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Shan Y, Li J, Duan X, Zhang X, Yu J. Elucidating the multichromosomal structure within the Brasenia schreberi mitochondrial genome through assembly and analysis. BMC Genomics 2024; 25:422. [PMID: 38684976 PMCID: PMC11059650 DOI: 10.1186/s12864-024-10331-0] [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] [Received: 12/19/2023] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Abstract
Brasenia schreberi, a plant species traditionally utilized in Chinese medicine and cuisine, represents an early evolutionary stage among flowering plants (angiosperms). While the plastid genome of this species has been published, its mitochondrial genome (mitogenome) has not been extensively explored, with a notable absence of thorough comparative analyses of its organellar genomes. In our study, we had assembled the entire mitogenome of B. schreberi utilizing the sequencing data derived from both Illumina platform and Oxford Nanopore. The B. schreberi mitogenome mostly exists as six circular DNA molecules, with the largest being 628,257 base pairs (bp) and the smallest 110,220 bp, amounting to 1.49 megabases (Mb). Then we annotated the mitogenome of B. schreberi. The mitogenome encompasses a total of 71 genes: 40 of these are coding proteins genes (PCGs), 28 are genes for transfer RNA (tRNA), and the remaining 3 are genes for ribosomal RNA (rRNA). In the analysis of codon usage, we noted a unique codon preference specific to each amino acid. The most commonly used codons exhibited an average RSCU of 1.36, indicating a noticeable bias in codon selection. In the repeat sequence analysis, a total of 553 simple sequence repeats (SSRs) were identified, 1,822 dispersed repeats (comprising 1,015 forward and 807 palindromic repeats), and 608 long terminal repeats (LTRs). Additionally, in the analysis of homologous sequences between organelle genomes, we detected 38 homologous sequences derived from the plastid genome, each exceeding 500 bp, within the B. schreberi mitochondrial genome. Notably, ten tRNA genes (trnC-GCA, trnM-CAU, trnI-CAU, trnQ-UUG, trnN-GUU, trnT-GGU, trnW-CCA, trnA-UGC, trnI-GAU, and trnV-GAC) appear to have been completely transferred from the chloroplast to the mitogenome. Utilizing the Deepred-mt to predict the RNA editing sites in the mitogenome, we have identified 675 high-quality RNA editing sites in the 40 mitochondrial PCGs. In the final stage of our study, we performed an analysis of colinearity and inferred the phylogenetic relationship of B. schreberi with other angiosperms, utilizing the mitochondrial PCGs as a basis. The results showed that the non-coding regions of the B. schreberi mitogenome are characterized by an abundance of repetitive sequences and exogenous sequences, and B. schreberi is more closely related with Euryale ferox.
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Affiliation(s)
- Yuanyu Shan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Xinmei Duan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Xue Zhang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China.
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing, 400715, China.
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Wu LF, Zhu WG, Yu EP, Cao HL, Wang ZF. Draft genome of Brasenia schreberi, a worldwide distributed and endangered aquatic plant. BMC Genom Data 2024; 25:24. [PMID: 38438998 PMCID: PMC10913576 DOI: 10.1186/s12863-024-01212-2] [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: 02/01/2024] [Accepted: 02/21/2024] [Indexed: 03/06/2024] Open
Abstract
OBJECTIVES Brasenia is a monotypic genus in the family of Cabombaceae. The only species, B. schreberi, is a macrophyte distributed worldwide. Because it requires good water quality, it is endangered in China and other countries due to the deterioration of aquatic habitats. The young leaves and stems of B. schreberi are covered by thick mucilage, which has high medical value. As an allelopathic aquatic plant, it can also be used in the management of aquatic weeds. Here, we present its assembled and annotated genome to help shed light on medial and allelopathic substrates and facilitate their conservation. DATA DESCRIPTION Genomic DNA and RNA extracted from B. schreberi leaf tissues were used for whole genome and RNA sequencing using a Nanopore and/or MGI sequencer. The assembly was 1,055,148,839 bp in length, with 92 contigs and an N50 of 22,379,495 bp. The repetitive elements in the assembly were 555,442,205 bp. A completeness assessment of the assembly with BUSCO and compleasm indicated 88.4 and 90.9% completeness in the Eudicots database and 95.4 and 96.6% completeness in the Embryphyta database. Gene annotation revealed 67,747 genes that coded for 73,344 proteins.
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Affiliation(s)
- Lin-Fang Wu
- Guangzhou Linfang Ecological Technology Co., Ltd, 510000, Guangzhou, China
| | - Wei-Guang Zhu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China
- South China National Botanical Garden, 510650, Guangzhou, China
| | - En-Ping Yu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China
- South China National Botanical Garden, 510650, Guangzhou, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Hong-Lin Cao
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China.
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China.
- South China National Botanical Garden, 510650, Guangzhou, China.
| | - Zheng-Feng Wang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China.
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China.
- South China National Botanical Garden, 510650, Guangzhou, China.
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Lu B, Shi T, Chen J. Chromosome-level genome assembly of watershield (Brasenia schreberi). Sci Data 2023; 10:467. [PMID: 37468511 PMCID: PMC10356934 DOI: 10.1038/s41597-023-02380-z] [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] [Received: 04/27/2023] [Accepted: 07/11/2023] [Indexed: 07/21/2023] Open
Abstract
Watershield (Brasenia schreberi) is an aquatic plant that belongs to the basal angiosperm family Cabombaceae. This species has been cultivated as an aquatic vegetable for more than 3000 years in East Asia, but the natural populations have greatly declined in recent decades and have become endangered in several countries of East Asia. In this study, by using PacBio long reads, Illumina short reads, and Hi-C sequencing data, we assembled the genome of B. schreberi, which was approximately 1170.4 Mb in size with a contig N50 of 7.1 Mb. Of the total assembled sequences, 93.6% were anchored to 36 pseudochromosomes with a scaffold N50 of 28.9 Mb. A total of 74,699 protein-coding genes were predicted in the B. schreberi genome, and 558 Mb of repetitive elements occupying 47.69% of the genome were identified. BUSCO analysis yielded a completeness score of 95.8%. The assembled high-quality genome of B. schreberi will be a valuable reference for the study of conservation, evolution and molecular breeding in this species.
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Affiliation(s)
- Bei Lu
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 4300074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Shi
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 4300074, China
| | - Jinming Chen
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 4300074, China.
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Zhu X, Tang J, Jiang H, Yang Y, Chen Z, Zou R, Xu A, Luo Y, Deng Z, Wei X, Chai S. Genomic evidence reveals high genetic diversity in a narrowly distributed species and natural hybridization risk with a widespread species in the genus Geodorum. BMC PLANT BIOLOGY 2023; 23:317. [PMID: 37316828 DOI: 10.1186/s12870-023-04285-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND Understanding genetic diversity is a core issue in conservation genetics. However, previous genetic diversity evaluations of narrowly distributed species have rarely used closely related widespread species as a reference. Furthermore, identifying natural hybridization signals between narrowly and widely distributed sympatric species is of great importance for the development of species conservation programs. METHODS In this study, population genotyping by sequencing (GBS) was performed for a narrowly distributed species, Geodorum eulophioides (endemic and endangered in Southwest China), and a widespread species, G. densiflorum. A total of 18,490 high-quality single nucleotide polymorphisms (SNPs) were identified at the whole-genome level. RESULTS The results showed that the nucleotide diversity and heterozygosity of G. eulophioides were significantly higher than those of G. densiflorum, confirming that narrowly distributed species can still preserve high genetic diversity. Consistent with taxonomic boundaries, all sampled individuals from the two species were divided into two genetic clusters and showed high genetic differentiation between species. However, in a sympatric population, a few G. eulophioides individuals were detected with genetic components from G. densiflorum, suggesting potential interspecific natural hybridization. This hypothesis was supported by Treemix analysis and hand-hybridization trials. Invasion of the habitat of G. eulophioides invasion by G. densiflorum under anthropogenic disturbance may be the main factor causing interspecific hybridization. CONCLUSIONS Therefore, reducing or avoiding habitat disturbance is a key measure to protect the G. eulophioides populations. This study provides valuable information for future conservation programs for narrowly distributed species.
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Affiliation(s)
- Xianliang Zhu
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Jianmin Tang
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Haidu Jiang
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Yishan Yang
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Zongyou Chen
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Rong Zou
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Aizhu Xu
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
- College of Tourism and Landscape Architecture, Guilin University of Technology, Guilin, Guangxi, 541006, China
| | - Yajin Luo
- Yachang Orchid National Nature Reserve Management Center, Baise, Guangxi, 533209, China
| | - Zhenhai Deng
- Yachang Orchid National Nature Reserve Management Center, Baise, Guangxi, 533209, China
| | - Xiao Wei
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China.
| | - Shengfeng Chai
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China.
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Wan J, Yu X, Liu J, Li J, Ai T, Yin C, Liu H, Qin R. A special polysaccharide hydrogel coated on Brasenia schreberi: preventive effects against ulcerative colitis via modulation of gut microbiota. Food Funct 2023; 14:3564-3575. [PMID: 36946057 DOI: 10.1039/d2fo03207d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Ulcerative colitis (UC) is a growing health concern in humans, but it can be prevented by using special dietary strategies. Young stems and leaves of Brasenia schreberi (BS) are coated with a special polysaccharide hydrogel (BS mucilage) which can be beneficial for colon health. The aim of this study was to investigate the preventive effects of BS mucilage against UC in a DSS-treated mouse model. Although containing only 0.3% solid content, our research showed that BS mucilage effectively attenuated the disease activity index (DAI) and the spleen index and downregulated IL-1β, IL-18, IL-6 and CAT mRNA levels in DSS-treated mice, which is a promising UC alleviation function. Additionally, BS mucilage also improved the propionate and butyrate levels in mouse feces and alleviated the imbalanced gut microbiota induced by DSS. The abundance of pro-inflammatory and colorectal cancer related bacteria, such as Prevotella, Ruminococcus, Acutalibacter and Christensenella, was decreased by BS mucilage feeding, whereas the abundance of anti-inflammatory and SCFA-producing bacteria including Alistipes and Odoribacter was increased. In conclusion, the current study shows that the daily consumption of BS mucilage could be an effective way to prevent UC in mice, via modulation of gut microbiota.
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Affiliation(s)
- Jiawei Wan
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, 430070, China.
| | - Xiujuan Yu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, 430070, China.
| | - Jiao Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, 430070, China.
| | - Jing Li
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tingyang Ai
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, 430070, China.
| | - Cong Yin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, 430070, China.
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, 430070, China.
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, 430070, China.
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Li J, Yi C, Zhang C, Pan F, Xie C, Zhou W, Zhou C. Effects of light quality on leaf growth and photosynthetic fluorescence of Brasenia schreberi seedlings. Heliyon 2021; 7:e06082. [PMID: 33553752 PMCID: PMC7848635 DOI: 10.1016/j.heliyon.2021.e06082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/23/2020] [Accepted: 01/20/2021] [Indexed: 11/24/2022] Open
Abstract
Brasenia schreberi J. F. Gmel, a perennial floating-leaved macrophyte with high economic value as an aquatic vegetable, has been listed as first-class endangered species in China, mainly due to its habitat loss. Protected cultivation is a potential strategy to meet the demand of both plant conservation and vegetable market, whereas pre-experiments are still needed before series of parameters can be properly set for the large-scale growth of the plants indoor. Light quality is one of the major factors controlling the development of plants and consequently becomes an important factor when planting B. schreberi indoor. This experiment used three artificial light sources to investigate the response of B. schreberi seedlings to different light qualities, including the red-blue LED light (red: blue = 5:1, RB-LED), the white LED light (W-LED) and the white fluorescent (W-Fluo). Our results indicated that the responses of B. schreberi towards varied light qualities differed from those of most terrestrial plants. The total leaf number of the RB-LED treatment was the highest; the number of the submerged leaf and the rolled leaf of the RB-LED treatment was higher than that of the other two treatments, but the number of floating leaves was the lowest. Both the specific leaf weight and the pigment contents per unit leaf area were the lowest in the RB-LED treatment. Quantum yield of PSⅡ (ΦPSⅡ), electron transport rate (ETR) and photochemical quenching (qP) measured through light induction curves followed the sequence from high to low as W-Fluo > W-LED > RB-LED, whereas the trend of non-photochemical quenching (NPQ) reversed. The maximum potential ETR (Ps) and maximum ETR (ETRm) derived from ETR curves further verified the trends.
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Affiliation(s)
- Jiafeng Li
- School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Cuiyu Yi
- School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Chenrong Zhang
- School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Fan Pan
- School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Chun Xie
- School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Wenzong Zhou
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Changfang Zhou
- School of Life Sciences, Nanjing University, Nanjing, 210023, China
- Corresponding author.
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7
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Senkoro AM, Talhinhas P, Simões F, Batista-Santos P, Shackleton CM, Voeks RA, Marques I, Ribeiro-Barros AI. The genetic legacy of fragmentation and overexploitation in the threatened medicinal African pepper-bark tree, Warburgia salutaris. Sci Rep 2020; 10:19725. [PMID: 33184322 PMCID: PMC7661512 DOI: 10.1038/s41598-020-76654-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/28/2020] [Indexed: 11/09/2022] Open
Abstract
The pepper-bark tree (Warburgia salutaris) is one of the most highly valued medicinal plant species worldwide. Native to southern Africa, this species has been extensively harvested for the bark, which is widely used in traditional health practices. Illegal harvesting coupled with habitat degradation has contributed to fragmentation of populations and a severe decline in its distribution. Even though the species is included in the IUCN Red List as Endangered, genetic data that would help conservation efforts and future re-introductions are absent. We therefore developed new molecular markers to understand patterns of genetic diversity, structure, and gene flow of W. salutaris in one of its most important areas of occurrence (Mozambique). In this study, we have shown that, despite fragmentation and overexploitation, this species maintains a relatively high level of genetic diversity supporting the existence of random mating. Two genetic groups were found corresponding to the northern and southern locations. Our study suggests that, if local extinctions occurred in Mozambique, the pepper-bark tree persisted in sufficient numbers to retain a large proportion of genetic diversity. Management plans should concentrate on maintaining this high level of genetic variability through both in and ex-situ conservation actions.
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Affiliation(s)
- Annae M Senkoro
- Department of Environmental Science, Rhodes University, Grahamstown, 6140, South Africa.,Departmento de Ciências Biológicas, Universidade Eduardo Mondlane CP 257, Maputo, Moçambique
| | - Pedro Talhinhas
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Fernanda Simões
- Instituto Nacional de Investigação Agrária E Veterinária, Av. da República, Quinta Marquês, Edificio Sede, 2780-157, Oeiras, Portugal
| | - Paula Batista-Santos
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Charlie M Shackleton
- Department of Environmental Science, Rhodes University, Grahamstown, 6140, South Africa
| | - Robert A Voeks
- Department of Geography and the Environment, California State University, 800 N State College Blvd, FullertonFullerton, CA, 92831, USA
| | - Isabel Marques
- Forest Research Centre (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal.
| | - Ana I Ribeiro-Barros
- Forest Research Centre (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal.
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Population Genetic Diversity and Structure of Ancient Tree Populations of Cryptomeria japonica var. sinensis Based on RAD-seq Data. FORESTS 2020. [DOI: 10.3390/f11111192] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Research highlights: Our study is the first to explore the genetic composition of ancient Cryptomeria trees across a distribution range in China. Background and objectives: Cryptomeria japonica var. sinensis is a native forest species of China; it is widely planted in the south of the country to create forests and for wood production. Unlike Cryptomeria in Japan, genetic Chinese Cryptomeria has seldom been studied, although there is ample evidence of its great ecological and economic value. Materials and methods: Because of overcutting, natural populations are rare in the wild. In this study, we investigated seven ancient tree populations to explore the genetic composition of Chinese Cryptomeria through ddRAD-seq technology. Results: The results reveal a lower genetic variation but higher genetic differentiation (Ho = 0.143, FST = 0.1204) than Japanese Cryptomeria (Ho = 0.245, FST = 0.0455). The 86% within-population variation is based on an analysis of molecular variance (AMOVA). Significant excess heterozygosity was detected in three populations and some outlier loci were found; these were considered to be the consequence of selection or chance. Structure analysis and dendrogram construction divided the seven ancient tree populations into four groups corresponding to the geographical provinces in which the populations are located, but there was no obvious correlation between genetic distance and geographic distance. A demographic history analysis conducted by a Stairway Plot showed that the effective population size of Chinese Cryptomeria had experienced a continuing decline from the mid-Pleistocene to the present. Our findings suggest that the strong genetic drift caused by climate fluctuation and intense anthropogenic disturbance together contributed to the current low diversity and structure. Considering the species’ unfavorable conservation status, strategies are urgently required to preserve the remaining genetic resources.
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Santos MP, Araujo JVSR, Lopes AVS, Vettorazzi JCF, Boechat MSB, Arêdes FA, Campos NV, Calderon EN, Santos FMG, Fernandes TN, da Fonseca RN, Pereira MG, Oliveira G, Zandonadi DB, Martins R, Esteves FDA. The genetic diversity and population structure of two endemic Amazonian quillwort ( Isoetes L.) species. PeerJ 2020; 8:e10274. [PMID: 33240624 PMCID: PMC7659625 DOI: 10.7717/peerj.10274] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 10/08/2020] [Indexed: 11/24/2022] Open
Abstract
Background Two endemic lycophyte species Isoetes cangae and Isoetes serracarajensis have been recently described in the State of Pará in the Amazon forest located in northern Brazil. Isoetes L. has survived through three mass extinctions. Plants are considered small-sized, heterosporous, and can display a great diversity of physiological adaptations to different environments. Thus, the current study aimed to estimate the genetic variation of the populations of I. cangae and I. serracarajensis to generate information about their different mechanisms for survival at the same geographical location that could point to different reproductive, adaptative and dispersal strategies and should be considered for effective conservation strategies. Methods The genetic diversity and population structure of I. cangae and I. serracarajensis were investigated using Inter Simple Sequence Repeat (ISSR) molecular markers. Total genomic DNA was isolated, and the genetic diversity parameters were calculated. Results The sixteen primers produced 115 reproducible bands, 87% of which were polymorphic. A high level of polymorphic loci (81.74% and 68.48%) and a high Shannon index (Sh = 0.376 and 0.289) were observed for I. cangae and I. serracarajensis, respectively. The coefficient of genetic differentiation between population areas (GST) showed a higher value in I. serracarajensis (0.5440). Gene flow was higher in I. cangae (1.715) and lower in I. serracarajensis populations (0.419). Overall, the results further show that I. serracarajensis and I. cangae are two species with considerable genetic variation and that these differences may reflect their habitats and modes of reproduction. These results should be considered in the development of effective conservation strategies for both species.
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Affiliation(s)
- Mirella Pupo Santos
- Instituto de Sustentabilidade e Biodiversidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - João V S Rabelo Araujo
- Instituto de Sustentabilidade e Biodiversidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Arthur V Sant'anna Lopes
- Instituto de Sustentabilidade e Biodiversidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Julio Cesar Fiorio Vettorazzi
- Laboratório de Melhoramento Genético Vegetal, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Marcela Santana Bastos Boechat
- Laboratório de Melhoramento Genético Vegetal, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Fernanda AbreuSantana Arêdes
- Laboratório de Melhoramento Genético Vegetal, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Naiara Viana Campos
- Instituto de Sustentabilidade e Biodiversidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Emiliano Nicolas Calderon
- Instituto de Sustentabilidade e Biodiversidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | | | | | - Rodrigo Nunes da Fonseca
- Instituto de Sustentabilidade e Biodiversidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Messias Gonzaga Pereira
- Laboratório de Melhoramento Genético Vegetal, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | | | - Daniel Basilio Zandonadi
- Instituto de Sustentabilidade e Biodiversidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - RodrigoLemes Martins
- Instituto de Sustentabilidade e Biodiversidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Francisco de Assis Esteves
- Instituto de Sustentabilidade e Biodiversidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
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10
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Zheng T, He X, Ye H, Fu W, Peng M, Gou G. Phylogeography of the rare and endangered lycophyte Isoetes yunguiensis. PeerJ 2020; 8:e8270. [PMID: 31915576 PMCID: PMC6944106 DOI: 10.7717/peerj.8270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/22/2019] [Indexed: 11/20/2022] Open
Abstract
Background Isoetes yunguiensis Q. F. Wang & W. C. Taylor is a lycophyte of an ancient genus, and it is endemic to China. It is a first-class protected plant in China. This living fossil is used in paleoecology and studies on the evolution of Lycophytes in the Yunnan-Guizhou Plateau. In recent years, human activities have caused the disappearance of several wild populations, and the number of plants in the existing populations is low. Study of the genetic structure, distribution pattern, and historical dynamics of I. yunguiensis in all areas of its distribution is of guiding significance for its rational and effective protection. Methods Expressed sequence tag-simple sequence repeat (EST-SSR) markers were used to study the genetic diversity and structure of I. yunguiensis, and noncoding chloroplast DNA (cpDNA) sequences were used to study the pedigree, population dynamics history, and glacial shelter of I. yunguiensis. A maximum entropy model was used to predict the past, present, and future distribution patterns of I. yunguiensis. Results Analysis with EST-SSR markers revealed that I. yunguiensis showed high genetic diversity and that genetic variation was significantly higher within populations than between populations. Based on cpDNA data, it was concluded that there was no significant geographic pedigree in the whole area of I. yunguiensis distribution (NST = 0.344 > GST = 0.183, p > 0.05); 21 haplotypes were detected using DnaSP v5. Neutral test and LAMARC simulation showed that I. yunguiensis has experienced rapid expansion in recent years. The maximum entropy model predicted that the potential distribution area of I. yunguiensis in the last glacial maximum period has increased significantly compared with the present distribution area, but the future distribution area did not show substantial changes.
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Affiliation(s)
- Tao Zheng
- College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Xuanze He
- College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Honghuan Ye
- College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Wei Fu
- College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Maimai Peng
- College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Guangqian Gou
- College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
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11
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Luo Q, Wu M, Sun Y, Lv J, Zhang Y, Cao H, Wu D, Lin D, Zhang Q, Liu Y, Qin W, Chen H. Optimizing the Extraction and Encapsulation of Mucilage from Brasenia Schreberi. Polymers (Basel) 2019; 11:E822. [PMID: 31067742 PMCID: PMC6571674 DOI: 10.3390/polym11050822] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/20/2019] [Accepted: 04/28/2019] [Indexed: 12/31/2022] Open
Abstract
The mucilage from Brasenia schreberi (BS) exhibits various biological activities, including antialgal, antibacterial, soluble-fiber properties, and excellent lubricating behavior. Thus, the extraction and wide use of mucilage in the food industry are crucial. In this study, the high-speed shear-assisted extraction of mucilage from BS was optimized by using response surface methodology (RSM). The optimal extraction conditions were as follows: Extraction temperature of 82 °C, extraction time of 113 min, liquid-solid ratio of 47 mL/g, and shear speed of 10,000 rpm. Under these conditions, the actual yield of BS mucilage was 71.67%, which highly matched the yield (73.44%) predicted by the regression model. Then, the BS mucilage extract was powdered to prepare the capsule, and the excipients of the capsule were screened using a single-factor test to improve the disintegration property and flowability. The final capsule formulation, which consisted of: 39% BS mucilage powder (60 meshes); 50% microcrystalline cellulose (60 meshes) as the filler; both 10% sodium starch glycolate and PVPP XL-10 (3:1, 60 meshes) as the disintegrant; both 1% colloidal silicon dioxide and sodium stearyl fumarate (1:1, 100 meshes) as the glidant by weight; were used for preparing the weights of a 320 mg/grain of capsule with 154.7 ± 0.95 mg/g polysaccharide content. Overall, the optimized extraction process had a high extraction rate for BS mucilage and the capsule formulation was designed reasonably.
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Affiliation(s)
- Qingying Luo
- College of Food Science, Sichuan Agricultural University, Yaan 625014, Sichuan, China.
| | - Min Wu
- College of Food Science, Sichuan Agricultural University, Yaan 625014, Sichuan, China.
| | - Yanan Sun
- College of Food Science, Sichuan Agricultural University, Yaan 625014, Sichuan, China.
| | - Junxia Lv
- College of Food Science, Sichuan Agricultural University, Yaan 625014, Sichuan, China.
| | - Yu Zhang
- College of Food Science, Sichuan Agricultural University, Yaan 625014, Sichuan, China.
| | - Hongfu Cao
- College of Food Science, Sichuan Agricultural University, Yaan 625014, Sichuan, China.
| | - Dingtao Wu
- College of Food Science, Sichuan Agricultural University, Yaan 625014, Sichuan, China.
| | - Derong Lin
- College of Food Science, Sichuan Agricultural University, Yaan 625014, Sichuan, China.
| | - Qing Zhang
- College of Food Science, Sichuan Agricultural University, Yaan 625014, Sichuan, China.
| | - Yuntao Liu
- College of Food Science, Sichuan Agricultural University, Yaan 625014, Sichuan, China.
| | - Wen Qin
- College of Food Science, Sichuan Agricultural University, Yaan 625014, Sichuan, China.
| | - Hong Chen
- College of Food Science, Sichuan Agricultural University, Yaan 625014, Sichuan, China.
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