansen RK. Divergence of RNA polymerase α subunits in angiosperm plastid genomes is mediated by genomic rearrangement. Sci Rep 2016; 6:24595. [PMID: 27087667 PMCID: PMC4834550 DOI: 10.1038/srep24595] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 04/01/2016] [Indexed: 12/20/2022] Open
Abstract
Genes for the plastid-encoded RNA polymerase (PEP) persist in the plastid genomes of all photosynthetic angiosperms. However, three unrelated lineages (Annonaceae, Passifloraceae and Geraniaceae) have been identified with unusually divergent open reading frames (ORFs) in the conserved region of rpoA, the gene encoding the PEP α subunit. We used sequence-based approaches to evaluate whether these genes retain function. Both gene sequences and complete plastid genome sequences were assembled and analyzed from each of the three angiosperm families. Multiple lines of evidence indicated that the rpoA sequences are likely functional despite retaining as low as 30% nucleotide sequence identity with rpoA genes from outgroups in the same angiosperm order. The ratio of non-synonymous to synonymous substitutions indicated that these genes are under purifying selection, and bioinformatic prediction of conserved domains indicated that functional domains are preserved. One of the lineages (Pelargonium, Geraniaceae) contains species with multiple rpoA-like ORFs that show evidence of ongoing inter-paralog gene conversion. The plastid genomes containing these divergent rpoA genes have experienced extensive structural rearrangement, including large expansions of the inverted repeat. We propose that illegitimate recombination, not positive selection, has driven the divergence of rpoA.
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Affiliation(s)
- J Chris Blazier
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Mao-Lun Weng
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Sumaiyah K Rehman
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Jamal S M Sabir
- Biotechnology Research Group, Department of Biological Science, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA.,Biotechnology Research Group, Department of Biological Science, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Zhang J, Ruhlman TA, Sabir JSM, Blazier JC, Weng ML, Park S, Jansen RK. Coevolution between Nuclear-Encoded DNA Replication, Recombination, and Repair Genes and Plastid Genome Complexity. Genome Biol Evol 2016; 8:622-34. [PMID: 26893456 PMCID: PMC4824065 DOI: 10.1093/gbe/evw033] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Disruption of DNA replication, recombination, and repair (DNA-RRR) systems has been hypothesized to cause highly elevated nucleotide substitution rates and genome rearrangements in the plastids of angiosperms, but this theory remains untested. To investigate nuclear–plastid genome (plastome) coevolution in Geraniaceae, four different measures of plastome complexity (rearrangements, repeats, nucleotide insertions/deletions, and substitution rates) were evaluated along with substitution rates of 12 nuclear-encoded, plastid-targeted DNA-RRR genes from 27 Geraniales species. Significant correlations were detected for nonsynonymous (dN) but not synonymous (dS) substitution rates for three DNA-RRR genes (uvrB/C, why1, and gyrA) supporting a role for these genes in accelerated plastid genome evolution in Geraniaceae. Furthermore, correlation between dN of uvrB/C and plastome complexity suggests the presence of nucleotide excision repair system in plastids. Significant correlations were also detected between plastome complexity and 13 of the 90 nuclear-encoded organelle-targeted genes investigated. Comparisons revealed significant acceleration of dN in plastid-targeted genes of Geraniales relative to Brassicales suggesting this correlation may be an artifact of elevated rates in this gene set in Geraniaceae. Correlation between dN of plastid-targeted DNA-RRR genes and plastome complexity supports the hypothesis that the aberrant patterns in angiosperm plastome evolution could be caused by dysfunction in DNA-RRR systems.
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Affiliation(s)
- Jin Zhang
- Department of Integrative Biology, University of Texas at Austin
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin
| | - Jamal S M Sabir
- The Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | | | - Mao-Lun Weng
- Department of Integrative Biology, University of Texas at Austin
| | - Seongjun Park
- Department of Integrative Biology, University of Texas at Austin
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin The Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
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Park S, Grewe F, Zhu A, Ruhlman TA, Sabir J, Mower JP, Jansen RK. Dynamic evolution of Geranium mitochondrial genomes through multiple horizontal and intracellular gene transfers. New Phytol 2015; 208:570-83. [PMID: 25989702 DOI: 10.1111/nph.13467] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/15/2015] [Indexed: 05/20/2023]
Abstract
The exchange of genetic material between cellular organelles through intracellular gene transfer (IGT) or between species by horizontal gene transfer (HGT) has played an important role in plant mitochondrial genome evolution. The mitochondrial genomes of Geraniaceae display a number of unusual phenomena including highly accelerated rates of synonymous substitutions, extensive gene loss and reduction in RNA editing. Mitochondrial DNA sequences assembled for 17 species of Geranium revealed substantial reduction in gene and intron content relative to the ancestor of the Geranium lineage. Comparative analyses of nuclear transcriptome data suggest that a number of these sequences have been functionally relocated to the nucleus via IGT. Evidence for rampant HGT was detected in several Geranium species containing foreign organellar DNA from diverse eudicots, including many transfers from parasitic plants. One lineage has experienced multiple, independent HGT episodes, many of which occurred within the past 5.5 Myr. Both duplicative and recapture HGT were documented in Geranium lineages. The mitochondrial genome of Geranium brycei contains at least four independent HGT tracts that are absent in its nearest relative. Furthermore, G. brycei mitochondria carry two copies of the cox1 gene that differ in intron content, providing insight into contrasting hypotheses on cox1 intron evolution.
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Affiliation(s)
- Seongjun Park
- Department of Integrative Biology, University of Texas, Austin, TX, 78712, USA
| | - Felix Grewe
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68588, USA
| | - Andan Zhu
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68588, USA
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas, Austin, TX, 78712, USA
| | - Jamal Sabir
- Department of Biological Science, Biotechnology Research Group, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Jeffrey P Mower
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68588, USA
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas, Austin, TX, 78712, USA
- Department of Biological Science, Biotechnology Research Group, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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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 Biol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Zhang J, Ruhlman TA, Sabir J, Blazier JC, Jansen RK. Coordinated rates of evolution between interacting plastid and nuclear genes in Geraniaceae. Plant Cell 2015; 27:563-73. [PMID: 25724640 PMCID: PMC4558654 DOI: 10.1105/tpc.114.134353] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/28/2015] [Accepted: 02/12/2015] [Indexed: 05/08/2023]
Abstract
Although gene coevolution has been widely observed within individuals and between different organisms, rarely has this phenomenon been investigated within a phylogenetic framework. The Geraniaceae is an attractive system in which to study plastid-nuclear genome coevolution due to the highly elevated evolutionary rates in plastid genomes. In plants, the plastid-encoded RNA polymerase (PEP) is a protein complex composed of subunits encoded by both plastid (rpoA, rpoB, rpoC1, and rpoC2) and nuclear genes (sig1-6). We used transcriptome and genomic data for 27 species of Geraniales in a systematic evaluation of coevolution between genes encoding subunits of the PEP holoenzyme. We detected strong correlations of dN (nonsynonymous substitutions) but not dS (synonymous substitutions) within rpoB/sig1 and rpoC2/sig2, but not for other plastid/nuclear gene pairs, and identified the correlation of dN/dS ratio between rpoB/C1/C2 and sig1/5/6, rpoC1/C2 and sig2, and rpoB/C2 and sig3 genes. Correlated rates between interacting plastid and nuclear sequences across the Geraniales could result from plastid-nuclear genome coevolution. Analyses of coevolved amino acid positions suggest that structurally mediated coevolution is not the major driver of plastid-nuclear coevolution. The detection of strong correlation of evolutionary rates between SIG and RNAP genes suggests a plausible explanation for plastome-genome incompatibility in Geraniaceae.
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Affiliation(s)
- Jin Zhang
- Department of Integrative Biology, University of Texas, Austin, Texas 78712
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas, Austin, Texas 78712
| | - Jamal Sabir
- Department of Biological Sciences, Biotechnology Research Group, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - J Chris Blazier
- Department of Integrative Biology, University of Texas, Austin, Texas 78712
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas, Austin, Texas 78712 Department of Biological Sciences, Biotechnology Research Group, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Ruhlman TA, Rajasekaran K, Cary JW. Expression of chloroperoxidase from Pseudomonas pyrrocinia in tobacco plastids for fungal resistance. Plant Sci 2014; 228:98-106. [PMID: 25438790 DOI: 10.1016/j.plantsci.2014.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 01/31/2014] [Accepted: 02/19/2014] [Indexed: 06/04/2023]
Abstract
The chloroperoxidase (cpo) gene from Pseudomonas pyrrocinia was transformed into the plastid genome (plastome) of Nicotiana tabacum var. Petit Havana and transplastomic lines were compared with a nuclear transformant for the same gene. Southern analysis confirmed integration in the plastome and western blotting confirmed the presence of the chloroperoxidase protein (CPO) in higher abundance in transplastomic plants than in cpo nuclear transformants. Northern analysis of primary plastome transformants for cpo showed 15-fold higher transcript abundance than in the nuclear transformant, yet this extent of enhancement was not observed in western blot, enzyme or bioassay, indicating a bottleneck at the post-transcriptional level. Representative plants from the two transplastomic lines showed resistance to fungal pathogens in vitro (Aspergillus flavus, Fusarium verticillioides, and Verticillium dahliae) and in planta (Alternaria alternata).
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Affiliation(s)
- Tracey A Ruhlman
- USDA, ARS, Southern Regional Research Center, 1100 Robert E. Lee Boulevard, New Orleans, LA 70124-4305, United States.
| | - Kanniah Rajasekaran
- USDA, ARS, Southern Regional Research Center, 1100 Robert E. Lee Boulevard, New Orleans, LA 70124-4305, United States.
| | - Jeffrey W Cary
- USDA, ARS, Southern Regional Research Center, 1100 Robert E. Lee Boulevard, New Orleans, LA 70124-4305, United States.
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Park S, Ruhlman TA, Sabir JSM, Mutwakil MHZ, Baeshen MN, Sabir MJ, Baeshen NA, Jansen RK. Complete sequences of organelle genomes from the medicinal plant Rhazya stricta (Apocynaceae) and contrasting patterns of mitochondrial genome evolution across asterids. BMC Genomics 2014; 15:405. [PMID: 24884625 PMCID: PMC4045975 DOI: 10.1186/1471-2164-15-405] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 05/15/2014] [Indexed: 11/17/2022] Open
Abstract
Background Rhazya stricta is native to arid regions in South Asia and the Middle East and is used extensively in folk medicine to treat a wide range of diseases. In addition to generating genomic resources for this medicinally important plant, analyses of the complete plastid and mitochondrial genomes and a nuclear transcriptome from Rhazya provide insights into inter-compartmental transfers between genomes and the patterns of evolution among eight asterid mitochondrial genomes. Results The 154,841 bp plastid genome is highly conserved with gene content and order identical to the ancestral organization of angiosperms. The 548,608 bp mitochondrial genome exhibits a number of phenomena including the presence of recombinogenic repeats that generate a multipartite organization, transferred DNA from the plastid and nuclear genomes, and bidirectional DNA transfers between the mitochondrion and the nucleus. The mitochondrial genes sdh3 and rps14 have been transferred to the nucleus and have acquired targeting presequences. In the case of rps14, two copies are present in the nucleus; only one has a mitochondrial targeting presequence and may be functional. Phylogenetic analyses of both nuclear and mitochondrial copies of rps14 across angiosperms suggests Rhazya has experienced a single transfer of this gene to the nucleus, followed by a duplication event. Furthermore, the phylogenetic distribution of gene losses and the high level of sequence divergence in targeting presequences suggest multiple, independent transfers of both sdh3 and rps14 across asterids. Comparative analyses of mitochondrial genomes of eight sequenced asterids indicates a complicated evolutionary history in this large angiosperm clade with considerable diversity in genome organization and size, repeat, gene and intron content, and amount of foreign DNA from the plastid and nuclear genomes. Conclusions Organelle genomes of Rhazya stricta provide valuable information for improving the understanding of mitochondrial genome evolution among angiosperms. The genomic data have enabled a rigorous examination of the gene transfer events. Rhazya is unique among the eight sequenced asterids in the types of events that have shaped the evolution of its mitochondrial genome. Furthermore, the organelle genomes of R. stricta provide valuable genomic resources for utilizing this important medicinal plant in biotechnology applications. Electronic supplementary material The online version of this article (doi: 10.1186/1471-2164-15-405) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA.
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Abstract
The plastid genome (plastome) has proved a valuable source of data for evaluating evolutionary relationships among angiosperms. Through basic and applied approaches, plastid transformation technology offers the potential to understand and improve plant productivity, providing food, fiber, energy and medicines to meet the needs of a burgeoning global population. The growing genomic resources available to both phylogenetic and biotechnological investigations are allowing novel insights and expanding the scope of plastome research to encompass new species. In this chapter we present an overview of some of the seminal and contemporary research that has contributed to our current understanding of plastome evolution and attempt to highlight the relationship between evolutionary mechanisms and tools of plastid genetic engineering.
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Affiliation(s)
- Tracey A Ruhlman
- Integrative Biology, University of Texas at Austin, Austin, TX, USA
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Abstract
The interest in producing pharmaceutical proteins in a nontoxic plant host has led to the development of an approach to express such proteins in transplastomic lettuce (Lactuca sativa L.). A number of therapeutic proteins and vaccine antigen candidates have been stably integrated into the lettuce plastid genome using biolistic DNA delivery. High levels of accumulation and retention of biological activity suggest that lettuce may provide an ideal platform for the production of biopharmaceuticals.
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Affiliation(s)
- Tracey A Ruhlman
- Integrative Biology, University of Texas at Austin, Austin, TX, USA
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Zhang J, Ruhlman TA, Mower JP, Jansen RK. Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing. BMC Plant Biol 2013; 13:228. [PMID: 24373163 PMCID: PMC3880972 DOI: 10.1186/1471-2229-13-228] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 12/20/2013] [Indexed: 05/24/2023]
Abstract
BACKGROUND Organelle genomes of Geraniaceae exhibit several unusual evolutionary phenomena compared to other angiosperm families including accelerated nucleotide substitution rates, widespread gene loss, reduced RNA editing, and extensive genomic rearrangements. Since most organelle-encoded proteins function in multi-subunit complexes that also contain nuclear-encoded proteins, it is likely that the atypical organellar phenomena affect the evolution of nuclear genes encoding organellar proteins. To begin to unravel the complex co-evolutionary interplay between organellar and nuclear genomes in this family, we sequenced nuclear transcriptomes of two species, Geranium maderense and Pelargonium x hortorum. RESULTS Normalized cDNA libraries of G. maderense and P. x hortorum were used for transcriptome sequencing. Five assemblers (MIRA, Newbler, SOAPdenovo, SOAPdenovo-trans [SOAPtrans], Trinity) and two next-generation technologies (454 and Illumina) were compared to determine the optimal transcriptome sequencing approach. Trinity provided the highest quality assembly of Illumina data with the deepest transcriptome coverage. An analysis to determine the amount of sequencing needed for de novo assembly revealed diminishing returns of coverage and quality with data sets larger than sixty million Illumina paired end reads for both species. The G. maderense and P. x hortorum transcriptomes contained fewer transcripts encoding the PLS subclass of PPR proteins relative to other angiosperms, consistent with reduced mitochondrial RNA editing activity in Geraniaceae. In addition, transcripts for all six plastid targeted sigma factors were identified in both transcriptomes, suggesting that one of the highly divergent rpoA-like ORFs in the P. x hortorum plastid genome is functional. CONCLUSIONS The findings support the use of the Illumina platform and assemblers optimized for transcriptome assembly, such as Trinity or SOAPtrans, to generate high-quality de novo transcriptomes with broad coverage. In addition, results indicated no major improvements in breadth of coverage with data sets larger than six billion nucleotides or when sampling RNA from four tissue types rather than from a single tissue. Finally, this work demonstrates the power of cross-compartmental genomic analyses to deepen our understanding of the correlated evolution of the nuclear, plastid, and mitochondrial genomes in plants.
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Affiliation(s)
- Jin Zhang
- Department of Integrative Biology and Institute of Cellular and Molecular Biology, The University of Texas at Austin, 205 W. 24th St. Stop C0930, Austin, TX 78712, USA
| | - Tracey A Ruhlman
- Department of Integrative Biology and Institute of Cellular and Molecular Biology, The University of Texas at Austin, 205 W. 24th St. Stop C0930, Austin, TX 78712, USA
| | - Jeffrey P Mower
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Robert K Jansen
- Department of Integrative Biology and Institute of Cellular and Molecular Biology, The University of Texas at Austin, 205 W. 24th St. Stop C0930, Austin, TX 78712, USA
- Genomics and Biotechnology Section, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Weng ML, Ruhlman TA, Gibby M, Jansen RK. Phylogeny, rate variation, and genome size evolution of Pelargonium (Geraniaceae). Mol Phylogenet Evol 2012; 64:654-70. [DOI: 10.1016/j.ympev.2012.05.026] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 05/17/2012] [Accepted: 05/22/2012] [Indexed: 11/28/2022]
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