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Qi X, Wang K, Yang L, Deng Z, Sun Z. The complete mitogenome sequence of the coral lily ( Lilium pumilum) and the Lanzhou lily ( Lilium davidii) in China. Open Life Sci 2021; 15:1060-1067. [PMID: 33817292 PMCID: PMC7874665 DOI: 10.1515/biol-2020-0102] [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: 11/21/2019] [Revised: 07/18/2020] [Accepted: 09/14/2020] [Indexed: 11/24/2022] Open
Abstract
Background The mitogenomes of higher plants are conserved. This study was performed to complete the mitogenome of two China Lilium species (Lilium pumilum Redouté and Lilium davidii var. unicolor (Hoog) cotton). Methods Genomic DNA was separately extracted from the leaves of L. pumilum and L. davidii in triplicate and used for sequencing. The mitogenome of Allium cepa was used as a reference. Genome assembly, annotation and phylogenetic tree were analyzed. Results The mitogenome of L. pumilum and L. davidii was 988,986 bp and 924,401 bp in length, respectively. There were 22 core protein-coding genes (including atp1, atp4, atp6, atp9, ccmB, ccmC, ccmFc, ccmFN1, ccmFN2, cob, cox3, matR, mttB, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7 and nad9), one open reading frame and one ribosomal protein-coding gene (rps12) in the mitogenomes. Compared with the A. cepa mitogenome, the coding sequence of the 24 genes and intergenic spacers in L. pumilum and L. davidii mitogenome contained 1,621 and 1,617 variable sites, respectively. In the phylogenetic tree, L. pumilum and L. davidii were distinct from A. cepa (NC_030100). Conclusions L. pumilum and L. davidii mitogenomes have far distances from other plants. This study provided additional information on the species resources of China Lilium.
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Affiliation(s)
- Xiangying Qi
- China Lily Laboratory, Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Kaiqi Wang
- China Lily Laboratory, Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Liping Yang
- School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, 408100, China
| | - Zhenshan Deng
- China Lily Laboratory, Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Zhihong Sun
- China Lily Laboratory, Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, 716000, Shaanxi, China
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Aquatic Plant Genomics: Advances, Applications, and Prospects. Int J Genomics 2017; 2017:6347874. [PMID: 28900619 PMCID: PMC5576420 DOI: 10.1155/2017/6347874] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 07/11/2017] [Accepted: 07/30/2017] [Indexed: 11/23/2022] Open
Abstract
Genomics is a discipline in genetics that studies the genome composition of organisms and the precise structure of genes and their expression and regulation. Genomics research has resolved many problems where other biological methods have failed. Here, we summarize advances in aquatic plant genomics with a focus on molecular markers, the genes related to photosynthesis and stress tolerance, comparative study of genomes and genome/transcriptome sequencing technology.
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Wang XC, Chen H, Yang D, Liu C. Diversity of mitochondrial plastid DNAs (MTPTs) in seed plants. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:635-642. [PMID: 28573928 DOI: 10.1080/24701394.2017.1334772] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Mitochondrial plastid DNAs (MTPTs) refer to plastid-derived DNA fragments in mitochondrial genomes. While the MTPTs have been described for numerous species, its overall patterns have not been examined in details. Here, we carried out a systematic analysis of MTPTs among 73 plant species, including 28 algae, 1 liverwort, 2 moss, 1 lycophyte, 1 gymnosperm, 1 magnoliid, 12 monocots, 26 eudicots and 1 relic angiosperm Amborella trichopoda. A total of 300 MTPT gene clusters were found in 39 seed plants, which represented 144 MTPT gene cluster types. The detected MTPT gene clusters were evaluated in seven aspects, and they were found to be enriched particularly in monocots and asterids of eudicots. Some MTPT gene clusters were found to be shared by closely related species. All chloroplast genes were found in MTPTs, suggesting that there is no functional relevancy for genes that were transferred. However, after calculation of the frequency of the 115 chloroplast genes, five hot spots and three cold spots were discovered in chloroplast genome. In summary, this study demonstrated the high degree of diversity in MTPTs. The discovered MTPTs would facilitate the accurate assembly of chloroplast and mitochondrial genomes as well as the understanding of organelle genome evolution.
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Affiliation(s)
- Xin-Cun Wang
- a Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing , P.R. China
| | - Haimei Chen
- a Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing , P.R. China
| | - Dan Yang
- a Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing , P.R. China
| | - Chang Liu
- a Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing , P.R. China
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Petersen G, Cuenca A, Zervas A, Ross GT, Graham SW, Barrett CF, Davis JI, Seberg O. Mitochondrial genome evolution in Alismatales: Size reduction and extensive loss of ribosomal protein genes. PLoS One 2017; 12:e0177606. [PMID: 28545148 PMCID: PMC5435185 DOI: 10.1371/journal.pone.0177606] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 04/28/2017] [Indexed: 11/18/2022] Open
Abstract
The order Alismatales is a hotspot for evolution of plant mitochondrial genomes characterized by remarkable differences in genome size, substitution rates, RNA editing, retrotranscription, gene loss and intron loss. Here we have sequenced the complete mitogenomes of Zostera marina and Stratiotes aloides, which together with previously sequenced mitogenomes from Butomus and Spirodela, provide new evolutionary evidence of genome size reduction, gene loss and transfer to the nucleus. The Zostera mitogenome includes a large portion of DNA transferred from the plastome, yet it is the smallest known mitogenome from a non-parasitic plant. Using a broad sample of the Alismatales, the evolutionary history of ribosomal protein gene loss is analyzed. In Zostera almost all ribosomal protein genes are lost from the mitogenome, but only some can be found in the nucleus.
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Affiliation(s)
- Gitte Petersen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Argelia Cuenca
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Athanasios Zervas
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Gregory T. Ross
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean W. Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Craig F. Barrett
- L. H. Bailey Hortorium and Plant Biology Section, Cornell University, Ithaca, New York, United States of America
| | - Jerrold I. Davis
- L. H. Bailey Hortorium and Plant Biology Section, Cornell University, Ithaca, New York, United States of America
| | - Ole Seberg
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Complete Sequence and Analysis of Coconut Palm (Cocos nucifera) Mitochondrial Genome. PLoS One 2016; 11:e0163990. [PMID: 27736909 PMCID: PMC5063475 DOI: 10.1371/journal.pone.0163990] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 09/19/2016] [Indexed: 11/19/2022] Open
Abstract
Coconut (Cocos nucifera L.), a member of the palm family (Arecaceae), is one of the most economically important crops in tropics, serving as an important source of food, drink, fuel, medicine, and construction material. Here we report an assembly of the coconut (C. nucifera, Oman local Tall cultivar) mitochondrial (mt) genome based on next-generation sequencing data. This genome, 678,653bp in length and 45.5% in GC content, encodes 72 proteins, 9 pseudogenes, 23 tRNAs, and 3 ribosomal RNAs. Within the assembly, we find that the chloroplast (cp) derived regions account for 5.07% of the total assembly length, including 13 proteins, 2 pseudogenes, and 11 tRNAs. The mt genome has a relatively large fraction of repeat content (17.26%), including both forward (tandem) and inverted (palindromic) repeats. Sequence variation analysis shows that the Ti/Tv ratio of the mt genome is lower as compared to that of the nuclear genome and neutral expectation. By combining public RNA-Seq data for coconut, we identify 734 RNA editing sites supported by at least two datasets. In summary, our data provides the second complete mt genome sequence in the family Arecaceae, essential for further investigations on mitochondrial biology of seed plants.
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Cuenca A, Ross TG, Graham SW, Barrett CF, Davis JI, Seberg O, Petersen G. Localized Retroprocessing as a Model of Intron Loss in the Plant Mitochondrial Genome. Genome Biol Evol 2016; 8:2176-89. [PMID: 27435795 PMCID: PMC4987113 DOI: 10.1093/gbe/evw148] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2016] [Indexed: 12/23/2022] Open
Abstract
Loss of introns in plant mitochondrial genes is commonly explained by retroprocessing. Under this model, an mRNA is reverse transcribed and integrated back into the genome, simultaneously affecting the contents of introns and edited sites. To evaluate the extent to which retroprocessing explains intron loss, we analyzed patterns of intron content and predicted RNA editing for whole mitochondrial genomes of 30 species in the monocot order Alismatales. In this group, we found an unusually high degree of variation in the intron content, even expanding the hitherto known variation among angiosperms. Some species have lost some two-third of the cis-spliced introns. We found a strong correlation between intron content and editing frequency, and detected 27 events in which intron loss is consistent with the presence of nucleotides in an edited state, supporting retroprocessing. However, we also detected seven cases of intron loss not readily being explained by retroprocession. Our analyses are also not consistent with the entire length of a fully processed cDNA copy being integrated into the genome, but instead indicate that retroprocessing usually occurs for only part of the gene. In some cases, several rounds of retroprocessing may explain intron loss in genes completely devoid of introns. A number of taxa retroprocessing seem to be very common and a possibly ongoing process. It affects the entire mitochondrial genome.
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Affiliation(s)
- Argelia Cuenca
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - T Gregory Ross
- Department of Botany, 6270 University Boulevard, University of British Columbia, Vancouver, British Columbia, Canada UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean W Graham
- Department of Botany, 6270 University Boulevard, University of British Columbia, Vancouver, British Columbia, Canada UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Craig F Barrett
- Department of Biological Sciences, California State University, Los Angeles, California
| | - Jerrold I Davis
- L.H. Bailey Hortorium and Plant Biology Section, Cornell University, Ithaca, New York
| | - Ole Seberg
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Gitte Petersen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Gui S, Wu Z, Zhang H, Zheng Y, Zhu Z, Liang D, Ding Y. The mitochondrial genome map of Nelumbo nucifera reveals ancient evolutionary features. Sci Rep 2016; 6:30158. [PMID: 27444405 PMCID: PMC4957087 DOI: 10.1038/srep30158] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 06/28/2016] [Indexed: 01/12/2023] Open
Abstract
Nelumbo nucifera is an evolutionary relic from the Late Cretaceous period. Sequencing the N. nucifera mitochondrial genome is important for elucidating the evolutionary characteristics of basal eudicots. Here, the N. nucifera mitochondrial genome was sequenced using single molecule real-time sequencing technology (SMRT), and the mitochondrial genome map was constructed after de novo assembly and annotation. The results showed that the 524,797-bp N. nucifera mitochondrial genome has a total of 63 genes, including 40 protein-coding genes, three rRNA genes and 20 tRNA genes. Fifteen collinear gene clusters were conserved across different plant species. Approximately 700 RNA editing sites in the protein-coding genes were identified. Positively selected genes were identified with selection pressure analysis. Nineteen chloroplast-derived fragments were identified, and seven tRNAs were derived from the chloroplast. These results suggest that the N. nucifera mitochondrial genome retains evolutionarily conserved characteristics, including ancient gene content and gene clusters, high levels of RNA editing, and low levels of chloroplast-derived fragment insertions. As the first publicly available basal eudicot mitochondrial genome, the N. nucifera mitochondrial genome facilitates further analysis of the characteristics of basal eudicots and provides clues of the evolutionary trajectory from basal angiosperms to advanced eudicots.
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Affiliation(s)
- Songtao Gui
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhihua Wu
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hongyuan Zhang
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yinzhen Zheng
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhixuan Zhu
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Dequan Liang
- Nextomics Biosciences Co., Ltd., Wuhan, 430075, China
| | - Yi Ding
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China
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Guo W, Grewe F, Fan W, Young GJ, Knoop V, Palmer JD, Mower JP. GinkgoandWelwitschiaMitogenomes Reveal Extreme Contrasts in Gymnosperm Mitochondrial Evolution. Mol Biol Evol 2016; 33:1448-60. [DOI: 10.1093/molbev/msw024] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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Transcriptome sequencing of three Ranunculus species (Ranunculaceae) reveals candidate genes in adaptation from terrestrial to aquatic habitats. Sci Rep 2015; 5:10098. [PMID: 25993393 PMCID: PMC4438715 DOI: 10.1038/srep10098] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 03/30/2015] [Indexed: 01/12/2023] Open
Abstract
Adaptation to aquatic habitats is a formidable challenge for terrestrial angiosperms that has long intrigued scientists. As part of a suite of work to explore the molecular mechanism of adaptation to aquatic habitats, we here sequenced the transcriptome of the submerged aquatic plant Ranunculus bungei, and two terrestrial relatives R. cantoniensis and R. brotherusii, followed by comparative evolutionary analyses to determine candidate genes for adaption to aquatic habitats. We obtained 126,037, 140,218 and 114,753 contigs for R. bungei, R. cantoniensis and R. brotherusii respectively. Bidirectional Best Hit method and OrthoMCL method identified 11,362 and 8,174 1:1:1 orthologous genes (one ortholog is represented in each of the three species) respectively. Non-synonymous/synonymous (dN/dS) analyses were performed with a maximum likelihood method and an approximate method for the three species-pairs. In total, 14 genes of R. bungei potentially involved in the adaptive transition from terrestrial to aquatic habitats were identified. Some of the homologs to these genes in model plants are involved in vacuole protein formation, regulating 'water transport process' and 'microtubule cytoskeleton organization'. Our study opens the door to understand the molecular mechanism of plant adaptation from terrestrial to aquatic habitats.
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Petersen G, Seberg O, Cuenca A, Stevenson DW, Thadeo M, Davis JI, Graham S, Ross TG. Phylogeny of the Alismatales (Monocotyledons) and the relationship ofAcorus(Acorales?). Cladistics 2015; 32:141-159. [DOI: 10.1111/cla.12120] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2015] [Indexed: 11/28/2022] Open
Affiliation(s)
- Gitte Petersen
- Natural History Museum of Denmark; University of Copenhagen; Sølvgade 83 Opg. S DK-1307 Copenhagen Denmark
| | - Ole Seberg
- Natural History Museum of Denmark; University of Copenhagen; Sølvgade 83 Opg. S DK-1307 Copenhagen Denmark
| | - Argelia Cuenca
- Natural History Museum of Denmark; University of Copenhagen; Sølvgade 83 Opg. S DK-1307 Copenhagen Denmark
| | | | | | - Jerrold I. Davis
- L. H. Bailey Hortorium and Section of Plant Biology; Cornell University; Ithaca NY 14853 USA
| | - Sean Graham
- Department of Botany; University of British Columbia; Vancouver BC V6T 1Z4 Canada
| | - T. Gregory Ross
- Department of Botany; University of British Columbia; Vancouver BC V6T 1Z4 Canada
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Takenaka M, Verbitskiy D, Zehrmann A, Härtel B, Bayer-Császár E, Glass F, Brennicke A. RNA editing in plant mitochondria—connecting RNA target sequences and acting proteins. Mitochondrion 2014; 19 Pt B:191-7. [PMID: 24732437 DOI: 10.1016/j.mito.2014.04.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/27/2014] [Accepted: 04/04/2014] [Indexed: 12/31/2022]
Abstract
RNA editing changes several hundred cytidines to uridines in the mRNAs of mitochondria in flowering plants. The target cytidines are identified by a subtype of PPR proteins characterized by tandem modules which each binds with a specific upstream nucleotide. Recent progress in correlating repeat structures with nucleotide identities allows to predict and identify target sites in mitochondrial RNAs. Additional proteins have been found to play a role in RNA editing; their precise function still needs to be elucidated. The enzymatic activity performing the C to U reaction may reside in the C-terminal DYW extensions of the PPR proteins; however, this still needs to be proven. Here we update recent progress in understanding RNA editing in flowering plant mitochondria.
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Affiliation(s)
| | | | - Anja Zehrmann
- Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany
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