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Fang J, Lin A, Yan H, Feng L, Lin S, Mason P, Zhou L, Xu X, Zhao K, Huang Y, Henry RJ. Cytoplasmic genomes of Jasminum sambac reveal divergent sub-mitogenomic conformations and a large nuclear chloroplast-derived insertion. BMC PLANT BIOLOGY 2024; 24:861. [PMID: 39272034 PMCID: PMC11401388 DOI: 10.1186/s12870-024-05557-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 08/30/2024] [Indexed: 09/15/2024]
Abstract
BACKGROUND Jasminum sambac, a widely recognized ornamental plant prized for its aromatic blossoms, exhibits three flora phenotypes: single-petal ("SP"), double-petal ("DP"), and multi-petal ("MP"). The lack of detailed characterization and comparison of J. sambac mitochondrial genomes (mitogenomes) hinders the exploration of the genetic and structural diversity underlying the varying floral phenotypes in jasmine accessions. RESULTS Here, we de novo assembled three mitogenomes of typical phenotypes of J. sambac, "SP", "DP", and "MP-hutou" ("HT"), with PacBio reads and the "HT" chloroplast (cp) genome with Illumina reads, and verified them with read mapping and fluorescence in situ hybridization (FISH). The three mitogenomes present divergent sub-genomic conformations, with two, two, and four autonomous circular chromosomes ranging in size from 35.7 kb to 405.3 kb. Each mitogenome contained 58 unique genes. Ribosome binding sites with conserved AAGAAx/AxAAAG motifs were detected upstream of uncanonical start codons TTG, CTG and GTG. The three mitogenomes were similar in genomic content but divergent in structure. The structural variations were mainly attributed to recombination mediated by a large (~ 5 kb) forward repeat pair and several short repeats. The three jasmine cp. genomes showed a well-conserved structure, apart from a 19.9 kb inversion in "HT". We identified a 14.3 kb "HT"-specific insertion on Chr7 of the "HT" nuclear genome, consisting of two 7 kb chloroplast-derived fragments with two intact ndhH and rps15 genes, further validated by polymerase chain reaction (PCR). The well-resolved phylogeny suggests faster mitogenome evolution in J. sambac compared to other Oleaceae species and outlines the mitogenome evolutionary trajectories within Lamiales. All evidence supports that "DP" and "HT" evolved from "SP", with "HT" being the most recent derivative of "DP". CONCLUSION The comprehensive characterization of jasmine organelle genomes has added to our knowledge of the structural diversity and evolutionary trajectories behind varying jasmine traits, paving the way for in-depth exploration of mechanisms and targeted genetic research.
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Affiliation(s)
- Jingping Fang
- College of Life Science, Fujian Normal University, Fuzhou, China.
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia.
| | - Aiting Lin
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hansong Yan
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liqing Feng
- College of Life Science, Fujian Normal University, Fuzhou, China
- Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, China
| | - Shaoqing Lin
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Patrick Mason
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Linwei Zhou
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Xiuming Xu
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kai Zhao
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Yongji Huang
- Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, China.
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia.
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Wang J, Kan S, Kong J, Nie L, Fan W, Ren Y, Reeve W, Mower JP, Wu Z. Accumulation of Large Lineage-Specific Repeats Coincides with Sequence Acceleration and Structural Rearrangement in Plantago Plastomes. Genome Biol Evol 2024; 16:evae177. [PMID: 39190481 PMCID: PMC11354287 DOI: 10.1093/gbe/evae177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2024] [Indexed: 08/29/2024] Open
Abstract
Repeats can mediate rearrangements and recombination in plant mitochondrial genomes and plastid genomes. While repeat accumulations are linked to heightened evolutionary rates and complex structures in specific lineages, debates persist regarding the extent of their influence on sequence and structural evolution. In this study, 75 Plantago plastomes were analyzed to investigate the relationships between repeats, nucleotide substitution rates, and structural variations. Extensive repeat accumulations were associated with significant rearrangements and inversions in the large inverted repeats (IRs), suggesting that repeats contribute to rearrangement hotspots. Repeats caused infrequent recombination that potentially led to substoichiometric shifting, supported by long-read sequencing. Repeats were implicated in elevating evolutionary rates by facilitating localized hypermutation, likely through DNA damage and repair processes. This study also observed a decrease in nucleotide substitution rates for loci translocating into IRs, supporting the role of biased gene conversion in maintaining lower substitution rates. Combined with known parallel changes in mitogenomes, it is proposed that potential dysfunction in nuclear-encoded genes associated with DNA replication, recombination, and repair may drive the evolution of Plantago organellar genomes. These findings contribute to understanding how repeats impact organellar evolution and stability, particularly in rapidly evolving plant lineages.
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Affiliation(s)
- Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Perth, WA 6150, Australia
- College of Environmental and Life Sciences, Murdoch University, Perth, WA 6150, Australia
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Marine College, Shandong University, Weihai 264209, China
| | - Jiali Kong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Liyun Nie
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Perth, WA 6150, Australia
| | - Weishu Fan
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yonglin Ren
- College of Environmental and Life Sciences, Murdoch University, Perth, WA 6150, Australia
| | - Wayne Reeve
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Perth, WA 6150, Australia
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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Jiang C, Zhao G, Wang H, Zheng W, Zhang R, Wang L, Zheng Z. Comparative genomics analysis and transposon mutagenesis provides new insights into high menaquinone-7 biosynthetic potential of Bacillus subtilis natto. Gene 2024; 907:148264. [PMID: 38346457 DOI: 10.1016/j.gene.2024.148264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/15/2024]
Abstract
This research combined Whole-Genome sequencing, intraspecific comparative genomics and transposon mutagenesis to investigate the menaquinone-7 (MK-7) synthesis potential in Bacillus subtilis natto. First, Whole-Genome sequencing showed that Bacillus subtilis natto BN-P15-11-1 contains one single circular chromosome in size of 3,982,436 bp with a GC content of 43.85 %, harboring 4,053 predicted coding genes. Next, the comparative genomics analysis among strain BN-P15-11-1 with model Bacillus subtilis 168 and four typical Bacillus subtilis natto strains proves that the closer evolutionary relationship Bacillus subtilis natto BN-P15-11-1 and Bacillus subtilis 168 both exhibit strong biosynthetic potential. To further dig for MK-7 biosynthesis latent capacity of BN-P15-11-1, we constructed a mutant library using transposons and a high throughput screening method using microplates. We obtained a YqgQ deficient high MK-7 yield strain F4 with a yield 3.02 times that of the parent strain. Experiments also showed that the high yield mutants had defects in different transcription and translation regulatory factor genes, indicating that regulatory factor defects may affect the biosynthesis and accumulation of MK-7 by altering the overall metabolic level. The findings of this study will provide more novel insights on the precise identification and rational utilization of the Bacillus subtilis subspecies for biosynthesis latent capacity.
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Affiliation(s)
- Chunxu Jiang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China; University of Science and Technology of China, Hefei, Anhui, PR China
| | - Genhai Zhao
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China
| | - Han Wang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China
| | - Wenqian Zheng
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China; University of Science and Technology of China, Hefei, Anhui, PR China
| | - Rui Zhang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China
| | - Li Wang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China.
| | - Zhiming Zheng
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China.
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Cai Q, Feng S, Zheng X. The complete chloroplast genome of Aristolochia fangchi provided insights into the phylogeny and species identification of Aristolochia. Genome 2024; 67:90-98. [PMID: 38091583 DOI: 10.1139/gen-2023-0068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Aristolochia fangchi is an important species within the family Aristolochiaceae, most of which contain nephrotoxic aristolochic acid. The inadvertent use of Aristolochiaceae plants as raw ingredients in the manufacturing of patent medicine poses a significant risk warranting considerable attention. In this study, we assembled and analyzed the complete chloroplast genome of Aristolochia fangchi, which is a 159 867 bp long circular molecule. Functional annotation of the A. fangchi plastome unveiled a total of 113 genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Subsequently, a series of genome structure and characteristic evaluations were conducted against the A. fangchi plastome. Further phylogenetic analysis suggested that a plausible phylogenetic relationship among Aristolochiaceae derived from the concatenated sequences of shared conserved genes rather than from the entire chloroplast genome with one IR copy. Finally, a DNA polymorphism assessment against a dozen Aristolochia plastomes yielded multiple potential regions for biomarker designation. Six pairs of primers were generated and underwent both in silico and actual PCR validations. In conclusion, this study identified the unique characteristics of the A. fangchi plastome, providing invaluable insights for further investigations on species identification and the phylogeny evolution between A. fangchi and its related species.
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Affiliation(s)
- Qingqun Cai
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- Guangdong Clinical Research Academy of Chinese Medicine, Guangzhou 510405, China
| | - Shiyin Feng
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- Guangdong Clinical Research Academy of Chinese Medicine, Guangzhou 510405, China
| | - Xiasheng Zheng
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
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Brito JBP, Antunes AM, Ferreira RDSB, de Campos Telles MP, Targueta CP, Soares TN. Complete Chloroplast Genomes of Pterodon emarginatus Vogel and Pterodon pubescens Benth: Comparative and Phylogenetic Analyses. Curr Genomics 2023; 24:236-249. [PMID: 38169762 PMCID: PMC10758126 DOI: 10.2174/0113892029244147231016050434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/03/2023] [Accepted: 07/17/2023] [Indexed: 01/05/2024] Open
Abstract
Background The species Pterodon emarginatus and P. pubescens, popularly known as white sucupira or faveira, are native to the Cerrado biome and have the potential for medicinal use and reforestation. They are sister species with evolutionary proximity. Objective Considering that the chloroplast genome exhibits a conserved structure and genes, the analysis of its sequences can contribute to the understanding of evolutionary, phylogenetic, and diversity issues. Methods The chloroplast genomes of P. emarginatus and P. pubescens were sequenced on the Illumina MiSeq platform. The genomes were assembled based on the de novo strategy. We performed the annotation of the genes and the repetitive regions of the genomes. The nucleotide diversity and phylogenetic relationships were analyzed using the gene sequences of these species and others of the Leguminosae family, whose genomes are available in databases. Results The complete chloroplast genome of P. emarginatus is 159,877 bp, and that of P. pubescens is 159,873 bp. The genomes of both species have circular and quadripartite structures. A total of 127 genes were predicted in both species, including 110 single-copy genes and 17 duplicated genes in the inverted regions. 141 microsatellite regions were identified in P. emarginatus and 140 in P. pubescens. The nucleotide diversity estimates of the gene regions in twenty-one species of the Leguminosae family were 0.062 in LSC, 0.086 in SSC, and 0.036 in IR. The phylogenetic analysis demonstrated the proximity between the genera Pterodon and Dipteryx, both from the clade Dipterygeae. Ten pairs of primers with potential for the development of molecular markers were designed. Conclusion The genetic information obtained on the chloroplast genomes of P. emarginatus and P. pubescens presented here reinforces the similarity and evolutionary proximity between these species, with a similarity percentage of 99.8%.
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Affiliation(s)
- Juliana Borges Pereira Brito
- Laboratory of Genetics and Biodiversity, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, CEP: 74001-970 Brazil
- Postgraduate Program in Genetics and Plant Breeding, School of Agronomy, Federal University of Goiás, Goiânia, Goiás , Brazil
| | - Adriana Maria Antunes
- Laboratory of Genetics and Biodiversity, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, CEP: 74001-970 Brazil
- Postgraduate Program in Genetics and Plant Breeding, School of Agronomy, Federal University of Goiás, Goiânia, Goiás , Brazil
| | - Ramilla dos Santos Braga Ferreira
- Laboratory of Genetics and Biodiversity, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, CEP: 74001-970 Brazil
| | - Mariana Pires de Campos Telles
- Laboratory of Genetics and Biodiversity, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, CEP: 74001-970 Brazil
- School of Medical and Life Sciences, Pontifical Catholic University of Goiás, Goiânia, Goiás, CEP: 74605-010 Brazil
| | - Cintia Pelegrineti Targueta
- Laboratory of Genetics and Biodiversity, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, CEP: 74001-970 Brazil
| | - Thannya Nascimento Soares
- Laboratory of Genetics and Biodiversity, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, CEP: 74001-970 Brazil
- Postgraduate Program in Genetics and Plant Breeding, School of Agronomy, Federal University of Goiás, Goiânia, Goiás , Brazil
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Raman G, Choi KS, Lee EM, Morden CW, Shim H, Kang JS, Yang TJ, Park S. Extensive characterization of 28 complete chloroplast genomes of Hydrangea species: A perspective view of their organization and phylogenetic and evolutionary relationships. Comput Struct Biotechnol J 2023; 21:5073-5091. [PMID: 37867966 PMCID: PMC10589384 DOI: 10.1016/j.csbj.2023.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023] Open
Abstract
The tribe Hydrangeeae displays a unique, distinctive disjunct distribution encompassing East Asia, North America and Hawaii. Despite its complex trait variations and polyphyletic nature, comprehensive phylogenomic and biogeographical studies on this tribe have been lacking. To address this gap, we sequenced and characterized 28 plastomes of Hydrangeeae. Our study highlights the highly conserved nature of Hydrangeaceae chloroplast (cp) genomes in terms of gene content and arrangement. Notably, synapomorphic characteristics of tandem repeats in the conserved domain of accD were observed in the Macrophyllae, Chinenses, and Dichroa sections within the Hydrangeeae tribe. Additionally, we found lower expression of accD in these sections using structure prediction and quantitative real-time PCR analysis. Phylogenomic analyses revealed the subdivision of the Hydrangeeae tribe into two clades with robust support values. Consistent with polyphyletic relationships, sect. Broussaisia was identified as the basal group in the tribe Hydrangeeae. Our study also provides insights into the phylogenetic relationships of Hydrangea petiolaris in the Jeju and Ulleung Island populations, suggesting the need for further studies with more samples and molecular data. Divergence time estimation and biogeographical analyses suggested that the common ancestors of the tribe Hydrangeeae likely originated from North America and East Asia during the Paleocene period via the Bering Land Bridge, potentially facilitating migration within the tribe between these regions. In conclusion, this study enhances our understanding of the evolutionary history and biogeography of the tribe Hydrangeeae, shedding light on the dispersal patterns and origins of this intriguing plant group with its unique disjunct distribution.
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Affiliation(s)
- Gurusamy Raman
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
| | - Kyoung-Su Choi
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
- Plant Research Team, Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - Eun Mi Lee
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
| | - Clifford W. Morden
- School of Life Sciences, University of Hawai]i at Mānoa, Honolulu, HI, USA
| | - Hyeonah Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jong-Soo Kang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
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Tan F, Li W, Feng H, Huang Y, Banerjee AK. Interspecific variation and phylogenetic relationship between mangrove and non-mangrove species of a same family (Meliaceae)-insights from comparative analysis of complete chloroplast genome. PeerJ 2023; 11:e15527. [PMID: 37397021 PMCID: PMC10309054 DOI: 10.7717/peerj.15527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 05/19/2023] [Indexed: 07/04/2023] Open
Abstract
The mahogany family, Meliaceae, contains 58 genera with only one mangrove genus: Xylocarpus. Two of the three species of the genus Xylocarpus are true mangroves (X. granatum and X. moluccensis), and one is a non-mangrove (X. rumphii). In order to resolve the phylogenetic relationship between the mangrove and non-mangrove species, we sequenced chloroplast genomes of these Xylocarpus species along with two non-mangrove species of the Meliaceae family (Carapa guianensis and Swietenia macrophylla) and compared the genome features and variations across the five species. The five Meliaceae species shared 130 genes (85 protein-coding genes, 37 tRNA, and eight rRNA) with identical direction and order, with a few variations in genes and intergenic spacers. The repetitive sequences identified in the rpl22 gene region only occurred in Xylocarpus, while the repetitive sequences in accD were found in X. moluccensis and X. rumphii. The TrnH-GUG and rpl32 gene regions and four non-coding gene regions showed high variabilities between X. granatum and the two non-mangrove species (S. macrophylla and C. guianensis). In addition, among the Xylocarpus species, only two genes (accD and clpP) showed positive selection. Carapa guianensis and S. macrophylla owned unique RNA editing sites. The above genes played an important role in acclimation to different stress factors like heat, low temperature, high UV light, and high salinity. Phylogenetic analysis with 22 species in the order Sapindales supported previous studies, which revealed that the non-mangrove species X. rumphii is closer to X. moluccensis than X. granatum. Overall, our results provided important insights into the variation of genetic structure and adaptation mechanism at interspecific (three Xylocarpus species) and intergeneric (mangrove and non-mangrove genera) levels.
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Affiliation(s)
- Fengxiao Tan
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Guangdong, China
| | - Weixi Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Hui Feng
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yelin Huang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
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Ahmad W, Asaf S, Al-Rawahi A, Al-Harrasi A, Khan AL. Comparative plastome genomics, taxonomic delimitation and evolutionary divergences of Tetraena hamiensis var. qatarensis and Tetraena simplex (Zygophyllaceae). Sci Rep 2023; 13:7436. [PMID: 37156827 PMCID: PMC10167353 DOI: 10.1038/s41598-023-34477-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 05/02/2023] [Indexed: 05/10/2023] Open
Abstract
The Zygophyllum and Tetraena genera are intriguingly important ecologically and medicinally. Based on morphological characteristics, T. hamiensis var. qatarensis, and T. simplex were transferred from Zygophyllum to Tetraena with the least genomic datasets available. Hence, we sequenced the T. hamiensis and T. simplex and performed in-depth comparative genomics, phylogenetic analysis, and estimated time divergences. The complete plastomes ranged between 106,720 and 106,446 bp-typically smaller than angiosperms plastomes. The plastome circular genomes are divided into large single-copy regions (~ 80,964 bp), small single-copy regions (~ 17,416 bp), and two inverted repeats regions (~ 4170 bp) in both Tetraena species. An unusual shrinkage of IR regions 16-24 kb was identified. This resulted in the loss of 16 genes, including 11 ndh genes which encode the NADH dehydrogenase subunits, and a significant size reduction of Tetraena plastomes compared to other angiosperms. The inter-species variations and similarities were identified using genome-wide comparisons. Phylogenetic trees generated by analyzing the whole plastomes, protein-coding genes, matK, rbcL, and cssA genes exhibited identical topologies, indicating that both species are sisters to the genus Tetraena and may not belong to Zygophyllum. Similarly, based on the entire plastome and proteins coding genes datasets, the time divergence of Zygophyllum and Tetraena was 36.6 Ma and 34.4 Ma, respectively. Tetraena stem ages were 31.7 and 18.2 Ma based on full plastome and protein-coding genes. The current study presents the plastome as a distinguishing and identification feature among the closely related Tetraena and Zygophyllum species. It can be potentially used as a universal super-barcode for identifying plants.
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Affiliation(s)
- Waqar Ahmad
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman
| | - Sajjad Asaf
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman
| | - Ahmed Al-Rawahi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman.
| | - Abdul Latif Khan
- Department of Engineering Technology, University of Houston, Sugar Land, TX, 77479, USA.
- Department of Biology and Biochemistry, University of Houston, Houston, USA.
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Zhai Y, Zhang T, Guo Y, Gao C, Zhou L, Feng L, Zhou T, Xumei W. Phylogenomics, phylogeography and germplasms authentication of the Rheum palmatum complex based on complete chloroplast genomes. JOURNAL OF PLANT RESEARCH 2023; 136:291-304. [PMID: 36808315 DOI: 10.1007/s10265-023-01440-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
As a traditional Chinese medicine, rhubarb is used to treat several diseases such as severe acute pancreatitis, sepsis and chronic renal failure. However, few studies focused on the authentication of germplasm for the Rheum palmatum complex, and no studies have been conducted to elucidate the evolutionary history of the R. palmatum complex using plastome datasets. Hence, we aim to develop the potential molecular markers to identify the elite germplasms of rhubarb and explore the divergence and biogeographic history of the R. palmatum complex based on the newly sequenced chloroplast genome datasets. Chloroplast genomes of thirty-five the R. palmatum complex germplasms were sequenced, and the length ranged from 160,858 to 161,204 bp. The structure, gene content and gene order were highly conserved across all genomes. Eight InDels and sixty-one SNPs loci could be used to authenticate the high-quality germplasms of rhubarb in specific areas. Phylogenetic analysis revealed that all rhubarb germplasms were clustered in the same clade with high bootstrap support values and Bayesian posterior probabilities. According to the molecular dating result, the intraspecific divergence of the complex occurred in the Quaternary, which might be affected by climatic fluctuation. The biogeography reconstruction indicated that the ancestor of the R. palmatum complex might originate from the Himalaya-Hengduan Mountains or/and Bashan-Qinling Mountains, and then spread to surrounding areas. Several useful molecular markers were developed to identify rhubarb germplasms, and our study will provide further understanding on speciation, divergence and biogeography of the R. palmatum complex.
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Affiliation(s)
- Yunyan Zhai
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Tianyi Zhang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yanbing Guo
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Chenxi Gao
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Lipan Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Li Feng
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Wang Xumei
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
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Li ZZ, Lehtonen S, Chen JM. The dynamic history of plastome structure across aquatic subclass Alismatidae. BMC PLANT BIOLOGY 2023; 23:125. [PMID: 36869282 PMCID: PMC9985265 DOI: 10.1186/s12870-023-04125-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND The rapidly increasing availability of complete plastomes has revealed more structural complexity in this genome under different taxonomic levels than expected, and this complexity provides important evidence for understanding the evolutionary history of angiosperms. To explore the dynamic history of plastome structure across the subclass Alismatidae, we sampled and compared 38 complete plastomes, including 17 newly assembled, representing all 12 recognized families of Alismatidae. RESULT We found that plastomes size, structure, repeat elements, and gene content were highly variable across the studied species. Phylogenomic relationships among families were reconstructed and six main patterns of variation in plastome structure were revealed. Among these, the inversion from rbcL to trnV-UAC (Type I) characterized a monophyletic lineage of six families, but independently occurred also in Caldesia grandis. Three independent ndh gene loss events were uncovered across the Alismatidae. In addition, we detected a positive correlation between the number of repeat elements and the size of plastomes and IR in Alismatidae. CONCLUSION In our study, ndh complex loss and repeat elements likely contributed to the size of plastomes in Alismatidae. Also, the ndh loss was more likely related to IR boundary changes than the adaptation of aquatic habits. Based on existing divergence time estimation, the Type I inversion may have occurred during the Cretaceous-Paleogene in response to the extreme paleoclimate changes. Overall, our findings will not only allow exploring the evolutionary history of Alismatidae plastome, but also provide an opportunity to test if similar environmental adaptations result in convergent restructuring in plastomes.
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Affiliation(s)
- Zhi-Zhong Li
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Samuli Lehtonen
- Herbarium, Biodiversity Unit, University of Turku, Turku, 20014, Finland.
| | - Jin-Ming Chen
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
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11
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Wang N, Chen S, Xie L, Wang L, Feng Y, Lv T, Fang Y, Ding H. The complete chloroplast genomes of three Hamamelidaceae species: Comparative and phylogenetic analyses. Ecol Evol 2022; 12:e8637. [PMID: 35222983 PMCID: PMC8848467 DOI: 10.1002/ece3.8637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/10/2022] [Accepted: 01/27/2022] [Indexed: 11/07/2022] Open
Abstract
Hamamelidaceae is an important group that represents the origin and early evolution of angiosperms. Its plants have many uses, such as timber, medical, spice, and ornamental uses. In this study, the complete chloroplast genomes of Loropetalum chinense (R. Br.) Oliver, Corylopsis glandulifera Hemsl., and Corylopsis velutina Hand.-Mazz. were sequenced using the Illumina NovaSeq 6000 platform. The sizes of the three chloroplast genomes were 159,402 bp (C. glandulifera), 159,414 bp (C. velutina), and 159,444 bp (L. chinense), respectively. These chloroplast genomes contained typical quadripartite structures with a pair of inverted repeat (IR) regions (26,283, 26,283, and 26,257 bp), a large single-copy (LSC) region (88,134, 88,146, and 88,160 bp), and a small single-copy (SSC) region (18,702, 18,702, and 18,770 bp). The chloroplast genomes encoded 132-133 genes, including 85-87 protein-coding genes, 37-38 tRNA genes, and 8 rRNA genes. The coding regions were composed of 26,797, 26,574, and 26,415 codons, respectively, most of which ended in A/U. A total of 37-43 long repeats and 175-178 simple sequence repeats (SSRs) were identified, and the SSRs contained a higher number of A + T than G + C bases. The genome comparison showed that the IR regions were more conserved than the LSC or SSC regions, while the noncoding regions contained higher variability than the gene coding regions. Phylogenetic analyses revealed that species in the same genus tended to cluster together. Chunia Hung T. Chang, Mytilaria Lecomte, and Disanthus Maxim. may have diverged early and Corylopsis Siebold & Zucc. was closely related to Loropetalum R. Br. This study provides valuable information for further species identification, evolution, and phylogenetic studies of Hamamelidaceae plants.
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Affiliation(s)
- NingJie Wang
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaCollege of Biology and the EnvironmentKey Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationNanjing Forestry UniversityNanjingChina
| | - ShuiFei Chen
- Research Center for Nature Conservation and BiodiversityState Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi MountainsState Environmental Protection Key Laboratory on BiosafetyNanjing Institute of Environmental Sciences, Ministry of Ecology and EnvironmentNanjingChina
| | - Lei Xie
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaCollege of Biology and the EnvironmentKey Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationNanjing Forestry UniversityNanjingChina
| | - Lu Wang
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaCollege of Biology and the EnvironmentKey Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationNanjing Forestry UniversityNanjingChina
| | - YueYao Feng
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaCollege of Biology and the EnvironmentKey Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationNanjing Forestry UniversityNanjingChina
| | - Ting Lv
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaCollege of Biology and the EnvironmentKey Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationNanjing Forestry UniversityNanjingChina
| | - YanMing Fang
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaCollege of Biology and the EnvironmentKey Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationNanjing Forestry UniversityNanjingChina
| | - Hui Ding
- Research Center for Nature Conservation and BiodiversityState Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi MountainsState Environmental Protection Key Laboratory on BiosafetyNanjing Institute of Environmental Sciences, Ministry of Ecology and EnvironmentNanjingChina
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12
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Hsieh CL, Yu CC, Huang YL, Chung KF. Mahonia vs. Berberis Unloaded: Generic Delimitation and Infrafamilial Classification of Berberidaceae Based on Plastid Phylogenomics. FRONTIERS IN PLANT SCIENCE 2022; 12:720171. [PMID: 35069611 PMCID: PMC8770955 DOI: 10.3389/fpls.2021.720171] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 10/15/2021] [Indexed: 05/12/2023]
Abstract
The early-diverging eudicot family Berberidaceae is composed of a morphologically diverse assemblage of disjunctly distributed genera long praised for their great horticultural and medicinal values. However, despite century-long studies, generic delimitation of Berberidaceae remains controversial and its tribal classification has never been formally proposed under a rigorous phylogenetic context. Currently, the number of accepted genera in Berberidaceae ranges consecutively from 13 to 19, depending on whether to define Berberis, Jeffersonia, and Podophyllum broadly, or to segregate these three genera further and recognize Alloberberis, Mahonia, and Moranothamnus, Plagiorhegma, and Dysosma, Diphylleia, and Sinopodophyllum, respectively. To resolve Berberidaceae's taxonomic disputes, we newly assembled 23 plastomes and, together with 85 plastomes from the GenBank, completed the generic sampling of the family. With 4 problematic and 14 redundant plastome sequences excluded, robust phylogenomic relationships were reconstructed based on 93 plastomes representing all 19 genera of Berberidaceae and three outgroups. Maximum likelihood phylogenomic relationships corroborated with divergence time estimation support the recognition of three subfamilies Berberidoideae, Nandinoideae, and Podophylloideae, with tribes Berberideae and Ranzanieae, Leonticeae and Nandineae, and Podophylleae, Achlydeae, Bongardieae tr. nov., Epimedieae, and Jeffersonieae tr. nov. in the former three subfamilies, respectively. By applying specifically stated criteria, our phylogenomic data also support the classification of 19 genera, recognizing Alloberberis, Mahonia, and Moranothamnus, Plagiorhegma, and Diphylleia, Dysosma, and Sinopodophyllum that are morphologically and evolutionarily distinct from Berberis, Jeffersonia, and Podophyllum, respectively. Comparison of plastome structures across Berberidaceae confirms inverted repeat expansion in the tribe Berberideae and reveals substantial length variation in accD gene caused by repeated sequences in Berberidoideae. Comparison of plastome tree with previous studies and nuclear ribosomal DNA (nrDNA) phylogeny also reveals considerable conflicts at different phylogenetic levels, suggesting that incomplete lineage sorting and/or hybridization had occurred throughout the evolutionary history of Berberidaceae and that Alloberberis and Moranothamnus could have resulted from reciprocal hybridization between Berberis and Mahonia in ancient times prior to the radiations of the latter two genera.
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Affiliation(s)
- Chia-Lun Hsieh
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chih-Chieh Yu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
| | - Yu-Lan Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Kuo-Fang Chung
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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13
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Lee SH, Kim J, Park HS, Koo H, Waminal NE, Pellerin RJ, Shim H, Lee HO, Kim E, Park JY, Yu HS, Kim HH, Lee J, Yang TJ. Genome structure and diversity among Cynanchum wilfordii accessions. BMC PLANT BIOLOGY 2022; 22:4. [PMID: 34979940 PMCID: PMC8722063 DOI: 10.1186/s12870-021-03390-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/06/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Cynanchum wilfordii (Cw) and Cynanchum auriculatum (Ca) have long been used in traditional medicine and as functional food in Korea and China, respectively. They have diverse medicinal functions, and many studies have been conducted, including pharmaceutical efficiency and metabolites. Especially, Cw is regarded as the most famous medicinal herb in Korea due to its menopausal symptoms relieving effect. Despite the high demand for Cw in the market, both species are cultivated using wild resources with rare genomic information. RESULTS We collected 160 Cw germplasm from local areas of Korea and analyzed their morphological diversity. Five Cw and one Ca of them, which were morphologically diverse, were sequenced, and nuclear ribosomal DNA (nrDNA) and complete plastid genome (plastome) sequences were assembled and annotated. We investigated the genomic characteristics of Cw as well as the genetic diversity of plastomes and nrDNA of Cw and Ca. The Cw haploid nuclear genome was approximately 178 Mbp. Karyotyping revealed the juxtaposition of 45S and 5S nrDNA on one of 11 chromosomes. Plastome sequences revealed 1226 interspecies polymorphisms and 11 Cw intraspecies polymorphisms. The 160 Cw accessions were grouped into 21 haplotypes based on seven plastome markers and into 108 haplotypes based on seven nuclear markers. Nuclear genotypes did not coincide with plastome haplotypes that reflect the frequent natural outcrossing events. CONCLUSIONS Cw germplasm had a huge morphological diversity, and their wide range of genetic diversity was revealed through the investigation with 14 molecular markers. The morphological and genomic diversity, chromosome structure, and genome size provide fundamental genomic information for breeding of undomesticated Cw plants.
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Affiliation(s)
- Sae Hyun Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jiseok Kim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hyun-Seung Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - HyunJin Koo
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Nomar Espinosa Waminal
- Department of Life Sciences, Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Remnyl Joyce Pellerin
- Department of Life Sciences, Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Hyeonah Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hyun-Oh Lee
- Phyzen Genomics Institute, Seongnam, 13558, Republic of Korea
| | - Eunbi Kim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jee Young Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hong Seob Yu
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hyun Hee Kim
- Department of Life Sciences, Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Jeonghoon Lee
- National Institute of Horticultural and Herbal Science, RDA, Eumseong, 27709, Republic of Korea
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
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14
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Asaf S, Khan AL, Jan R, Khan A, Khan A, Kim KM, Lee IJ. The dynamic history of gymnosperm plastomes: Insights from structural characterization, comparative analysis, phylogenomics, and time divergence. THE PLANT GENOME 2021; 14:e20130. [PMID: 34505399 DOI: 10.1002/tpg2.20130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/08/2021] [Indexed: 05/25/2023]
Abstract
Gymnosperms are among the most endangered groups of plant species; they include ginkgo, pines (Conifers I), cupressophytes (Conifers II), cycads, and gnetophytes. The relationships among the five extant gymnosperm groups remain equivocal. We analyzed 167 available gymnosperm plastomes and investigated their diversity and phylogeny. We found that plastome size, structure, and gene order were highly variable in the five gymnosperm groups, of which Parasitaxus usta (Vieill.) de Laub. and Macrozamia mountperriensis F.M.Bailey had the smallest and largest plastomes, respectively. The inverted repeats (IRs) of the five groups were shown to have evolved through distinctive evolutionary scenarios. The IRs have been lost in all conifers but retained in cycads and gnetophytes. A positive association between simple sequence repeat (SSR) abundance and plastome size was observed, and the SSRs with the most variation were found in Pinaceae. Furthermore, the number of repeats was negatively correlated with IR length; thus, the highest number of repeats was detected in Conifers I and II, in which the IRs had been lost. We constructed a phylogeny based on 29 shared genes from 167 plastomes. With the plastome tree and 13 calibrations, we estimated the tree height between present-day angiosperms and gymnosperms to be ∼380 million years ago (mya). The placement of Gnetales in the tree agreed with the Gnetales-other gymnosperms hypothesis. The divergence between Ginkgo and cycads was estimated as ∼284 mya; the crown age of the cycads was 251 mya. Our time-calibrated plastid-based phylogenomic tree provides a framework for comparative studies of gymnosperm evolution.
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Affiliation(s)
- Sajjad Asaf
- Natural and Medical Sciences Research Center, Univ. of Nizwa, Nizwa, 616, Oman
| | - Abdul Latif Khan
- Dep. of Biotechnology, College of Technology, Univ. of Houston, Houston, TX, 77204, USA
| | - Rahmatullah Jan
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life Science, Kyungpook National Univ., Daegu, 41566, Republic of Korea
| | - Arif Khan
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord Univ., Bodø, 8049, Norway
| | - Adil Khan
- Institute of Genomics for Crop Abiotic Stress Tolerance, Dep. of Plant and Soil Science, Texas Tech Univ., Lubbock, TX, 79409, USA
| | - Kyung-Min Kim
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life Science, Kyungpook National Univ., Daegu, 41566, Republic of Korea
| | - In-Jung Lee
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life Science, Kyungpook National Univ., Daegu, 41566, Republic of Korea
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15
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Abdullah, Henriquez CL, Croat TB, Poczai P, Ahmed I. Mutational Dynamics of Aroid Chloroplast Genomes II. Front Genet 2021; 11:610838. [PMID: 33552129 PMCID: PMC7854696 DOI: 10.3389/fgene.2020.610838] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/16/2020] [Indexed: 01/30/2023] Open
Abstract
The co-occurrence among single nucleotide polymorphisms (SNPs), insertions-deletions (InDels), and oligonucleotide repeats has been reported in prokaryote, eukaryote, and chloroplast genomes. Correlations among SNPs, InDels, and repeats have been investigated in the plant family Araceae previously using pair-wise sequence alignments of the chloroplast genomes of two morphotypes of one species, Colocasia esculenta belonging to subfamily Aroideae (crown group), and four species from the subfamily Lemnoideae, a basal group. The family Araceae is a large family comprising 3,645 species in 144 genera, grouped into eight subfamilies. In the current study, we performed 34 comparisons using 27 species from 7 subfamilies of Araceae to determine correlation coefficients among the mutational events at the family, subfamily, and genus levels. We express strength of the correlations as: negligible or very weak (0.10–0.19), weak (0.20–0.29), moderate (0.30–0.39), strong (0.40–0.69), very strong (0.70–0.99), and perfect (1.00). We observed strong/very strong correlations in most comparisons, whereas a few comparisons showed moderate correlations. The average correlation coefficient was recorded as 0.66 between “SNPs and InDels,” 0.50 between “InDels and repeats,” and 0.42 between “SNPs and repeats.” In qualitative analyses, 95–100% of the repeats at family and sub-family level, while 36–86% of the repeats at genus level comparisons co-occurred with SNPs in the same bins. Our findings show that such correlations among mutational events exist throughout Araceae and support the hypothesis of distribution of oligonucleotide repeats as a proxy for mutational hotspots.
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Affiliation(s)
- Abdullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Claudia L Henriquez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | | | - Peter Poczai
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, Pakistan
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16
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Wu CS, Sudianto E, Hung YM, Wang BC, Huang CJ, Chen CT, Chaw SM. Genome skimming and exploration of DNA barcodes for Taiwan endemic cypresses. Sci Rep 2020; 10:20650. [PMID: 33244113 PMCID: PMC7693304 DOI: 10.1038/s41598-020-77492-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 09/16/2020] [Indexed: 11/23/2022] Open
Abstract
Cypresses are characterized by their longevity and valuable timber. In Taiwan, two endemic cypress species, Chamaecyparis formosensis and C. obtusa var. formosana, are threatened by prevalent illegal logging. A DNA barcode system is urgently needed for reforestation and conservation of these two cypresses. In this study, both plastomes and 35S rDNAs from 16, 10, and 6 individuals of C. formosensis, C. obtusa var. formosana, and C. obtusa var. obtusa were sequenced, respectively. We show that the loss of plastid trnT-GGU readily distinguishes C. formosensis from its congeneric species. We demonstrate that entire sequences of plastomes or 35S rDNAs are capable of correctly identifying cypress species and varieties, suggesting that they are effective super-barcodes. We also discover three short hypervariable loci (i.e., 3′ETS, ITS1, and trnH-psbA) that are promising barcodes for identifying cypress species and varieties. Moreover, nine species-specific indels of > 100 bp were detected in the cypress plastomes. These indels, together with the three aforementioned short barcodes, constitute an alternative and powerful barcode system crucial for identifying specimens that are fragmentary or contain degraded/poor DNA. Our sequenced data and barcode systems not only enrich the genetic reference for cypresses, but also contribute to future reforestation, conservation, and forensic investigations.
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Affiliation(s)
- Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Edi Sudianto
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Yu-Mei Hung
- Department of Forensic Science Investigation Bureau, Ministry of Justice, New Taipei City, 231209, Taiwan
| | - Bo-Cyun Wang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chiun-Jr Huang
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, 10617, Taiwan
| | - Chi-Tsong Chen
- Department of Forensic Science Investigation Bureau, Ministry of Justice, New Taipei City, 231209, Taiwan.
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
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17
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Sudianto E, Chaw SM. Two Independent Plastid accD Transfers to the Nuclear Genome of Gnetum and Other Insights on Acetyl-CoA Carboxylase Evolution in Gymnosperms. Genome Biol Evol 2019; 11:1691-1705. [PMID: 30924880 PMCID: PMC6595918 DOI: 10.1093/gbe/evz059] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2019] [Indexed: 12/26/2022] Open
Abstract
Acetyl-CoA carboxylase (ACCase) is the key regulator of fatty acid biosynthesis. In most plants, ACCase exists in two locations (cytosol and plastids) and in two forms (homomeric and heteromeric). Heteromeric ACCase comprises four subunits, three of them (ACCA-C) are nuclear encoded (nr) and the fourth (ACCD) is usually plastid encoded. Homomeric ACCase is encoded by a single nr-gene (ACC). We investigated the ACCase gene evolution in gymnosperms by examining the transcriptomes of newly sequenced Gnetum ula, combined with 75 transcriptomes and 110 plastomes of other gymnosperms. AccD-coding sequences are elongated through the insertion of repetitive DNA in four out of five cupressophyte families (except Sciadopityaceae) and were functionally transferred to the nucleus of gnetophytes and Sciadopitys. We discovered that, among the three genera of gnetophytes, only Gnetum has two copies of nr-accD. Furthermore, using protoplast transient expression assays, we experimentally verified that the nr-accD precursor proteins in Gnetum and Sciadopitys can be delivered to the plastids. Of the two nr-accD copies of Gnetum, one dually targets plastids and mitochondria, whereas the other potentially targets plastoglobuli. The distinct transit peptides, gene architectures, and flanking sequences between the two Gnetum accDs suggest that they have independent origins. Our findings are the first account of two distinctly targeted nr-accDs of any green plants and the most comprehensive analyses of ACCase evolution in gymnosperms to date.
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Affiliation(s)
- Edi Sudianto
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shu-Miaw Chaw
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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18
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Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus bawanglingensis Huang, Li et Xing, a Vulnerable Oak Tree in China. FORESTS 2019. [DOI: 10.3390/f10070587] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Quercus bawanglingensis Huang, Li et Xing, an endemic evergreen oak of the genus Quercus (Fagaceae) in China, is currently listed in the Red List of Chinese Plants as a vulnerable (VU) plant. No chloroplast (cp) genome information is currently available for Q. bawanglingensis, which would be essential for the establishment of guidelines for its conservation and breeding. In the present study, the cp genome of Q. bawanglingensis was sequenced and assembled into double-stranded circular DNA with a length of 161,394 bp. Two inverted repeats (IRs) with a total of 51,730 bp were identified, and the rest of the sequence was separated into two single-copy regions, namely, a large single-copy (LSC) region (90,628 bp) and a small single-copy (SSC) region (19,036 bp). The genome of Q. bawanglingensis contains 134 genes (86 protein-coding genes, 40 tRNAs and eight rRNAs). More forward (29) than inverted long repeats (21) are distributed in the cp genome. A simple sequence repeat (SSR) analysis showed that the genome contains 82 SSR loci, involving 84.15% A/T mononucleotides. Sequence comparisons among the nine complete cp genomes, including the genomes of Q. bawanglingensis, Q. tarokoensis Hayata (NC036370), Q. aliena var. acutiserrata Maxim. ex Wenz. (KU240009), Q. baronii Skan (KT963087), Q. aquifolioides Rehd. et Wils. (KX911971), Q. variabilis Bl. (KU240009), Fagus engleriana Seem. (KX852398), Lithocarpus balansae (Drake) A. Camus (KP299291) and Castanea mollissima Bl. (HQ336406), demonstrated that the diversity of SC regions was higher than that of IR regions, which might facilitate identification of the relationships within this extremely complex family. A phylogenetic analysis showed that Fagus engleriana and Trigonobalanus doichangensis form the basis of the produced evolutionary tree. Q. bawanglingensis and Q. tarokoensis, which belong to the group Ilex, share the closest relationship. The analysis of the cp genome of Q. bawanglingensis provides crucial genetic information for further studies of this vulnerable species and the taxonomy, phylogenetics and evolution of Quercus.
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19
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Nováková E, Zablatzká L, Brus J, Nesrstová V, Hanáček P, Kalendar R, Cvrčková F, Majeský Ľ, Smýkal P. Allelic Diversity of Acetyl Coenzyme A Carboxylase accD/ bccp Genes Implicated in Nuclear-Cytoplasmic Conflict in the Wild and Domesticated Pea ( Pisum sp.). Int J Mol Sci 2019; 20:E1773. [PMID: 30974846 PMCID: PMC6480052 DOI: 10.3390/ijms20071773] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/04/2019] [Accepted: 04/08/2019] [Indexed: 01/09/2023] Open
Abstract
Reproductive isolation is an important component of species differentiation. The plastid accD gene coding for the acetyl-CoA carboxylase subunit and the nuclear bccp gene coding for the biotin carboxyl carrier protein were identified as candidate genes governing nuclear-cytoplasmic incompatibility in peas. We examined the allelic diversity in a set of 195 geographically diverse samples of both cultivated (Pisum sativum, P. abyssinicum) and wild (P. fulvum and P. elatius) peas. Based on deduced protein sequences, we identified 34 accD and 31 bccp alleles that are partially geographically and genetically structured. The accD is highly variable due to insertions of tandem repeats. P. fulvum and P. abyssinicum have unique alleles and combinations of both genes. On the other hand, partial overlap was observed between P. sativum and P. elatius. Mapping of protein sequence polymorphisms to 3D structures revealed that most of the repeat and indel polymorphisms map to sequence regions that could not be modeled, consistent with this part of the protein being less constrained by requirements for precise folding than the enzymatically active domains. The results of this study are important not only from an evolutionary point of view but are also relevant for pea breeding when using more distant wild relatives.
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Affiliation(s)
- Eliška Nováková
- Department of Botany, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
| | - Lenka Zablatzká
- Department of Botany, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
| | - Jan Brus
- Department of Geoinformatics, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
| | - Viktorie Nesrstová
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University, 78371 Olomouc, Czech Republic.
| | - Pavel Hanáček
- Department of Plant Biology, Faculty of Agronomy, Mendel University, 61300 Brno, Czech Republic.
| | - Ruslan Kalendar
- National Center for Biotechnology, Astana 010000, Kazakhstan.
- Department of Agricultural Sciences, Viikki Plant Science Centre and Helsinki Sustainability Centre, University of Helsinki, FI-00014 Helsinki, Finland.
| | - Fatima Cvrčková
- Department of Experimental Plant Biology, Faculty of Sciences, Charles University, 12844 Prague, Czech Republic.
| | - Ľuboš Majeský
- Department of Botany, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
| | - Petr Smýkal
- Department of Botany, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
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