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Liu H, Wagutu GK, Chen Y, Li X, Fan X. The complete chloroplast genome sequence of Myricaria wardii Marquand 1929 (Tamaricaceae): a shrub species endemic to the Tibet Plateau. Mitochondrial DNA B Resour 2024; 9:367-370. [PMID: 38529113 PMCID: PMC10962288 DOI: 10.1080/23802359.2024.2329666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 03/07/2024] [Indexed: 03/27/2024] Open
Abstract
Myricaria wardii Marquand 1929, endemic to the Tibet Plateau, is a perennial shrub with important medicinal and ecological values. In this study, the complete chloroplast (cp) genome of M. wardii was assembled, and the phylogenetic tree was reconstructed to evaluate the phylogenetic location of the species. The results showed that the cp genome size of the M. wardii was 155,299 bp, which contained a pair of inverted repeat (IR) regions (26,150 bp), a large single copy (LSC) region (84,715 bp), and a small single copy (SSC) region (18,284 bp). The total GC content of the cp genome was 36.30%. A total of 128 genes were annotated, consisting of 83 protein-coding genes, 37 tRNA genes and 8 rRNA genes. The phylogenetic analysis showed that M. wardii was closely related to M. prostrata. This study provides useful information for the conservation of this species and the phylogenetic analysis of Tamaricaceae.
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Affiliation(s)
- Haoran Liu
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, Shandong, China
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Godfrey Kinyori Wagutu
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, Hubei, China
- Wuhan Botanical Garden, University of Chinese Academy of Sciences, Beijing, Beijing, China
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yuanyuan Chen
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xiuling Li
- College of Life Science, Linyi University, Linyi, Shandong, China
- National Forest Eco-system Research Station of Linyi City, Linyi, Shandong, China
| | - Xiangrong Fan
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
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Ochieng WA, Wei L, Wagutu GK, Xian L, Muthui SW, Ogada S, Otieno DO, Linda EL, Liu F. Transcriptome Analysis of Macrophytes' Myriophyllum spicatum Response to Ammonium Nitrogen Stress Using the Whole Plant Individual. Plants (Basel) 2023; 12:3875. [PMID: 38005772 PMCID: PMC10675724 DOI: 10.3390/plants12223875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/11/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023]
Abstract
Ammonium toxicity in macrophytes reduces growth and development due to a disrupted metabolism and high carbon requirements for internal ammonium detoxification. To provide more molecular support for ammonium detoxification in the above-ground and below-ground parts of Myriophyllum spicatum, we separated (using hermetic bags) the aqueous medium surrounding the below-ground from that surrounding the above-ground and explored the genes in these two regions. The results showed an upregulation of asparagine synthetase genes under high ammonium concentrations. Furthermore, the transcriptional down and/or upregulation of other genes involved in nitrogen metabolism, including glutamate dehydrogenase, ammonium transporter, and aspartate aminotransferase in above-ground and below-ground parts were crucial for ammonium homeostasis under high ammonium concentrations. The results suggest that, apart from the primary pathway and alternative pathway, the asparagine metabolic pathway plays a crucial role in ammonium detoxification in macrophytes. Therefore, the complex genetic regulatory network in M. spicatum contributes to its ammonium tolerance, and the above-ground part is the most important in ammonium detoxification. Nevertheless, there is a need to incorporate an open-field experimental setup for a conclusive picture of nitrogen dynamics, toxicity, and the molecular response of M. spicatum in the natural environment.
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Affiliation(s)
- Wyckliffe Ayoma Ochieng
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.A.O.); (G.K.W.); (L.X.); (S.W.M.); (D.O.O.)
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan 430074, China
- University of the Chinese Academy of Sciences, Beijing 101408, China
| | - Li Wei
- Changjiang Water Resources and Hydropower Development Group (Hubei) Co., Ltd., Wuhan 430010, China;
| | - Godfrey Kinyori Wagutu
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.A.O.); (G.K.W.); (L.X.); (S.W.M.); (D.O.O.)
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan 430074, China
- University of the Chinese Academy of Sciences, Beijing 101408, China
| | - Ling Xian
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.A.O.); (G.K.W.); (L.X.); (S.W.M.); (D.O.O.)
| | - Samuel Wamburu Muthui
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.A.O.); (G.K.W.); (L.X.); (S.W.M.); (D.O.O.)
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan 430074, China
- University of the Chinese Academy of Sciences, Beijing 101408, China
| | - Stephen Ogada
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi 00200, Kenya;
| | - Duncan Ochieng Otieno
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.A.O.); (G.K.W.); (L.X.); (S.W.M.); (D.O.O.)
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan 430074, China
- University of the Chinese Academy of Sciences, Beijing 101408, China
| | - Elive Limunga Linda
- School of Resources and Environmental Science, Hubei University, Wuhan 430062, China;
| | - Fan Liu
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.A.O.); (G.K.W.); (L.X.); (S.W.M.); (D.O.O.)
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan 430074, China
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Cheptoo Rono P, Munyao Mutie F, Kathambi V, Wei N, Muema Watuma B, Nanjala C, Wagutu GK, Kirika PM, Malombe I, Hu GW, Wang QF. An annotated plant checklist of the transboundary volcanic Mt Elgon, East Africa. PhytoKeys 2023; 223:1-174. [PMID: 37252062 PMCID: PMC10209612 DOI: 10.3897/phytokeys.223.97401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/02/2023] [Indexed: 05/31/2023]
Abstract
Mt Elgon is an ancient transboundary volcanic mountain found at the Kenya-Uganda boarder possessing high plant diversity. This study documents an updated checklist of the mountain's vascular plants obtained through random-walk field excursions and retrieval of herbarium specimen tracing back to 1900. We compiled 1709 species from 673 genera in 131 families. One new species of the family Cucurbitaceae was also reported. This checklist records respective habitat, habits, elevation ranges, voucher numbers and global distribution ranges of each species. Native and exotic species were also distinguished, where 8.4% of the total species in 49 families were exotic species. There were 103 endemic species, while 14 species were found to be both rare and endemic. IUCN conservation status revealed 2 Critically Endangered, 4 Endangered, 9 Vulnerable and 2 Near Threatened species. This study presents the first and most comprehensive plant inventory of Mt Elgon that will facilitate further ecological and phylogenetic studies.
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Affiliation(s)
- Peninah Cheptoo Rono
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, ChinaUniversity of Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of Sciences, Beijing 100049, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhanChina
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, Hubei, ChinaSino-Africa Joint Research Center, Chinese Academy of SciencesWuhanChina
| | - Fredrick Munyao Mutie
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, ChinaUniversity of Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of Sciences, Beijing 100049, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhanChina
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, Hubei, ChinaSino-Africa Joint Research Center, Chinese Academy of SciencesWuhanChina
| | - Vivian Kathambi
- East African Herbarium, National Museums of Kenya, P.O. Box 45166 00100, Nairobi, KenyaEast African Herbarium, National Museums of KenyaNairobiKenya
| | - Neng Wei
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, ChinaUniversity of Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of Sciences, Beijing 100049, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhanChina
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, Hubei, ChinaSino-Africa Joint Research Center, Chinese Academy of SciencesWuhanChina
| | - Benjamin Muema Watuma
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, ChinaUniversity of Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of Sciences, Beijing 100049, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhanChina
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, Hubei, ChinaSino-Africa Joint Research Center, Chinese Academy of SciencesWuhanChina
| | - Consolata Nanjala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, ChinaUniversity of Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of Sciences, Beijing 100049, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhanChina
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, Hubei, ChinaSino-Africa Joint Research Center, Chinese Academy of SciencesWuhanChina
| | - Godfrey Kinyori Wagutu
- University of Chinese Academy of Sciences, Beijing 100049, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhanChina
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, Hubei, ChinaSino-Africa Joint Research Center, Chinese Academy of SciencesWuhanChina
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, ChineseAcademy of Sciences, Wuhan, ChinaKey Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, ChineseAcademy of SciencesWuhanChina
| | - Paul M. Kirika
- East African Herbarium, National Museums of Kenya, P.O. Box 45166 00100, Nairobi, KenyaEast African Herbarium, National Museums of KenyaNairobiKenya
| | - Itambo Malombe
- East African Herbarium, National Museums of Kenya, P.O. Box 45166 00100, Nairobi, KenyaEast African Herbarium, National Museums of KenyaNairobiKenya
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, ChinaUniversity of Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of Sciences, Beijing 100049, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhanChina
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, Hubei, ChinaSino-Africa Joint Research Center, Chinese Academy of SciencesWuhanChina
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, ChinaUniversity of Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of Sciences, Beijing 100049, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhanChina
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, Hubei, ChinaSino-Africa Joint Research Center, Chinese Academy of SciencesWuhanChina
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Wagutu GK, Fan X, Fu W, Tengwer MC, Li W, Chen Y. Genetic structure of wild rice Zizania latifolia in an expansive heterogeneous landscape along a latitudinal gradient. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.929944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Global aquatic habitats are undergoing rapid degradation and fragmentation as a result of climate change and changes in land use. Understanding the genetic variability and adaptive potential of aquatic plant species is thus important for conservation purposes. In this study, we investigated the genetic diversity and structure of the extant natural populations of Zizania latifolia from five river basins in China based on 46 microsatellite markers. We tested isolation by environment (IBE), isolation by resistance (IBR), and isolation by distance (IBD) patterns using a reciprocal causal model (RCM). Furthermore, we elucidated the impact of the environment on Z. latifolia genetic diversity using generalized linear models (GLMs) and spatially explicit mixed models. Low genetic diversity (HE = 0.125–0.433) and high genetic differentiation (FST = 0.641, Øpt = 0.654) were found. Higher historical gene flow (MH = 0.212–2.354) than contemporary gene flow (MC = 0.0112–0.0247) and significant bottlenecks in almost all populations were identified, highlighting the negative impact of wetland fragmentation. The IBE model was exclusively supported for all populations and in three river basins. The IBD and IBR models were supported in one river basin each. The maximum temperature of the warmest month and precipitation seasonality were the plausible environmental parameters responsible for the observed pattern of genetic diversity. Local adaptation signatures were found, with nine loci identified as outliers, four of which were gene-linked and associated with environmental variables. Based on these findings, IBE is more important than IBD and IBR in shaping the genetic structure of Z. latifolia.
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Abstract
Trapa (Lythraceae) is an economically important aquatic genus used for food and medicine, with wide distribution in Asia, Africa, and Europe. Identification of species, genetic studies and utilization of Trapa are limited by lack of molecular data. Herein, we report the complete chloroplast (cp) genome sequence of a wild species, Trapa kozhevnikoviorum Pshenn. The cp genome size of T. kozhevnikoviorum is 155,545 bp, consisting of a pair of inverted repeat regions (IRa/IRb) of length 24,388 bp, separated by the small single copy (SSC) region of 18,275 bp and a large single copy (LSC) region of 88,494 bp. A total of 113 unique genes, including 79 protein-coding, 30 tRNA, and four rRNA were annotated. Phylogenetic analysis based on 15 whole cp genomes of Lythraceae species supported the monophyletic clustering of Trapa. A cladal relationship among T. kozhevnikoviorum, T. bicornis, and T. natans was revealed.
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Affiliation(s)
- Godfrey Kinyori Wagutu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Wuhan Botanical Garden, University of Chinese Academy of Sciences, Beijing, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Xiangrong Fan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,College of Science, Tibet University, Lhasa, Tibet Autonomous Region, China.,Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa, Tibet Autonomous Region, China
| | - Wuchao Wang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Wuhan Botanical Garden, University of Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Wuhan Botanical Garden, University of Chinese Academy of Sciences, Beijing, China
| | - Yuanyuan Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
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