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Zhuang Y, Wang X, Li X, Hu J, Fan L, Landis JB, Cannon SB, Grimwood J, Schmutz J, Jackson SA, Doyle JJ, Zhang XS, Zhang D, Ma J. Phylogenomics of the genus Glycine sheds light on polyploid evolution and life-strategy transition. NATURE PLANTS 2022; 8:233-244. [PMID: 35288665 DOI: 10.1038/s41477-022-01102-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
Polyploidy and life-strategy transitions between annuality and perenniality often occur in flowering plants. However, the evolutionary propensities of polyploids and the genetic bases of such transitions remain elusive. We assembled chromosome-level genomes of representative perennial species across the genus Glycine including five diploids and a young allopolyploid, and constructed a Glycine super-pangenome framework by integrating 26 annual soybean genomes. These perennial diploids exhibit greater genome stability and possess fewer centromere repeats than the annuals. Biased subgenomic fractionation occurred in the allopolyploid, primarily by accumulation of small deletions in gene clusters through illegitimate recombination, which was associated with pre-existing local subgenomic differentiation. Two genes annotated to modulate vegetative-reproductive phase transition and lateral shoot outgrowth were postulated as candidates underlying the perenniality-annuality transition. Our study provides insights into polyploid genome evolution and lays a foundation for unleashing genetic potential from the perennial gene pool for soybean improvement.
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Affiliation(s)
- Yongbin Zhuang
- College of Agriculture, and State Key Laboratory of Crop Biology, Shangdong Agricultural University, Tai'an, China
| | - Xutong Wang
- Department of Agronomy, and Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Xianchong Li
- College of Agriculture, and State Key Laboratory of Crop Biology, Shangdong Agricultural University, Tai'an, China
| | - Junmei Hu
- College of Agriculture, and State Key Laboratory of Crop Biology, Shangdong Agricultural University, Tai'an, China
| | - Lichuan Fan
- College of Agriculture, and State Key Laboratory of Crop Biology, Shangdong Agricultural University, Tai'an, China
| | - Jacob B Landis
- School of Integrative Plant Science Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Steven B Cannon
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Jeffrey J Doyle
- School of Integrative Plant Science Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Xian Sheng Zhang
- College of Life Sciences, and State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Dajian Zhang
- College of Agriculture, and State Key Laboratory of Crop Biology, Shangdong Agricultural University, Tai'an, China.
| | - Jianxin Ma
- Department of Agronomy, and Center for Plant Biology, Purdue University, West Lafayette, IN, USA.
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2
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Doyle JJ. Defining coalescent genes: Theory meets practice in organelle phylogenomics. Syst Biol 2021; 71:476-489. [PMID: 34191012 DOI: 10.1093/sysbio/syab053] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 11/13/2022] Open
Abstract
The species tree paradigm that dominates current molecular systematic practice infers species trees from collections of sequences under assumptions of the multispecies coalescent (MSC), i.e., that there is free recombination between the sequences and no (or very low) recombination within them. These coalescent genes (c-genes) are thus defined in an historical rather than molecular sense, and can in theory be as large as an entire genome or as small as a single nucleotide. A debate about how to define c-genes centers on the contention that nuclear gene sequences used in many coalescent analyses undergo too much recombination, such that their introns comprise multiple c-genes, violating a key assumption of the MSC. Recently a similar argument has been made for the genes of plastid (e.g., chloroplast) and mitochondrial genomes, which for the last 30 or more years have been considered to represent a single c-gene for the purposes of phylogeny reconstruction because they are non-recombining in a historical sense. Consequently, it has been suggested that these genomes should be analyzed using coalescent methods that treat their genes-over 70 protein-coding genes in the case of most plastid genomes (plastomes)-as independent estimates of species phylogeny, in contrast to the usual practice of concatenation, which is appropriate for generating gene trees. However, although recombination certainly occurs in the plastome, as has been recognized since the 1970's, it is unlikely to be phylogenetically relevant. This is because such historically effective recombination can only occur when plastomes with incongruent histories are brought together in the same plastid. However, plastids sort rapidly into different cell lineages and rarely fuse. Thus, because of plastid biology, the plastome is a more canonical c-gene than is the average multi-intron mammalian nuclear gene. The plastome should thus continue to be treated as a single estimate of the underlying species phylogeny, as should the mitochondrial genome. The implications of this long-held insight of molecular systematics for studies in the phylogenomic era are explored.
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Affiliation(s)
- Jeff J Doyle
- Plant Biology Section, Plant Breeding & Genetics Section, and L. H. Bailey Hortorium, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
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Liu Q, Li X, Li M, Xu W, Schwarzacher T, Heslop-Harrison JS. Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny. BMC PLANT BIOLOGY 2020; 20:406. [PMID: 32878602 PMCID: PMC7466839 DOI: 10.1186/s12870-020-02621-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 08/25/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Oat (Avena sativa L.) is a recognized health-food, and the contributions of its different candidate A-genome progenitor species remain inconclusive. Here, we report chloroplast genome sequences of eleven Avena species, to examine the plastome evolutionary dynamics and analyze phylogenetic relationships between oat and its congeneric wild related species. RESULTS The chloroplast genomes of eleven Avena species (size range of 135,889-135,998 bp) share quadripartite structure, comprising of a large single copy (LSC; 80,014-80,132 bp), a small single copy (SSC; 12,575-12,679 bp) and a pair of inverted repeats (IRs; 21,603-21,614 bp). The plastomes contain 131 genes including 84 protein-coding genes, eight ribosomal RNAs and 39 transfer RNAs. The nucleotide sequence diversities (Pi values) range from 0.0036 (rps19) to 0.0093 (rpl32) for ten most polymorphic genes and from 0.0084 (psbH-petB) to 0.0240 (petG-trnW-CCA) for ten most polymorphic intergenic regions. Gene selective pressure analysis shows that all protein-coding genes have been under purifying selection. The adjacent position relationships between tandem repeats, insertions/deletions and single nucleotide polymorphisms support the evolutionary importance of tandem repeats in causing plastome mutations in Avena. Phylogenomic analyses, based on the complete plastome sequences and the LSC intermolecular recombination sequences, support the monophyly of Avena with two clades in the genus. CONCLUSIONS Diversification of Avena plastomes is explained by the presence of highly diverse genes and intergenic regions, LSC intermolecular recombination, and the co-occurrence of tandem repeat and indels or single nucleotide polymorphisms. The study demonstrates that the A-genome diploid-polyploid lineage maintains two subclades derived from different maternal ancestors, with A. longiglumis as the first diverging species in clade I. These genome resources will be helpful in elucidating the chloroplast genome structure, understanding the evolutionary dynamics at genus Avena and family Poaceae levels, and are potentially useful to exploit plastome variation in making hybrids for plant breeding.
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Affiliation(s)
- Qing Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
- Center for Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China.
| | - Xiaoyu Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingzhi Li
- Independent Researcher, Guangzhou, China
| | - Wenkui Xu
- Independent Researcher, Guangzhou, China
| | - Trude Schwarzacher
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - John Seymour Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
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Boutanaev AM, Nemchinov LG. Genome Size Dynamics within Multiple Genera of Diploid Seed Plants. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420060046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Grehl C, Wagner M, Lemnian I, Glaser B, Grosse I. Performance of Mapping Approaches for Whole-Genome Bisulfite Sequencing Data in Crop Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:176. [PMID: 32256504 PMCID: PMC7093021 DOI: 10.3389/fpls.2020.00176] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 02/05/2020] [Indexed: 05/09/2023]
Abstract
DNA methylation is involved in many different biological processes in the development and well-being of crop plants such as transposon activation, heterosis, environment-dependent transcriptome plasticity, aging, and many diseases. Whole-genome bisulfite sequencing is an excellent technology for detecting and quantifying DNA methylation patterns in a wide variety of species, but optimized data analysis pipelines exist only for a small number of species and are missing for many important crop plants. This is especially important as most existing benchmark studies have been performed on mammals with hardly any repetitive elements and without CHG and CHH methylation. Pipelines for the analysis of whole-genome bisulfite sequencing data usually consists of four steps: read trimming, read mapping, quantification of methylation levels, and prediction of differentially methylated regions (DMRs). Here we focus on read mapping, which is challenging because un-methylated cytosines are transformed to uracil during bisulfite treatment and to thymine during the subsequent polymerase chain reaction, and read mappers must be capable of dealing with this cytosine/thymine polymorphism. Several read mappers have been developed over the last years, with different strengths and weaknesses, but their performances have not been critically evaluated. Here, we compare eight read mappers: Bismark, BismarkBwt2, BSMAP, BS-Seeker2, Bwameth, GEM3, Segemehl, and GSNAP to assess the impact of the read-mapping results on the prediction of DMRs. We used simulated data generated from the genomes of Arabidopsis thaliana, Brassica napus, Glycine max, Solanum tuberosum, and Zea mays, monitored the effects of the bisulfite conversion rate, the sequencing error rate, the maximum number of allowed mismatches, as well as the genome structure and size, and calculated precision, number of uniquely mapped reads, distribution of the mapped reads, run time, and memory consumption as features for benchmarking the eight read mappers mentioned above. Furthermore, we validated our findings using real-world data of Glycine max and showed the influence of the mapping step on DMR calling in WGBS pipelines. We found that the conversion rate had only a minor impact on the mapping quality and the number of uniquely mapped reads, whereas the error rate and the maximum number of allowed mismatches had a strong impact and leads to differences of the performance of the eight read mappers. In conclusion, we recommend BSMAP which needs the shortest run time and yields the highest precision, and Bismark which requires the smallest amount of memory and yields precision and high numbers of uniquely mapped reads.
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Affiliation(s)
- Claudius Grehl
- Institute of Computer Science, Bioinformatics, Martin Luther University Halle–Wittenberg, Von Seckendorff-Platz 1, Halle (Saale), Germany
- Institute of Agronomy and Nutritional Sciences, Soil Biogeochemistry, Martin Luther University Halle–Wittenberg, Von Seckendorff-Platz 3, Halle (Saale), Germany
- *Correspondence: Claudius Grehl,
| | - Marc Wagner
- Institute of Mathematics and Informatics, Freie Universität Berlin, Berlin, Germany
| | - Ioana Lemnian
- Institute of Computer Science, Bioinformatics, Martin Luther University Halle–Wittenberg, Von Seckendorff-Platz 1, Halle (Saale), Germany
- Institute of Human Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Bruno Glaser
- Institute of Agronomy and Nutritional Sciences, Soil Biogeochemistry, Martin Luther University Halle–Wittenberg, Von Seckendorff-Platz 3, Halle (Saale), Germany
| | - Ivo Grosse
- Institute of Computer Science, Bioinformatics, Martin Luther University Halle–Wittenberg, Von Seckendorff-Platz 1, Halle (Saale), Germany
- Bioinformatics Unit, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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6
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Genetic Diversity and Phylogenetic Relationships of Annual and Perennial Glycine Species. G3-GENES GENOMES GENETICS 2019; 9:2325-2336. [PMID: 31097479 PMCID: PMC6643897 DOI: 10.1534/g3.119.400220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We have estimated the average genetic diversity of two Glycine annual and six perennial species based upon 76 orthologous gene sets and performed phylogenetic analysis, divergence analysis and tests for departure from neutrality of the eight species using 52 orthologous gene sets. In addition, 367 orthologous gene sets were used to estimate the relationships of 11 G. canescens accessions. Among the perennials, G. canescens showed the highest nucleotide diversity. The other perennials, except for G. tomentella, had higher nucleotide diversity than the two annuals. Phylogenetic analysis of the Glycine showed a similar genome grouping with the previous report except for G. cyrtoloba and G. stenophita which formed a sister clade in the study. Divergence analysis supported the phylogenetic relationships that G. falcata was the most divergent from G. max, followed by G. cyrtoloba, G. syndetika, G. tomentella D3, G. stenophita and G. canescens. Most genic sequences were homogeneous in the levels of polymorphism and divergence between G. max and other Glycine species based on the HKA test, thus, Glycine perennials may have experienced a very similar evolution as inferred by trans-specific mutation analysis. The greater genetic diversity of most perennial Glycine species and their origins from the warmer and drier climates of Australia suggests the perennials maybe a potential source of heat and drought resistance that will be of value in the face of climate change.
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Liu Q, Chang S, Hartman GL, Domier LL. Assembly and annotation of a draft genome sequence for Glycine latifolia, a perennial wild relative of soybean. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:71-85. [PMID: 29671916 DOI: 10.1111/tpj.13931] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/12/2018] [Accepted: 03/22/2018] [Indexed: 05/14/2023]
Abstract
Glycine latifolia (Benth.) Newell & Hymowitz (2n = 40), one of the 27 wild perennial relatives of soybean, possesses genetic diversity and agronomically favorable traits that are lacking in soybean. Here, we report the 939-Mb draft genome assembly of G. latifolia (PI 559298) using exclusively linked-reads sequenced from a single Chromium library. We organized scaffolds into 20 chromosome-scale pseudomolecules utilizing two genetic maps and the Glycine max (L.) Merr. genome sequence. High copy numbers of putative 91-bp centromere-specific tandem repeats were observed in consecutive blocks within predicted pericentromeric regions on several pseudomolecules. No 92-bp putative centromeric repeats, which are abundant in G. max, were detected in G. latifolia or Glycine tomentella. Annotation of the assembled genome and subsequent filtering yielded a high confidence gene set of 54 475 protein-coding loci. In comparative analysis with five legume species, genes related to defense responses were significantly overrepresented in Glycine-specific orthologous gene families. A total of 304 putative nucleotide-binding site (NBS)-leucine-rich-repeat (LRR) genes were identified in this genome assembly. Different from other legume species, we observed a scarcity of TIR-NBS-LRR genes in G. latifolia. The G. latifolia genome was also predicted to contain genes encoding 367 LRR-receptor-like kinases, a family of proteins involved in basal defense responses and responses to abiotic stress. The genome sequence and annotation of G. latifolia provides a valuable source of alternative alleles and novel genes to facilitate soybean improvement. This study also highlights the efficacy and cost-effectiveness of the application of Chromium linked-reads in diploid plant genome de novo assembly.
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Affiliation(s)
- Qiong Liu
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Sungyul Chang
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Glen L Hartman
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
- USDA ARS, Urbana, IL, 61801, USA
| | - Leslie L Domier
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
- USDA ARS, Urbana, IL, 61801, USA
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8
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Kang SH, Lee JH, Lee HO, Ahn BO, Won SY, Sohn SH, Kim JS. Complete chloroplast genome and 45S nrDNA sequences of the medicinal plant species Glycyrrhiza glabra and Glycyrrhiza uralensis. Genes Genet Syst 2018; 93:83-89. [DOI: 10.1266/ggs.17-00002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences
| | - Jeong-Hoon Lee
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science
| | - Hyun Oh Lee
- Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University
- Phyzen Genomics Institute
| | - Byoung Ohg Ahn
- R&D Coordination Division, Rural Development Administration
| | - So Youn Won
- Genomics Division, National Institute of Agricultural Sciences
| | - Seong-Han Sohn
- Genomics Division, National Institute of Agricultural Sciences
| | - Jung Sun Kim
- Genomics Division, National Institute of Agricultural Sciences
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9
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Tian N, Han L, Chen C, Wang Z. The complete chloroplast genome sequence of Epipremnum aureum and its comparative analysis among eight Araceae species. PLoS One 2018. [PMID: 29529038 PMCID: PMC5846728 DOI: 10.1371/journal.pone.0192956] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Epipremnum aureum is an important foliage plant in the Araceae family. In this study, we have sequenced the complete chloroplast genome of E. aureum by using Illumina Hiseq sequencing platforms. This genome is a double-stranded circular DNA sequence of 164,831 bp that contains 35.8% GC. The two inverted repeats (IRa and IRb; 26,606 bp) are spaced by a small single-copy region (22,868 bp) and a large single-copy region (88,751 bp). The chloroplast genome has 131 (113 unique) functional genes, including 86 (79 unique) protein-coding genes, 37 (30 unique) tRNA genes, and eight (four unique) rRNA genes. Tandem repeats comprise the majority of the 43 long repetitive sequences. In addition, 111 simple sequence repeats are present, with mononucleotides being the most common type and di- and tetranucleotides being infrequent events. Positive selection pressure on rps12 in the E. aureum chloroplast has been demonstrated via synonymous and nonsynonymous substitution rates and selection pressure sites analyses. Ycf15 and infA are pseudogenes in this species. We constructed a Maximum Likelihood phylogenetic tree based on the complete chloroplast genomes of 38 species from 13 families. Those results strongly indicated that E. aureum is positioned as the sister of Colocasia esculenta within the Araceae family. This work may provide information for further study of the molecular phylogenetic relationships within Araceae, as well as molecular markers and breeding novel varieties by chloroplast genetic-transformation of E. aureum in particular.
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Affiliation(s)
- Na Tian
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, P.R. China
| | - Limin Han
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, P.R. China
- Department of Bioscience and Biotechnology, Shaanxi Xueqian Normal University, Xi’an, Shaanxi, P.R. China
| | - Chen Chen
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, P.R. China
- Institute of Botany of Shaanxi Province, Xi’an Botanical Garden of Shaanxi Province, Xi’an, Shaanxi, P.R. China
| | - Zhezhi Wang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, P.R. China
- * E-mail:
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10
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Keller J, Rousseau-Gueutin M, Martin GE, Morice J, Boutte J, Coissac E, Ourari M, Aïnouche M, Salmon A, Cabello-Hurtado F, Aïnouche A. The evolutionary fate of the chloroplast and nuclear rps16 genes as revealed through the sequencing and comparative analyses of four novel legume chloroplast genomes from Lupinus. DNA Res 2017; 24:343-358. [PMID: 28338826 PMCID: PMC5737547 DOI: 10.1093/dnares/dsx006] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 02/02/2017] [Indexed: 01/21/2023] Open
Abstract
The Fabaceae family is considered as a model system for understanding chloroplast genome evolution due to the presence of extensive structural rearrangements, gene losses and localized hypermutable regions. Here, we provide sequences of four chloroplast genomes from the Lupinus genus, belonging to the underinvestigated Genistoid clade. Notably, we found in Lupinus species the functional loss of the essential rps16 gene, which was most likely replaced by the nuclear rps16 gene that encodes chloroplast and mitochondrion targeted RPS16 proteins. To study the evolutionary fate of the rps16 gene, we explored all available plant chloroplast, mitochondrial and nuclear genomes. Whereas no plant mitochondrial genomes carry an rps16 gene, many plants still have a functional nuclear and chloroplast rps16 gene. Ka/Ks ratios revealed that both chloroplast and nuclear rps16 copies were under purifying selection. However, due to the dual targeting of the nuclear rps16 gene product and the absence of a mitochondrial copy, the chloroplast gene may be lost. We also performed comparative analyses of lupine plastomes (SNPs, indels and repeat elements), identified the most variable regions and examined their phylogenetic utility. The markers identified here will help to reveal the evolutionary history of lupines, Genistoids and closely related clades.
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Affiliation(s)
- J Keller
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - M Rousseau-Gueutin
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France.,IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, BP35327, 35653 Le Rheu Cedex, France
| | - G E Martin
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398 Montpellier, France
| | - J Morice
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, BP35327, 35653 Le Rheu Cedex, France
| | - J Boutte
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - E Coissac
- Laboratoire d'Ecologie Alpine, CNRS - Université de Grenoble 1 - Université de Savoie, 38041 Grenoble, France
| | - M Ourari
- Département des Sciences Biologiques, Faculté des Sciences de la Nature et de la Vie, Université Abderrahmane Mira, 06000 Bejaia, Algeria
| | - M Aïnouche
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - A Salmon
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - F Cabello-Hurtado
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - A Aïnouche
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
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11
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Asaf S, Khan AL, Aaqil Khan M, Muhammad Imran Q, Kang SM, Al-Hosni K, Jeong EJ, Lee KE, Lee IJ. Comparative analysis of complete plastid genomes from wild soybean (Glycine soja) and nine other Glycine species. PLoS One 2017; 12:e0182281. [PMID: 28763486 PMCID: PMC5538705 DOI: 10.1371/journal.pone.0182281] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/14/2017] [Indexed: 11/19/2022] Open
Abstract
The plastid genomes of different plant species exhibit significant variation, thereby providing valuable markers for exploring evolutionary relationships and population genetics. Glycine soja (wild soybean) is recognized as the wild ancestor of cultivated soybean (G. max), representing a valuable genetic resource for soybean breeding programmes. In the present study, the complete plastid genome of G. soja was sequenced using Illumina paired-end sequencing and then compared it for the first time with previously reported plastid genome sequences from nine other Glycine species. The G. soja plastid genome was 152,224 bp in length and possessed a typical quadripartite structure, consisting of a pair of inverted repeats (IRa/IRb; 25,574 bp) separated by small (178,963 bp) and large (83,181 bp) single-copy regions, with a 51-kb inversion in the large single-copy region. The genome encoded 134 genes, including 87 protein-coding genes, eight ribosomal RNA genes, and 39 transfer RNA genes, and possessed 204 randomly distributed microsatellites, including 15 forward, 25 tandem, and 34 palindromic repeats. Whole-plastid genome comparisons revealed an overall high degree of sequence similarity between G. max and G. gracilis and some divergence in the intergenic spacers of other species. Greater numbers of indels and SNP substitutions were observed compared with G. cyrtoloba. The sequence of the accD gene from G. soja was highly divergent from those of the other species except for G. max and G. gracilis. Phylogenomic analyses of the complete plastid genomes and 76 shared genes yielded an identical topology and indicated that G. soja is closely related to G. max and G. gracilis. The complete G. soja genome sequenced in the present study is a valuable resource for investigating the population and evolutionary genetics of Glycine species and can be used to identify related species.
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Affiliation(s)
- Sajjad Asaf
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Abdul Latif Khan
- Chair of Oman's Medicinal Plants & Marine Natural Products, University of Nizwa, Nizwa, Oman
| | - Muhammad Aaqil Khan
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Qari Muhammad Imran
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Sang-Mo Kang
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Khdija Al-Hosni
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Eun Ju Jeong
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Ko Eun Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
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Marriboina S, Sengupta D, Kumar S, Reddy AR. Physiological and molecular insights into the high salinity tolerance of Pongamia pinnata (L.) pierre, a potential biofuel tree species. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 258:102-111. [PMID: 28330553 DOI: 10.1016/j.plantsci.2017.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 02/15/2017] [Accepted: 02/21/2017] [Indexed: 05/23/2023]
Abstract
Soil salinity is gradually becoming a threat to the global economy by affecting agricultural productivity worldwide. Here, we analyze the salinity tolerance of Pongamia pinnata with an insight into the underlying physiological and molecular responses. Despite a reduction in net photosynthetic rate, P. pinnata efficiently maintained its leaf water potentials even at 500mM NaCl for 15days and displayed no visible stress symptoms. Na+ localization analysis using CoroNa-Green AM revealed effective Na+ sequestration in the roots when compared to leaves. Elemental analysis demonstrated that roots accumulated more of Na+ while K+ content was higher in leaves. At the molecular level, salt stress significantly induced the expression levels of salt overly sensitive1 (SOS1), SOS2, SOS3, high affinity K+ transporter (HKT1), ABA biosynthetic and receptor genes (NCED and PYL4), guaiacol peroxidase (POD) exclusively in roots while tonoplast localized Na+/H+ exchanger (NHX1) was significantly enhanced in leaves. Our results clearly demonstrate that leaves and roots of Pongamia exhibit differential responses under salt stress although roots are more efficient in sequestering the Na+ ions. The present study provides crucial inputs for understanding salt tolerance in a tree species which can be further utilized for developing salt tolerance in higher plants.
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Affiliation(s)
- Sureshbabu Marriboina
- Photosynthesis and Stress Biology Laboratory, Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Debashree Sengupta
- Photosynthesis and Stress Biology Laboratory, Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Sumit Kumar
- Photosynthesis and Stress Biology Laboratory, Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Attipalli R Reddy
- Photosynthesis and Stress Biology Laboratory, Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, India.
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Daniell H, Lin CS, Yu M, Chang WJ. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol 2016; 17:134. [PMID: 27339192 PMCID: PMC4918201 DOI: 10.1186/s13059-016-1004-2] [Citation(s) in RCA: 738] [Impact Index Per Article: 92.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chloroplasts play a crucial role in sustaining life on earth. The availability of over 800 sequenced chloroplast genomes from a variety of land plants has enhanced our understanding of chloroplast biology, intracellular gene transfer, conservation, diversity, and the genetic basis by which chloroplast transgenes can be engineered to enhance plant agronomic traits or to produce high-value agricultural or biomedical products. In this review, we discuss the impact of chloroplast genome sequences on understanding the origins of economically important cultivated species and changes that have taken place during domestication. We also discuss the potential biotechnological applications of chloroplast genomes.
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Affiliation(s)
- Henry Daniell
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, South 40th St, Philadelphia, PA, 19104-6030, USA.
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ming Yu
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, South 40th St, Philadelphia, PA, 19104-6030, USA
| | - Wan-Jung Chang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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