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Huang L, Xu Y, Valcárcel V, Lutz S, Wen J, Ren Z. Three complete chloroplast genomes from two north American Rhus species and phylogenomics of Anacardiaceae. BMC Genom Data 2024; 25:30. [PMID: 38491489 PMCID: PMC10943888 DOI: 10.1186/s12863-024-01200-6] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/30/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND The suamc genus Rhus (sensu stricto) includes two subgenera, Lobadium (ca. 25 spp.) and Rhus (ca. 10 spp.). Their members, R. glabra and R. typhina (Rosanae: Sapindales: Anacardiaceae), are two economic important species. Chloroplast genome information is of great significance for the study of plant phylogeny and taxonomy. RESULTS The three complete chloroplast genomes from two Rhus glabra and one R. typhina accessions were obtained with a total of each about 159k bp in length including a large single-copy region (LSC, about 88k bp), a small single-copy regions (SSC, about 19k bp) and a pair of inverted repeats regions (IRa/IRb, about 26k bp), to form a canonical quadripartite structure. Each genome contained 88 protein-coding genes, 37 transfer RNA genes, eight ribosomal RNA genes and two pseudogenes. The overall GC content of the three genomes all were same (37.8%), and RSCU values showed that they all had the same codon prefers, i.e., to use codon ended with A/U (93%) except termination codon. Three variable hotspots, i.e., ycf4-cemA, ndhF-rpl32-trnL and ccsA-ndhD, and a total of 152-156 simple sequence repeats (SSR) were identified. The nonsynonymous (Ka)/synonymous (Ks) ratio was calculated, and cemA and ycf2 genes are important indicators of gene evolution. The phylogenetic analyses of the family Anacardiaceae showed that the eight genera were grouped into three clusters, and supported the monophyly of the subfamilies and all the genera. The accessions of five Rhus species formed four clusters, while, one individual of R. typhina grouped with the R. glabra accessions instead of clustering into the two other individuals of R. typhina in the subgenus Rhus, which showed a paraphyletic relationship. CONCLUSIONS Comparing the complete chloroplast genomes of the Rhus species, it was found that most SSRs were A/T rich and located in the intergenic spacer, and the nucleotide divergence exhibited higher levels in the non-coding region than in the coding region. The Ka/Ks ratio of cemA gene was > 1 for species collected in America, while it was < 1 for other species in China, which dedicated that the Rhus species from North America and East Asia have different evolutionary pressure. The phylogenetic analysis of the complete chloroplast genome clarified the Rhus placement and relationship. The results obtained in this study are expected to provide valuable genetic resources to perform species identification, molecular breeding, and intraspecific diversity of the Rhus species.
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Affiliation(s)
- Lan Huang
- School of Life Science, Shanxi University, 030006, Taiyuan, Shanxi, China
| | - Yujie Xu
- School of Geosciences, Qinghai Normal University, 810008, Xining, Qinghai, China
| | - Virginia Valcárcel
- Departamento de Biología, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Centro de Investigación en Biodiversidady Cambio Global (CIBC-UAM) , Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Sue Lutz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, 20013, Washington, DC, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, 20013, Washington, DC, USA.
| | - Zhumei Ren
- School of Life Science, Shanxi University, 030006, Taiyuan, Shanxi, China.
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Ma K, Fu Y, Liu Y. The effects of microplastics on crop variation depend on polymer types and their interactions with soil nutrient availability and weed competition. Plant Biol (Stuttg) 2024; 26:223-231. [PMID: 38198234 DOI: 10.1111/plb.13612] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 11/13/2023] [Indexed: 01/12/2024]
Abstract
Microplastics pollution of agricultural soil is a global environmental concern because of its potential risk to food security and human health. Although many studies have tested the direct effects of microplastics on growth of Eruca sativa Mill., little is known about whether these effects are regulated by fertilization and weed competition in field management practices. Here, we performed a greenhouse experiment growing E. sativa as target species in a three-factorial design with two levels of fertilization (low versus. high), two levels of weed competition treatments (weed competition versus no weed competition) and five levels of microplastic treatments (no microplastics, Polybutylene adipate-co-terephthalate [PBAT], Polybutylene succinate [PBS], Polycaprolactone [PCL] or Polypropylene [PP]). Compared to the soil without microplastics, PBS and PCL reduced aboveground biomass and leaf number of the E. sativa. PBS also resulted in increased root allocation and thicker roots in E. sativa. In addition, fertilization significantly mitigated the negative effects of PBS and PCL on aboveground biomass of E. sativa, but weed competition significantly promoted these effects. Although fertilization alleviated the negative effect of PBS on aboveground biomass, such alleviation became weaker under weed competition than when E. sativa grew alone. The results indicate that the effects of specific polymer types on E. sativa growth could be regulated by fertilization, weed management, and even their interactions. Therefore, reasonable on-farm management practices may help in mitigating the negative effects of microplastics pollution on E. sativa growth in agricultural fields.
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Affiliation(s)
- K Ma
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Y Fu
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Y Liu
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
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Xiao F, Zhao Y, Wang X, Jian X. Characterization of the chloroplast genome of Gleditsia species and comparative analysis. Sci Rep 2024; 14:4262. [PMID: 38383559 PMCID: PMC10881578 DOI: 10.1038/s41598-024-54608-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 02/14/2024] [Indexed: 02/23/2024] Open
Abstract
The genus Gleditsia has significant medicinal and economic value, but information about the chloroplast genomic characteristics of Gleditsia species has been limited. Using the Illumina sequencing, we assembled and annotated the whole chloroplast genomes of seven Gleditsia species (Gleditsia sinensis, Gleditsia japonica var. delavayi (G. delavayi), G. fera, G. japonica, G. microphylla, Fructus Gleditsiae Abnormalis (Zhū Yá Zào), G. microphylla mutant). The assembled genomes revealed that Gleditsia species have a typical circular tetrad structure, with genome sizes ranging from 162,746 to 170,907 bp. Comparative genomic analysis showed that most (65.8-75.8%) of the abundant simple sequence repeats in Gleditsia and Gymnocladus species were located in the large single copy region. The Gleditsia chloroplast genome prefer T/A-ending codons and avoid C/G-ending codons, positive selection was acting on the rpoA, rpl20, atpB, ndhA and ycf4 genes, most of the chloroplast genes of Gleditsia species underwent purifying selection. Expansion and contraction of the inverted repeat (IR)/single copy (SC) region showed similar patterns within the Gleditsia genus. Polymorphism analysis revealed that coding regions were more conserved than non-coding regions, and the IR region was more conserved than the SC region. Mutational hotspots were mostly found in intergenic regions such as "rps16-trnQ", "trnT-trnL", "ndhG-ndhI", and "rpl32-trnL" in Gleditsia. Phylogenetic analysis showed that G. fera is most closely related to G. sinensis,G. japonica and G. delavayi are relatively closely related. Zhū Yá Zào can be considered a bud mutation of the G. sinensis. The albino phenotype of G. microphylla mutant is not caused by variations in the chloroplast genome, and that the occurrence of the albino phenotype may be due to mutations in chloroplast-related genes involved in splicing or localization functions. This study will help us enhance our exploration of the genetic evolution and geographical origins of the Gleditsia genus.
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Affiliation(s)
- Feng Xiao
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Yang Zhao
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China.
| | - Xiurong Wang
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Xueyan Jian
- College of Continuing Education, Yanbian University, Yanji, 133002, Jilin, China
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Shim D, Jeon SH, Kim JC, Yoon DK. Comparative Phylogenetic Analysis of Ancient Korean Tea "Hadong Cheon-Nyeon Cha ( Camellia sinensis var. sinensis)" Using Complete Chloroplast Genome Sequences. Curr Issues Mol Biol 2024; 46:1091-1106. [PMID: 38392187 PMCID: PMC10888334 DOI: 10.3390/cimb46020069] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
Wild teas are valuable genetic resources for studying evolution and breeding. Here, we report the complete chloroplast genome of the ancient Korean tea 'Hadong Cheon-nyeon Cha' (C. sinensis var. sinensis), which is known as the oldest tea tree in Korea. This study determined seven Camellia sinensis var. sinenesis, including Hadong Cheon-nyeon Cha (HCNC) chloroplast genome sequences, using Illumina sequencing technology via de novo assembly. The chloroplast genome sizes ranged from 157,019 to 157,114 bp and were organized into quadripartite regions with the typical chloroplast genomes. Further, differences in SNPs and InDels were detected across the seven chloroplast genomes through variance analysis. Principal component and phylogenetic analysis suggested that regional constraints, rather than functional constraints, strongly affected the sequence evolution of the cp genomes in this study. These genomic resources provide evolutionary insight into Korean tea plant cultivars and lay the foundation for a better understanding of the ancient Korean tea plant HCNC.
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Affiliation(s)
- Doobo Shim
- Institute of Hadong Green Tea, Hadong 52304, Republic of Korea
| | - Seung Ho Jeon
- Department of Agricultural Life Science, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Jong Cheol Kim
- Institute of Hadong Green Tea, Hadong 52304, Republic of Korea
| | - Dong-Kyung Yoon
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea
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Javaid N, Ramzan M, Jabeen S, Shah MN, Danish S, Hirad AH. Genomic exploration of Sesuvium sesuvioides: comparative study and phylogenetic analysis within the order Caryophyllales from Cholistan desert, Pakistan. BMC Plant Biol 2023; 23:658. [PMID: 38124056 PMCID: PMC10731703 DOI: 10.1186/s12870-023-04670-5] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND The Aizoaceae family's Sesuvium sesuvioides (Fenzl) Verdc is a medicinal species of the Cholistan desert, Pakistan. The purpose of this study was to determine the genomic features and phylogenetic position of the Sesuvium genus in the Aizoaceae family. We used the Illumina HiSeq2500 and paired-end sequencing to publish the complete chloroplast sequence of S. sesuvioides. RESULTS The 155,849 bp length cp genome sequence of S. sesuvioides has a 36.8% GC content. The Leucine codon has the greatest codon use (10.6%), 81 simple sequence repetitions of 19 kinds, and 79 oligonucleotide repeats. We investigated the phylogeny of the order Caryophyllales' 27 species from 23 families and 25 distinct genera. The maximum likelihood tree indicated Sesuvium as a monophyletic genus, and sister to Tetragonia. A comparison of S. sesuvioides, with Sesuvium portulacastrum, Mesembryanthemum crystallinum, Mesembryanthemum cordifolium, and Tetragonia tetragonoides was performed using the NCBI platform. In the comparative investigation of genomes, all five genera revealed comparable cp genome structure, gene number and composition. All five species lacked the rps15 gene and the rpl2 intron. In most comparisons with S. sesuvioides, transition substitutions (Ts) were more frequent than transversion substitutions (Tv), producing Ts/Tv ratios larger than one, and the Ka/Ks ratio was lower than one. We determined ten highly polymorphic regions, comprising rpl22, rpl32-trnL-UAG, trnD-GUC-trnY-GUA, trnE-UUC-trnT-GGU, trnK-UUU-rps16, trnM-CAU-atpE, trnH-GUG-psbA, psaJ-rpl33, rps4-trnT-UGU, and trnF-GAA-ndhJ. CONCLUSION The whole S. sesuvioides chloroplast will be examined as a resource for in-depth taxonomic research of the genus when more Sesuvium and Aizoaceae species are sequenced in the future. The chloroplast genomes of the Aizoaceae family are well preserved, with little alterations, indicating the family's monophyletic origin. This study's highly polymorphic regions could be utilized to build realistic and low-cost molecular markers for resolving taxonomic discrepancies, new species identification, and finding evolutionary links among Aizoaceae species. To properly comprehend the evolution of the Aizoaceae family, further species need to be sequenced.
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Affiliation(s)
- Nida Javaid
- Department of Botany, Faculty of Chemical and Biological Sciences, The Islamia University Bahawalpur, Bahawalpur, Punjab, Pakistan
| | - Musarrat Ramzan
- Department of Botany, Faculty of Chemical and Biological Sciences, The Islamia University Bahawalpur, Bahawalpur, Punjab, Pakistan.
| | - Shagufta Jabeen
- Government Associate College for Women Ahmedpur East, Bahawalpur, Punjab, Pakistan
| | - Muhammad Nadeem Shah
- Department of Agriculture, Government College University Lahore, Lahore, Punjab, Pakistan
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, Florida, USA
| | - Subhan Danish
- Department of Soil Science, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, Punjab, Pakistan.
| | - Abdurahman Hajinur Hirad
- Department of Botany and Microbiology, College of Science, King Saud University, P. O. Box.2455, Riyadh, 11451, Saudi Arabia
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Feng L, Zhao G, An M, Wang C, Yin Y. Complete chloroplast genome sequences of the ornamental plant Prunus cistena and comparative and phylogenetic analyses with its closely related species. BMC Genomics 2023; 24:739. [PMID: 38053028 DOI: 10.1186/s12864-023-09838-9] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 11/23/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Prunus cistena is an excellent color leaf configuration tree for urban landscaping in the world, which has purplish red leaves, light pink flowers, plant shape and high ornamental value. Genomic resources for P. cistena are scarce, and a clear phylogenetic and evolutionary history for this species has yet to be elucidated. Here, we sequenced and analyzed the complete chloroplast genome of P. cistena and compared it with related species of the genus Prunus based on the chloroplast genome. RESULTS The complete chloroplast genome of P. cistena is a 157,935 bp long typical tetrad structure, with an overall GC content of 36.72% and higher GC content in the in the inverted repeats (IR) regions than in the large single-copy (LSC) and small single-copy (SSC) regions. It contains 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The ycf3 and clpP genes have two introns, with the longest intron in the trnK-UUU gene in the LSC region. Moreover, the genome has a total of 253SSRs, with the mononucleotide SSRs being the most abundant. The chloroplast sequences and gene arrangements of P. cistena are highly conserved, with the overall structure and gene order similar to other Prunus species. The atpE, ccsA, petA, rps8, and matK genes have undergone significant positive selection in Prunus species. P. cistena has a close evolutionary relationship with P. jamasakura. The coding and IR regions are more conserved than the noncoding regions, and the chloroplast DNA sequences are highly conserved throughout the genus Prunus. CONCLUSIONS The current genomic datasets provide valuable information for further species identification, evolution, and phylogenetic research of the genus Prunus.
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Affiliation(s)
- Lijuan Feng
- Shandong Institute of Pomology, Taian, 271000, Shandong, China
| | - Guopeng Zhao
- Yantai Testing Center for Food and Drug, Yantai, 264005, Shandong, China
| | - Mengmeng An
- Zibo Academy of Agricultural Sciences, Zibo, 255000, Shandong, China
| | - Chuanzeng Wang
- Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China.
| | - Yanlei Yin
- Shandong Institute of Pomology, Taian, 271000, Shandong, China.
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Yan R, Geng Y, Jia Y, Xiang C, Zhou X, Hu G. Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution. Front Plant Sci 2023; 14:1265641. [PMID: 37828930 PMCID: PMC10565954 DOI: 10.3389/fpls.2023.1265641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/01/2023] [Indexed: 10/14/2023]
Abstract
Introduction The recently established Linderniaceae, separated from the traditionally defined Scrophulariaceae, is a taxonomically complicated family. Although previous phylogenetic studies based on a few short DNA markers have made great contributions to the taxonomy of Linderniaceae, limited sampling and low resolution of the phylogenetic tree have failed to resolve controversies between some generic circumscriptions. The plastid genome exhibits a powerful ability to solve phylogenetic relationships ranging from shallow to deep taxonomic levels. To date, no plastid phylogenomic studies have been carried out in Linderniaceae. Methods In this study, we newly sequenced 26 plastid genomes of Linderniaceae, including eight genera and 25 species, to explore the phylogenetic relationships and genome evolution of the family through plastid phylogenomic and comparative genomic analyses. Results The plastid genome size of Linderniaceae ranged from 152,386 bp to 154,402 bp, exhibiting a typical quartile structure. All plastomes encoded 114 unique genes, comprising 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The inverted repeat regions were more conserved compared with the single-copy regions. A total of 1803 microsatellites and 1909 long sequence repeats were identified, and five hypervariable regions (petN-psbM, rps16-trnQ, rpl32-trnL, rpl32, and ycf1) were screened out. Most protein-coding genes were relatively conserved, with only the ycf2 gene found under positive selection in a few species. Phylogenomic analyses confirmed that Linderniaceae was a distinctive lineage and revealed that the presently circumscribed Vandellia and Torenia were non-monophyletic. Discussion Comparative analyses showed the Linderniaceae plastomes were highly conservative in terms of structure, gene order, and gene content. Combining morphological and molecular evidence, we supported the newly established Yamazakia separating from Vandellia and the monotypic Picria as a separate genus. These findings provide further evidence to recognize the phylogenetic relationships among Linderniaceae and new insights into the evolution of the plastid genomes.
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Affiliation(s)
- Rongrong Yan
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, China
- College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Yanfei Geng
- College of Tea Science, Guizhou University, Guiyang, Guizhou, China
| | - Yuhuan Jia
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, China
- College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Chunlei Xiang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xinxin Zhou
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Guoxiong Hu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, China
- College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
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Kashyap A, Kumari S, Garg P, Kushwaha R, Tripathi S, Sharma J, Gupta NC, Kumar RR, Yadav R, Vishwakarma H, Rana JC, Bhattacharya R, Rao M. Indexing Resilience to Heat and Drought Stress in the Wild Relatives of Rapeseed-Mustard. Life (Basel) 2023; 13:738. [PMID: 36983893 PMCID: PMC10055847 DOI: 10.3390/life13030738] [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] [Received: 01/11/2023] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 03/11/2023] Open
Abstract
Wild species are weedy relatives and progenitors of cultivated crops, usually maintained in their centres of origin. They are rich sources of diversity as they possess many agriculturally important traits. In this study, we analysed 25 wild species and 5 U triangle species of Brassica for their potential tolerance against heat and drought stress during germination and in order to examine the early seedling stage. We identified the germplasms based on the mean membership function value (MFV), which was calculated from the tolerance index of shoot length, root length, and biochemical analysis. The study revealed that B. napus (GSC-6) could withstand high temperatures and drought. Other genotypes that were tolerant to the impact of heat stress were B. tournefortii (RBT 2002), D. gomez-campoi, B. tournefortii (Rawa), L. sativum, and B. carinata (PC-6). C. sativa resisted drought but did not perform well when subjected to high temperatures. Tolerance to drought was observed in B. fruticulosa (Spain), B. tournefortii (RBT 2003), C. bursa-pastoris (late), D. muralis, C. abyssinica (EC694145), C. abyssinica (EC400058) and B. juncea (Pusa Jaikisan). This investigation contributes to germplasm characterization and the identification of the potential source of abiotic stress tolerance in the Brassica breeding programme. These identified genotypes can be potential sources for transferring the gene(s)/genomic regions that determine tolerance to the elite cultivars.
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Fu X, Xie DF, Zhou YY, Cheng RY, Zhang XY, Zhou SD, He XJ. Phylogeny and adaptive evolution of subgenus Rhizirideum (Amaryllidaceae, Allium) based on plastid genomes. BMC Plant Biol 2023; 23:70. [PMID: 36726056 PMCID: PMC9890777 DOI: 10.1186/s12870-022-03993-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 12/09/2022] [Indexed: 06/01/2023]
Abstract
The subgenus Rhizirideum in the genus Allium consists of 38 species worldwide and forms five sections (A. sect. Rhizomatosa, A. sect. Tenuissima, A. sect. Rhizirideum, A. sect. Eduardia, and A. sect. Caespitosoprason), A. sect. Caespitosoprason being merged into A. sect. Rhizomatosa recently. Previous studies on this subgenus mainly focused on separate sections. To investigate the inter-section and inter-subgenera phylogenetic relationships and adaptive evolution of A. subg. Rhizirideum, we selected thirteen representative species, which cover five sections of this subgenus and can represent four typical phenotypes of it. We conducted the comparative plastome analysis with our thirteen plastomes. And phylogenetic inferences with CDSs and complete sequences of plastomes of our thirteen species and another fifty-four related species were also performed. As a result, the A. subg. Rhizirideum plastomes were relatively conservative in structure, IR/SC borders, codon usage, and repeat sequence. In phylogenetic results, the inter-subgenera relationships among A. subg. Rhizirideum and other genus Allium subgenera were generally similar to the previous reports. In contrast, the inter-section relationships within our subgenus A. subg. Rhizirideum were newly resolved in this study. A. sect. Rhizomatosa and A. sect. Tenuissima were sister branches, which were then clustered with A. sect. Rhizirideum and A. sect. Eduardia successively. However, Allium Polyrhizum Turcz. ex Regel, type species of A. sect. Caespitosoprason, was resolved as the basal taxon of A. subg. Rhizirideum. Allium siphonanthum J. M. Xu was also found in clade A. subg. Cyathophora instead of clade A. subg. Rhizirideum. The selective pressure analysis was also conducted, and most protein-coding genes were under purifying selection. At the same time, just one gene, ycf2, was found under positive selection, and another three genes (rbcL, ycf1a, ycf1b) presented relaxed selection, which were all involved in the photosynthesis. The low temperature, dry climate, and high altitude of the extreme habitats where A. subg. Rhizirideum species grow might impose intense natural selection forces on their plastome genes for photosynthesis. In summary, our research provides new insights into the phylogeny and adaptive evolution of A. subg. Rhizirideum. Moreover, we suggest that the positions of the A. subg. Rhizirideum species A. polyrhizum and A. siphonanthum should be reconsidered.
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Affiliation(s)
- Xiao Fu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, The People's Republic of China
| | - Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, The People's Republic of China
| | - Yu-Yang Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, The People's Republic of China
| | - Rui-Yu Cheng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, The People's Republic of China
| | - Xiang-Yi Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, The People's Republic of China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, The People's Republic of China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, The People's Republic of China.
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Song B, Liu C, Xie D, Xiao Y, Tian R, Li Z, Zhou S, He X. Plastid Phylogenomic Analyses Reveal the Taxonomic Position of Peucedanum franchetii. Plants (Basel) 2022; 12:97. [PMID: 36616226 PMCID: PMC9824613 DOI: 10.3390/plants12010097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Peucedanum franchetii is a famous folk medicinal plant in China. However, the taxonomy of the P. franchetii has not been sufficiently resolved. Due to similar morphological features between P. franchetii and Ligusticopsis members, the World Flora Online (WFO) Plant List suggested that this species transformed into the genus Ligusticopsis and merged with Ligusticopsis likiangensis. However, both species are obviously diverse in leaf shape, bracts, and bracteoles. To check the taxonomic position of P. franchetii, we newly sequenced and assembled the plastome of P. franchetii and compared it with nine other plastomes of the genus Ligusticopsis. Ten plastomes were highly conserved and similar in gene order, codon bias, RNA editing sites, IR borders, and SSRs. Nevertheless, 10 mutation hotspot regions (infA, rps8, matK, ndhF, rps15, psbA-trnH, rps2-rpoC2, psbA-trnK, ycf2-trnL, and ccsA-ndhD) were still detected. In addition, both phylogenetic analyses based on plastome data and ITS sequences robustly supported that P. franchetii was not clustered with members of Peucedanum but nested in Ligusticopsis. P. franchetii was sister to L. likiangensis in the ITS topology but clustered with L. capillacea in the plastome tree. These findings implied that P. franchetii should be transferred to genus Ligusticopsis and not merged with L. likiangensis, but as an independent species, which was further verified by morphological evidences. Therefore, transferring P. franchetii under the genus Ligusticopsis as an independent species was reasonable, and a new combination was presented.
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Bai X, Peng J, Yang Y, Xiong B. The Complete Chloroplast Genome Sequence of Machilus chuanchienensis (Lauraceae): Genome Structure and Phylogenetic Analysis. Genes (Basel) 2022; 13. [PMID: 36553669 DOI: 10.3390/genes13122402] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Machilus chuanchienensis is an ecological tree distributed in southwestern China. It has a significant valuation with making Hawk tea using its leaves, an ethnic traditional tea-like beverage with a long history in Chinese tea culture. The whole chloroplast (cp) genome is an ideal model for the phylogenetic study of Lauraceae because of its simple structure and highly conserved features. There have been numerous reports of complete cp genome sequences in Lauraceae, but little is known about M. chuanchienensis. Here, the next-generation sequencing (NGS) was used to sequence the M. chuanchienensis cp genome. Then, a comprehensive comparative genome analysis was performed. The results revealed that the M. chuanchienensis's cp genome measured 152,748 base pairs (bp) with a GC content of 39.15% and coded 126 genes annotated, including comprising eight ribosomal RNA (rRNA), 36 transporter RNA (tRNA), and 82 protein-coding genes. In addition, the cp genome presented a typical quadripartite structure comprising a large single-copy (LSC; 93,811) region, a small single-copy (SSC; 18,803) region, and the inverted repeats (IRs; 20,067) region and contained 92 simple sequence repeat (SSR) locus in total. Phylogenetic relationships of 37 species indicated that M. chuanchienensis was a sister to M. balansae, M. melanophylla, and M. minutiflora. Further research on this crucial species may benefit significantly from these findings.
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Tayşi N, Kaymaz Y, Ateş D, Sari H, Toker C, Tanyolaç MB. Complete chloroplast genome sequence of Lens ervoides and comparison to Lens culinaris. Sci Rep 2022; 12:15068. [PMID: 36064865 PMCID: PMC9445179 DOI: 10.1038/s41598-022-17877-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 08/02/2022] [Indexed: 12/05/2022] Open
Abstract
Lens is a member of the Papilionoideae subfamily of Fabaceae and is generally used as a source of vegetable protein as part of human diets in many regions worldwide. Chloroplast (cp) genomes are highly active genetic components of plants and can be utilized as molecular markers for various purposes. As one of the wild lentil species, the Lens ervoides cp genome has been sequenced for the first time in this study using next-generation sequencing. The de novo assembly of the cp genome resulted in a single 122,722 bp sequence as two separate coexisting structural haplotypes with similar lengths. Results indicated that the cp genome of L. ervoides belongs to the inverted repeat lacking clade. Several noteworthy divergences within the coding regions were observed in ndhB, ndhF, rbcL, rpoC2, and ycf2 genes. Analysis of relative synonymous codon usage showed that certain genes, psbN, psaI, psbI, psbE, psbK, petD, and ndhC, preferred using biased codons more often and therefore might have elevated expression and translation efficiencies. Overall, this study exhibited the divergence level between the wild-type and cultured lentil cp genomes and pointed to certain regions that can be utilized as distinction markers for various goals.
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Affiliation(s)
- Nurbanu Tayşi
- Bioengineering Department, Faculty of Engineering, Ege University, Izmir, Turkey
| | - Yasin Kaymaz
- Bioengineering Department, Faculty of Engineering, Ege University, Izmir, Turkey
| | - Duygu Ateş
- Bioengineering Department, Faculty of Engineering, Ege University, Izmir, Turkey
| | - Hatice Sari
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - Cengiz Toker
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - M Bahattin Tanyolaç
- Bioengineering Department, Faculty of Engineering, Ege University, Izmir, Turkey.
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13
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Li DM, Zhu GF, Yu B, Huang D. Comparative chloroplast genomes and phylogenetic relationships of Aglaonema modestum and five variegated cultivars of Aglaonema. PLoS One 2022; 17:e0274067. [PMID: 36054201 PMCID: PMC9439221 DOI: 10.1371/journal.pone.0274067] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/19/2022] [Indexed: 11/30/2022] Open
Abstract
Aglaonema, commonly called Chinese evergreens, are widely used for ornamental purposes. However, attempts to identify Aglaonema species and cultivars based on leaf morphology have been challenging. In the present study, chloroplast sequences were used to elucidate the phylogenetic relationships of cultivated Aglaonema in South China. The chloroplast genomes of one green species and five variegated cultivars of Aglaonema, Aglaonema modestum, ‘Red Valentine’, ‘Lady Valentine’, ‘Hong Yan’, ‘Hong Jian’, and ‘Red Vein’, were sequenced for comparative and phylogenetic analyses. The six chloroplast genomes of Aglaonema had typical quadripartite structures, comprising a large single copy (LSC) region (91,092–91,769 bp), a small single copy (SSC) region (20,816–26,501 bp), and a pair of inverted repeat (IR) regions (21,703–26,732 bp). The genomes contained 112 different genes, including 79–80 protein coding genes, 28–29 tRNAs and 4 rRNAs. The molecular structure, gene order, content, codon usage, long repeats, and simple sequence repeats (SSRs) were generally conserved among the six sequenced genomes, but the IR-SSC boundary regions were significantly different, and ‘Red Vein’ had a distinct long repeat number and type frequency. For comparative and phylogenetic analyses, Aglaonema costatum was included; it was obtained from the GenBank database. Single-nucleotide polymorphisms (SNPs) and insertions/deletions (indels) were determined among the seven Aglaonema genomes studied. Nine divergent hotspots were identified: trnH-GUG-CDS1_psbA, trnS-GCU_trnS-CGA-CDS1, rps4-trnT-UGU, trnF-GAA-ndhJ, petD-CDS2-rpoA, ycf1-ndhF, rps15-ycf1-D2, ccsA-ndhD, and trnY-GUA-trnE-UUC. Additionally, positive selection was found for rpl2, rps2, rps3, ycf1 and ycf2 based on the analyses of Ka/Ks ratios among 16 Araceae chloroplast genomes. The phylogenetic tree based on whole chloroplast genomes strongly supported monophyletic Aglaonema and clear relationships among Aroideae, Lasioideae, Lemnoideae, Monsteroideae, Orontioideae, Pothoideae and Zamioculcadoideae in the family Araceae. By contrast, protein coding gene phylogenies were poorly to strongly supported and incongruent with the whole chloroplast genome phylogenetic tree. This study provided valuable genome resources and helped identify Aglaonema species and cultivars.
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Affiliation(s)
- Dong-Mei Li
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- * E-mail: (D-ML); (G-FZ)
| | - Gen-Fa Zhu
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- * E-mail: (D-ML); (G-FZ)
| | - Bo Yu
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Dan Huang
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
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Pei J, Wang Y, Zhuo J, Gao H, Vasupalli N, Hou D, Lin X. Complete Chloroplast Genome Features of Dendrocalamusfarinosus and Its Comparison and Evolutionary Analysis with Other Bambusoideae Species. Genes (Basel) 2022; 13:1519. [PMID: 36140690 PMCID: PMC9498922 DOI: 10.3390/genes13091519] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/16/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Dendrocalamus farinosus is one of the essential bamboo species mainly used for food and timber in the southwestern region of China. In this study, the complete chloroplast (cp) genome of D. farinosus is sequenced, assembled, and the phylogenetic relationship analyzed. The cp genome has a circular and quadripartite structure, has a total length of 139,499 bp and contains 132 genes: 89 protein-coding genes, eight rRNAs and 35 tRNAs. The repeat analyses showed that three types of repeats (palindromic, forward and reverse) are present in the genome. A total of 51 simple sequence repeats are identified in the cp genome. The comparative analysis between different species belonging to Dendrocalamus revealed that although the cp genomes are conserved, many differences exist between the genomes. The analysis shows that the non-coding regions were more divergent than the coding regions, and the inverted repeat regions are more conserved than the single-copy regions. Moreover, these results also indicate that rpoC2 may be used to distinguish between different bamboo species. Phylogenetic analysis results supported that D. farinosus was closely related to D. latiflorus. Furthermore, these bamboo species’ geographical distribution and rhizome types indicate two evolutionary pathways: one is from the tropics to the alpine zone, and the other is from the tropics to the warm temperate zone. Our study will be helpful in the determination of the cp genome sequences of D. farinosus, and provides new molecular data to understand the Bambusoideae evolution.
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Wan D, Bao H, Danzeng Q, Guo X, Li Q. Chloroplast genome of Corydalis impatiens (Pall.) Fisch. ex DC. (Papaveraceae), a Tibetan medical herb. Mitochondrial DNA B Resour 2022; 7:1413-1415. [PMID: 35937907 PMCID: PMC9347461 DOI: 10.1080/23802359.2022.2104668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Corydalis impatiens (Pall.) Fisch. 1821. (Papaveraceae) is a Tibetan medical herb used to reduce pain, treat skin injuries, cure hepatitis, and benefit the circulatory system. In the current study, the chloroplast genome of C. impatiens was sequenced. This complete genome is a circular 197,317 bp sequence consisting of a small single-copy (SSC, 3105 bp) region, a large single-copy (LSC, 89,790 bp) region, and a pair of inverted repeats (IRs, 52,211 bp). This chloroplast genome encodes a total of 127 functional genes, including 81 protein-coding, 38 transfer RNA, and eight ribosomal RNA genes. Furthermore, this chloroplast genome contains six pseudogenes, including a pair of ndhB a pair of ndhD, one ndhC, and one ndhK. The phylogenetic relationship within the genus Corydalis was inferred with the maximum-likelihood method, and the result showed that C. impatiens was most closely related to C. conspersa.
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Affiliation(s)
- Digao Wan
- Tibetan Medicine Research Center, Tibetan Medical College, Qinghai University, Xining, People’s Republic of China
| | - Haijuan Bao
- College of Ecological Environment and Resources, Qinghai Minzu University, Xining, People’s Republic of China
| | - Qupei Danzeng
- University Tibetan Medicine, Lhasa, People’s Republic of China
| | - Xiao Guo
- Tibetan Medicine Research Center, Tibetan Medical College, Qinghai University, Xining, People’s Republic of China
| | - Qien Li
- Tibetan Medicine Research Center, Tibetan Medical College, Qinghai University, Xining, People’s Republic of China
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Javaid N, Ramzan M, Khan IA, Alahmadi TA, Datta R, Fahad S, Danish S. The chloroplast genome of Farsetia hamiltonii Royle, phylogenetic analysis, and comparative study with other members of Clade C of Brassicaceae. BMC Plant Biol 2022; 22:384. [PMID: 35918648 PMCID: PMC9344719 DOI: 10.1186/s12870-022-03750-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 07/13/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Farsetia hamiltonii Royle is a medicinally important annual plant from the Cholistan desert that belongs to the tribe Anastaticeae and clade C of the Brassicaceae family. We provide the entire chloroplast sequence of F.hamiltonii, obtained using the Illumina HiSeq2500 and paired-end sequencing. We compared F. hamiltonii to nine other clade C species, including Farsetia occidentalis, Lobularia libyca, Notoceras bicorne, Parolinia ornata, Morettia canescens, Cochlearia borzaeana, Megacarpaea polyandra, Biscutella laevigata, and Iberis amara. We conducted phylogenetic research on the 22 Brassicaceae species, which included members from 17 tribes and six clades. RESULTS The chloroplast genome sequence of F.hamiltonii of 154,802 bp sizes with 36.30% GC content and have a typical structure comprised of a Large Single Copy (LSC) of 83,906 bp, a Small Single Copy (SSC) of 17,988 bp, and two copies of Inverted Repeats (IRs) of 26,454 bp. The genomes of F. hamiltonii and F. occidentalis show shared amino acid frequencies and codon use, RNA editing sites, simple sequence repeats, and oligonucleotide repeats. The maximum likelihood tree revealed Farsetia as a monophyletic genus, closely linked to Morettia, with a bootstrap score of 100. The rate of transversion substitutions (Tv) was higher than the rate of transition substitutions (Ts), resulting in Ts/Tv less than one in all comparisons with F. hamiltonii, indicating that the species are closely related. The rate of synonymous substitutions (Ks) was greater than non-synonymous substitutions (Ka) in all comparisons with F. hamiltonii, with a Ka/Ks ratio smaller than one, indicating that genes underwent purifying selection. Low nucleotide diversity values range from 0.00085 to 0.08516, and IR regions comprise comparable genes on junctions with minimal change, supporting the conserved status of the selected chloroplast genomes of the clade C of the Brassicaceae family. We identified ten polymorphic regions, including rps8-rpl14, rps15-ycf1, ndhG-ndhI, psbK-psbI, ccsA-ndhD, rpl36-rps8, petA-psbJ, ndhF-rpl32, psaJ-rpl3, and ycf1 that might be exploited to construct genuine and inexpensive to solve taxonomic discrepancy and understand phylogenetic relationship amongst Brassicaceae species. CONCLUSION The entire chloroplast sequencing of F. hamiltonii sheds light on the divergence of genic chloroplast sequences among members of the clade C. When other Farsetia species are sequenced in the future, the full F. hamiltonii chloroplast will be used as a source for comprehensive taxonomical investigations of the genus. The comparison of F. hamiltonii and other clade C species adds new information to the phylogenetic data and evolutionary processes of the clade. The results of this study will also provide further molecular uses of clade C chloroplasts for possible plant genetic modifications and will help recognise more Brassicaceae family species.
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Affiliation(s)
- Nida Javaid
- Department of Botany, The Islamia University, Bahawalpur, Pakistan
| | - Musarrat Ramzan
- Department of Botany, The Islamia University, Bahawalpur, Pakistan
| | - Ishtiaq Ahmad Khan
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences University of Karachi, Karachi, 75270 Pakistan
| | - Tahani Awad Alahmadi
- Department of Pediatrics, College of Medicine and King Khalid University Hospital, King Saud University, Medical City, PO Box-2925, Riyadh, 11461 Saudi Arabia
| | - Rahul Datta
- Department of Geology and Pedology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemedelska1, 61300 Brno, Czech Republic
| | - Shah Fahad
- Department of Agronomy, The University of Haripur, Khyber Pakhtunkhwa, Haripur, 22620 Pakistan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, 570228 China
| | - Subhan Danish
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, 570228 China
- Department of Soil Science, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, 60800 Punjab Pakistan
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Cay SB, Cinar YU, Kuralay SC, Inal B, Zararsiz G, Ciftci A, Mollman R, Obut O, Eldem V, Bakir Y, Erol O. Genome skimming approach reveals the gene arrangements in the chloroplast genomes of the highly endangered Crocus L. species: Crocus istanbulensis (B.Mathew) Rukšāns. PLoS One 2022; 17:e0269747. [PMID: 35704623 PMCID: PMC9200356 DOI: 10.1371/journal.pone.0269747] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/27/2022] [Indexed: 11/19/2022] Open
Abstract
Crocus istanbulensis (B.Mathew) Rukšāns is one of the most endangered Crocus species in the world and has an extremely limited distribution range in Istanbul. Our recent field work indicates that no more than one hundred individuals remain in the wild. In the present study, we used genome skimming to determine the complete chloroplast (cp) genome sequences of six C. istanbulensis individuals collected from the locus classicus. The cp genome of C. istanbulensis has 151,199 base pairs (bp), with a large single-copy (LSC) (81,197 bp), small single copy (SSC) (17,524 bp) and two inverted repeat (IR) regions of 26,236 bp each. The cp genome contains 132 genes, of which 86 are protein-coding (PCGs), 8 are rRNA and 38 are tRNA genes. Most of the repeats are found in intergenic spacers of Crocus species. Mononucleotide repeats were most abundant, accounting for over 80% of total repeats. The cp genome contained four palindrome repeats and one forward repeat. Comparative analyses among other Iridaceae species identified one inversion in the terminal positions of LSC region and three different gene (psbA, rps3 and rpl22) arrangements in C. istanbulensis that were not reported previously. To measure selective pressure in the exons of chloroplast coding sequences, we performed a sequence analysis of plastome-encoded genes. A total of seven genes (accD, rpoC2, psbK, rps12, ccsA, clpP and ycf2) were detected under positive selection in the cp genome. Alignment-free sequence comparison showed an extremely low sequence diversity across naturally occurring C. istanbulensis specimens. All six sequenced individuals shared the same cp haplotype. In summary, this study will aid further research on the molecular evolution and development of ex situ conservation strategies of C. istanbulensis.
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Affiliation(s)
- Selahattin Baris Cay
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Yusuf Ulas Cinar
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Selim Can Kuralay
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Behcet Inal
- Department of Agricultural Biotechnology, Faculty of Agriculture, University of Siirt, Siirt, Turkey
| | - Gokmen Zararsiz
- Department of Biostatistics, Erciyes University, Kayseri, Turkey
- Drug Application and Research Center (ERFARMA), Erciyes University, Kayseri, Turkey
| | - Almila Ciftci
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Rachel Mollman
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Onur Obut
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Vahap Eldem
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
- * E-mail:
| | - Yakup Bakir
- Department of Plant Bioactive Metabolites, ACTV Biotechnology, Inc., Istanbul, Turkey
| | - Osman Erol
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
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Sheikh-Assadi M, Naderi R, Kafi M, Fatahi R, Salami SA, Shariati V. Complete chloroplast genome of Lilium ledebourii (Baker) Boiss and its comparative analysis: lights into selective pressure and adaptive evolution. Sci Rep 2022; 12:9375. [PMID: 35672390 PMCID: PMC9174193 DOI: 10.1038/s41598-022-13449-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/24/2022] [Indexed: 01/02/2023] Open
Abstract
Lilium ledebourii (Baker) Boiss is a rare species, which exhibits valuable traits. However, before its genetic diversity and evolutionary were uncovered, its wild resources were jeopardized. Moreover, some ambiguities in phylogenetic relationships of this genus remain unresolved. Therefore, obtaining the whole chloroplast sequences of L. ledebourii and its comparative analysis along with other Lilium species is crucial and pivotal to understanding the evolution of this genus as well as the genetic populations. A multi-scale genome-level analysis, especially selection pressure, was conducted. Detailed third‑generation sequencing and analysis revealed a whole chloroplast genome of 151,884 bp, with an ordinary quadripartite and protected structure comprising 37.0% GC. Overall, 113 different genes were recognized in the chloroplast genome, consisting of 30 distinct tRNA genes, four distinct ribosomal RNAs genes, and 79 unique protein-encoding genes. Here, 3234 SSRs and 2053 complex repeats were identified, and a comprehensive analysis was performed for IR expansion and contraction, and codon usage bias. Moreover, genome-wide sliding window analysis revealed the variability of rpl32-trnL-ccsA, petD-rpoA, ycf1, psbI-trnS-trnG, rps15-ycf1, trnR, trnT-trnL, and trnP-psaJ-rpl33 were higher among the 48 Lilium cp genomes, displaying higher variability of nucleotide in SC regions. Following 1128 pairwise comparisons, ndhB, psbJ, psbZ, and ycf2 exhibit zero synonymous substitution, revealing divergence or genetic restriction. Furthermore, out of 78 protein-coding genes, we found that accD and rpl36 under positive selection: however, at the entire-chloroplast protein scale, the Lilium species have gone through a purifying selection. Also, a new phylogenetic tree for Lilium was rebuilt, and we believe that the Lilium classification is clearer than before. The genetic resources provided here will aid future studies in species identification, population genetics, and Lilium conservation.
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Affiliation(s)
- Morteza Sheikh-Assadi
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj, Iran.
| | - Roohangiz Naderi
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj, Iran.
| | - Mohsen Kafi
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj, Iran
| | - Reza Fatahi
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj, Iran
| | - Seyed Alireza Salami
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj, Iran
| | - Vahid Shariati
- NIGEB Genome Center, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
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Song W, Chen Z, He L, Feng Q, Zhang H, Du G, Shi C, Wang S. Comparative Chloroplast Genome Analysis of Wax Gourd (Benincasa hispida) with Three Benincaseae Species, Revealing Evolutionary Dynamic Patterns and Phylogenetic Implications. Genes (Basel) 2022; 13:461. [PMID: 35328015 PMCID: PMC8954987 DOI: 10.3390/genes13030461] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/01/2022] [Indexed: 12/13/2022] Open
Abstract
Benincasa hispida (wax gourd) is an important Cucurbitaceae crop, with enormous economic and medicinal importance. Here, we report the de novo assembly and annotation of the complete chloroplast genome of wax gourd with 156,758 bp in total. The quadripartite structure of the chloroplast genome comprises a large single-copy (LSC) region with 86,538 bp and a small single-copy (SSC) region with 18,060 bp, separated by a pair of inverted repeats (IRa and IRb) with 26,080 bp each. Comparison analyses among B. hispida and three other species from Benincaseae presented a significant conversion regarding nucleotide content, genome structure, codon usage, synonymous and non-synonymous substitutions, putative RNA editing sites, microsatellites, and oligonucleotide repeats. The LSC and SSC regions were found to be much more varied than the IR regions through a divergent analysis of the species within Benincaseae. Notable IR contractions and expansions were observed, suggesting a difference in genome size, gene duplication and deletion, and the presence of pseudogenes. Intronic gene sequences, such as trnR-UCU–atpA and atpH–atpI, were observed as highly divergent regions. Two types of phylogenetic analysis based on the complete cp genome and 72 genes suggested sister relationships between B. hispida with the Citrullus, Lagenaria, and Cucumis. Variations and consistency with previous studies regarding phylogenetic relationships are discussed. The cp genome of B. hispida provides valuable genetic information for the detection of molecular markers, research on taxonomic discrepancies, and the inference of the phylogenetic relationships of Cucurbitaceae.
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Song W, Ji C, Chen Z, Cai H, Wu X, Shi C, Wang S. Comparative Analysis the Complete Chloroplast Genomes of Nine Musa Species: Genomic Features, Comparative Analysis, and Phylogenetic Implications. Front Plant Sci 2022; 13:832884. [PMID: 35222490 PMCID: PMC8866658 DOI: 10.3389/fpls.2022.832884] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/07/2022] [Indexed: 06/12/2023]
Abstract
Musa (family Musaceae) is monocotyledonous plants in order Zingiberales, which grows in tropical and subtropical regions. It is one of the most important tropical fruit trees in the world. Herein, we used next-generation sequencing technology to assemble and perform in-depth analysis of the chloroplast genome of nine new Musa plants for the first time, including genome structure, GC content, repeat structure, codon usage, nucleotide diversity and etc. The entire length of the Musa chloroplast genome ranged from 167,975 to 172,653 bp, including 113 distinct genes comprising 79 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. In comparative analysis, we found that the contraction and expansion of the inverted repeat (IR) regions resulted in the doubling of the rps19 gene. The several non-coding sites (psbI-atpA, atpH-atpI, rpoB-petN, psbM-psbD, ndhf-rpl32, and ndhG-ndhI) and three genes (ycf1, ycf2, and accD) showed significant variation, indicating that they have the potential of molecular markers. Phylogenetic analysis based on the complete chloroplast genome and coding sequences of 77 protein-coding genes confirmed that Musa can be mainly divided into two groups. These genomic sequences provide molecular foundation for the development and utilization of Musa plants resources. This result may contribute to the understanding of the evolution pattern, phylogenetic relationships as well as classification of Musa plants.
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Affiliation(s)
- Weicai Song
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Chuxuan Ji
- Department of Life Sciences, Imperial College London, Silwood Park, London, United Kingdom
| | - Zimeng Chen
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Haohong Cai
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Xiaomeng Wu
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Chao Shi
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Shuo Wang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
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Lu Y, Wang W, Yu Y, Ma Q, Wang H. The chloroplast genome of Fallopia aubertii (Polygonaceae) from Xining, China. Mitochondrial DNA B Resour 2021; 6:3458-3460. [PMID: 34869874 PMCID: PMC8635536 DOI: 10.1080/23802359.2021.2001390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Fallopia aubertii (L.Henry) Holub (Polygonaceae), a woody plant with a voluble stem, is used as a folk herbal medicines for the treatment of gout, fever and pneumonia. To better understand the molecular genetics of F. aubertii, its complete chloroplast genome was sequenced and annotated. The assembled chloroplast genome is a circular 160,951 bp sequence consisting of large single copy (87,279 bp) and small single copy (13,394 bp) regions, separated by two inverted repeat regions (30,860 bp each). The genome contains 131 genes including 86 protein-coding, 37 tRNA and 8 tRNA genes. Phylogenetic analysis based on the complete chloroplast genome showed that F. aubertii is more closely related to M. australis than to F. sachalinensis, which exhibited a polyphyletic relationship with respect to F. aubertii. These results require further analyses. This study provides additional data for reconstructing species relationships in Fallopia.
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Affiliation(s)
- Yongchang Lu
- Collage of Pharmacy, Qinghai Minzu University, Xining, China
- Key Laboratory for Tibet Plateau Phytochemistry of Qinghai Province, Xining, China
| | - Wancui Wang
- Collage of Pharmacy, Qinghai Minzu University, Xining, China
- Key Laboratory for Tibet Plateau Phytochemistry of Qinghai Province, Xining, China
| | - Yingxiang Yu
- Collage of Pharmacy, Qinghai Minzu University, Xining, China
- Key Laboratory for Tibet Plateau Phytochemistry of Qinghai Province, Xining, China
| | - Qian Ma
- Collage of Pharmacy, Qinghai Minzu University, Xining, China
- Key Laboratory for Tibet Plateau Phytochemistry of Qinghai Province, Xining, China
| | - Huan Wang
- Collage of Pharmacy, Qinghai Minzu University, Xining, China
- Key Laboratory for Tibet Plateau Phytochemistry of Qinghai Province, Xining, China
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