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Almerekova S, Yermagambetova M, Ivaschenko A, Turuspekov Y, Abugalieva S. Comparative Analysis of Plastome Sequences of Seven Tulipa L. (Liliaceae Juss.) Species from Section Kolpakowskianae Raamsd. Ex Zonn and Veldk. Int J Mol Sci 2024; 25:7874. [PMID: 39063115 PMCID: PMC11277319 DOI: 10.3390/ijms25147874] [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: 07/04/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Tulipa L. is a genus of significant economic, environmental, and cultural importance in several parts of the world. The exact number of species in the genus remains uncertain due to inherent taxonomic challenges. We utilized next-generation sequencing technology to sequence and assemble the plastid genomes of seven Tulipa species collected in Kazakhstan and conducted a comparative analysis. The total number of annotated genes was 136 in all seven studied Tulipa species, 114 of which were unique, including 80 protein-coding, 30 tRNA, and 4 rRNA genes. Nine regions (petD, ndhH, ycf2-ycf3, ndhA, rpl16, clpP, ndhD-ndhF, rpoC2, and ycf1) demonstrated significant nucleotide variability, suggesting their potential as molecular markers. A total of 1388 SSRs were identified in the seven Tulipa plastomes, with mononucleotide repeats being the most abundant (60.09%), followed by dinucleotide (34.44%), tetranucleotide (3.90%), trinucleotide (1.08%), pentanucleotide (0.22%), and hexanucleotide (0.29%). The Ka/Ks values of the protein-coding genes ranged from 0 to 3.9286, with the majority showing values <1. Phylogenetic analysis based on a complete plastid genome and protein-coding gene sequences divided the species into three major clades corresponding to their subgenera. The results obtained in this study may contribute to understanding the phylogenetic relationships and molecular taxonomy of Tulipa species.
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Affiliation(s)
- Shyryn Almerekova
- Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (S.A.); (M.Y.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Moldir Yermagambetova
- Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (S.A.); (M.Y.); (Y.T.)
| | | | - Yerlan Turuspekov
- Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (S.A.); (M.Y.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Saule Abugalieva
- Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (S.A.); (M.Y.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
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Huang Y, Jin XJ, Zhang CY, Li P, Meng HH, Zhang YH. Plastome evolution of Engelhardia facilitates phylogeny of Juglandaceae. BMC PLANT BIOLOGY 2024; 24:634. [PMID: 38971744 PMCID: PMC11227234 DOI: 10.1186/s12870-024-05293-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 06/12/2024] [Indexed: 07/08/2024]
Abstract
BACKGROUND Engelhardia (Juglandaceae) is a genus of significant ecological and economic importance, prevalent in the tropics and subtropics of East Asia. Although previous efforts based on multiple molecular markers providing profound insights into species delimitation and phylogeography of Engelhardia, the maternal genome evolution and phylogeny of Engelhardia in Juglandaceae still need to be comprehensively evaluated. In this study, we sequenced plastomes from 14 samples of eight Engelhardia species and the outgroup Rhoiptelea chiliantha, and incorporated published data from 36 Juglandaceae and six outgroup species to test phylogenetic resolution. Moreover, comparative analyses of the plastomes were conducted to investigate the plastomes evolution of Engelhardia and the whole Juglandaceae family. RESULTS The 13 Engelhardia plastomes were highly similar in genome size, gene content, and order. They exhibited a typical quadripartite structure, with lengths from 161,069 bp to 162,336 bp. Three mutation hotspot regions (TrnK-rps16, ndhF-rpl32, and ycf1) could be used as effective molecular markers for further phylogenetic analyses and species identification. Insertion and deletion (InDels) may be an important driving factor for the evolution of plastomes in Juglandoideae and Engelhardioideae. A total of ten codons were identified as the optimal codons in Juglandaceae. The mutation pressure mostly contributed to shaping codon usage. Seventy-eight protein-coding genes in Juglandaceae experienced relaxed purifying selection, only rpl22 and psaI genes showed positive selection (Ka/Ks > 1). Phylogenetic results fully supported Engelhardia as a monophyletic group including two sects and the division of Juglandaceae into three subfamilies. The Engelhardia originated in the Late Cretaceous and diversified in the Late Eocene, and Juglandaceae originated in the Early Cretaceous and differentiated in Middle Cretaceous. The phylogeny and divergence times didn't support rapid radiation occurred in the evolution history of Engelhardia. CONCLUSION Our study fully supported the taxonomic treatment of at the section for Engelhardia species and three subfamilies for Juglandaceae and confirmed the power of phylogenetic resolution using plastome sequences. Moreover, our results also laid the foundation for further studying the course, tempo and mode of plastome evolution of Engelhardia and the whole Juglandaceae family.
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Affiliation(s)
- Yue Huang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Xin-Jie Jin
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, 325035, China
| | - Can-Yu Zhang
- Yunnan Normal University, Kunming, 650500, Yunnan, China
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hong-Hu Meng
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation & Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China.
| | - Yong-Hua Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China.
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, 325035, China.
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Hai Y, Qian Y, Yang M, Zhang Y, Xu H, Yang Y, Xia C. The chloroplast genomes of two medicinal species (Veronica anagallis-aquatica L. and Veronica undulata Wall.) and its comparative analysis with related Veronica species. Sci Rep 2024; 14:13945. [PMID: 38886540 PMCID: PMC11183227 DOI: 10.1038/s41598-024-64896-7] [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: 12/25/2023] [Accepted: 06/13/2024] [Indexed: 06/20/2024] Open
Abstract
Veronica anagallis-aquatica L. and Veronica undulata Wall. are widely used ethnomedicinal plants in China. The two species have different clinical efficacies, while their extremely similar morphology and unclear interspecific relationship make it difficult to accurately identify them, leading to increased instances of mixed usage. This article reports on the complete chloroplast genomes sequence of these two species and their related Veronica species to conduct a comparative genomics analysis and phylogenetic construction. The results showed that the chloroplast (cp) genomes of Veronica exhibited typical circular quadripartite structures, with total lengths of 149,386 to 152,319 base pairs (bp), and GC content of 37.9 to 38.1%, and the number of genes was between 129-134. The total number of simple sequence repeats (SSRs) in V. anagallis-aquatica and V. undulata is 37 and 36, while V. arvensis had the highest total number of 56, predominantly characterized by A/T single bases. The vast majority of long repeat sequence types are forward repeats and palindromic repeats. Selective Ka/Ks values showed that three genes were under positive selection. Sequence differences often occur in the non-coding regions of the large single-copy region (LSC) and small single-copy region (SSC), with the lowest sequence variation in the inverted repeat regions (IR). Seven highly variable regions (trnT-GGU-psbD, rps8-rpl16, trnQ-UUG, trnN-GUU-ndhF, petL, ycf3, and ycf1) were detected, which may be potential molecular markers for identifying V. anagallis-aquatica and V. undulata. The phylogenetic tree indicates that there is a close genetic relationship between the genera Veronica and Neopicrorhiza, and V. anagallis-aquatica and V. undulata are sister groups. The molecular clock analysis results indicate that the divergence time of Veronica may occur at ∼ 9.09 Ma, and the divergence time of these two species occurs at ∼ 0.48 Ma. It is speculated that climate change may be the cause of Veronica species diversity and promote the radiation of the genus. The chloroplast genome data of nine Veronica specie provides important insights into the characteristics and evolution of the chloroplast genome of this genus, as well as the phylogenetic relationships of the genus Veronica.
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Affiliation(s)
- Yonglin Hai
- College of Pharmacy, Dali University, Dali, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China
| | - Yan Qian
- College of Pharmacy, Dali University, Dali, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China
| | - Meihua Yang
- College of Pharmacy, Dali University, Dali, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China
| | - Yue Zhang
- College of Pharmacy, Dali University, Dali, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China
| | - Huimei Xu
- College of Pharmacy, Dali University, Dali, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China
| | - Yongcheng Yang
- College of Pharmacy, Dali University, Dali, 671000, China.
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China.
| | - Conglong Xia
- College of Pharmacy, Dali University, Dali, 671000, China.
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China.
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Lu Q, Tian Q, Gu W, Yang CX, Wang DJ, Yi TS. Comparative genomics on chloroplasts of Rubus (Rosaceae). Genomics 2024; 116:110845. [PMID: 38614287 DOI: 10.1016/j.ygeno.2024.110845] [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: 12/13/2023] [Revised: 04/02/2024] [Accepted: 04/10/2024] [Indexed: 04/15/2024]
Abstract
Rubus, the largest genus in Rosaceae, contains over 1400 species that distributed in multiple habitats across the world, with high species diversity in the temperate regions of Northern Hemisphere. Multiple Rubus species are cultivated for their valuable fruits. However, the intrageneric classification and phylogenetic relationships are still poorly understood. In this study, we sequenced, assembled, and characterized 17 plastomes of Rubus, and conducted comparative genomics integrating with 47 previously issued plastomes of this genus. The 64 plastomes of Rubus exhibited typical quadripartite structure with sizes ranging from 155,144 to 156,700 bp, and contained 132 genes including 87 protein-coding genes, 37 tRNA genes and eight rRNA genes. All plastomes are conservative in the gene order, the frequency of different types of long repeats and simple sequence repeats (SSRs), the codon usage, and the selection pressure of protein-coding genes. However, there are also some differences in the Rubus plastomes, including slight contraction and expansion of the IRs, a variation in the numbers of SSRs and long repeats, and some genes in certain clades undergoing intensified or relaxed purifying selection. Phylogenetic analysis based on whole plastomes showed that the monophyly of Rubus was strongly supported and resolved it into six clades corresponding to six subgenera. Moreover, we identified 12 highly variable regions that could be potential molecular markers for phylogenetic, population genetic, and barcoding studies. Overall, our study provided insight into plastomic structure and sequence diversification of Rubus, which could be beneficial for future studies on identification, evolution, and phylogeny in this genus.
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Affiliation(s)
- Qing Lu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qin Tian
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Gu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen-Xuan Yang
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ding-Jie Wang
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Zhang S, Yu Z, Sun L, Liang S, Xu F, Li S, Zheng X, Yan L, Huang Y, Qi X, Ren H. T2T reference genome assembly and genome-wide association study reveal the genetic basis of Chinese bayberry fruit quality. HORTICULTURE RESEARCH 2024; 11:uhae033. [PMID: 38495030 PMCID: PMC10940123 DOI: 10.1093/hr/uhae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 01/23/2024] [Indexed: 03/19/2024]
Abstract
Chinese bayberry (Myrica rubra or Morella rubra; 2n = 16) produces fruit with a distinctive flavor, high nutritional, and economic value. However, previous versions of the bayberry genome lack sequence continuity. Moreover, to date, no large-scale germplasm resource association analysis has examined the allelic and genetic variations determining fruit quality traits. Therefore, in this study, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the cultivar 'Zaojia' using PacBio HiFi long reads. The resulting 292.60 Mb T2T genome, revealed 8 centromeric regions, 15 telomeres, and 28 345 genes. This represents a substantial improvement in the genome continuity and integrity of Chinese bayberry. Subsequently, we re-sequenced 173 accessions, identifying 6 649 674 single nucleotide polymorphisms (SNPs). Further, the phenotypic analyses of 29 fruit quality-related traits enabled a genome-wide association study (GWAS), which identified 1937 SNPs and 1039 genes significantly associated with 28 traits. An SNP cluster pertinent to fruit color was identified on Chr6: 3407532 to 5 153 151 bp region, harboring two MYB genes (MrChr6G07650 and MrChr6G07660), exhibiting differential expression in extreme phenotype transcriptomes, linked to anthocyanin synthesis. An adjacent, closely linked gene, MrChr6G07670 (MLP-like protein), harbored an exonic missense variant and was shown to increase anthocyanin production in tobacco leaves tenfold. This SNP cluster, potentially a quantitative trait locus (QTL), collectively regulates bayberry fruit color. In conclusion, our study presented a complete reference genome, uncovered a suite of allelic variations related to fruit-quality traits, and identified functional genes that could be harnessed to enhance fruit quality and breeding efficiency of bayberries.
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Affiliation(s)
- Shuwen Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
| | - Zheping Yu
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
| | - Li Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
| | - Senmiao Liang
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
| | - Fei Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
| | - Sujuan Li
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
| | - Xiliang Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
| | - Lijv Yan
- Linhai Specialty and Technology Extension Station, 219 Dongfang Avenue, Linhai 317000, Zhejiang, China
| | - Yinghong Huang
- Jiangsu Taihu Evergreen Fruit Tree Technology Promotion Center, Dongshan Town, Wuzhong District, Suzhou 215107, Jiangsu, China
| | - Xingjiang Qi
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
- Xianghu Laboratory, 168 Gengwen Road, Xiaoshan District, Hangzhou 311231, Zhejiang, China
| | - Haiying Ren
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
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Zhang H, Li Z, Wang M, Yang Y, Wang Y, Nie Q, Liang F, Qin H, Zhang Z. The chromosome-level genome assembly of Fraxinus americana provides insights into the evolution of Oleaceae plants. Int J Biol Macromol 2023; 253:127132. [PMID: 37778585 DOI: 10.1016/j.ijbiomac.2023.127132] [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: 07/17/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/03/2023]
Abstract
White ash (Fraxinus americana linn.) originates from the southeastern United States. It is a tall and fast-growing tree species with strong salt-alkali resistance and cold tolerance, making it an important reforestation species and widely planted worldwide. Here, we completed the chromosome-level reference genome assembly of F. americana based on Illumina, PacBio, and Hi-C reads, with a genome size of 878.98 Mb, an N50 of 3.27 Mb, and a heterozygosity rate of 0.3 %. Based on de novo prediction, transcriptome prediction, and homology-based protein prediction, we obtained 39,538 genes. Approximately 843.21 Mb of the assembly genome was composed of 37,928 annotated protein-coding genes, with a gene function annotation rate of 95.93 %. 99.94 % of the overlap clusters (877.44 Mb) were anchored to 23 chromosomes. Synteny analysis of F. americana and other Oleaceae plants showed that F. americana underwent frequent chromosome rearrangements. The amplification of the Ale transposons effectively promoted the genome size of F. americana. Compared with other Oleaceae plants, the Glutathione S-transferase (GST) gene family in the F. americana genome has undergone significant expansion, which may help F. americana cope with adverse natural environments. Furthermore, we found that key enzyme-coding gene families related to lignin biosynthesis were expanded and highly expressed in F. americana leaves. These key genes drive lignin synthesis and benefit F. americana in fast-growing, as well as resisting biotic and abiotic stress. Overall, the F. americana genome assembly provides insights into the evolution of Oleaceae plants and provides abundant resources for breeding and germplasm conservation of white ash.
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Affiliation(s)
- Hua Zhang
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China.
| | - Zhiqi Li
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China; Sanya Institute of China Agricultural University, Sanya 572024, China
| | - Maoliang Wang
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Yipeng Yang
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Yongge Wang
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Qiufeng Nie
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Fang Liang
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Helan Qin
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Zhao Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China; Sanya Institute of China Agricultural University, Sanya 572024, China; Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou 570228, China.
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Yuan S, Nie C, Jia S, Liu T, Zhao J, Peng J, Kong W, Liu W, Gou W, Lei X, Xiong Y, Xiong Y, Yu Q, Ling Y, Ma X. Complete chloroplast genomes of three wild perennial Hordeum species from Central Asia: genome structure, mutation hotspot, phylogenetic relationships, and comparative analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1170004. [PMID: 37554563 PMCID: PMC10405828 DOI: 10.3389/fpls.2023.1170004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/05/2023] [Indexed: 08/10/2023]
Abstract
Hordeum L. is widely distributed in mountain or plateau of subtropical and warm temperate regions around the world. Three wild perennial Hordeum species, including H. bogdanii, H. brevisubulatum, and H. violaceum, have been used as forage and for grassland ecological restoration in high-altitude areas in recent years. To date, the degree of interspecies sequence variation in the three Hordeum species within existing gene pools is still not well-defined. Herein, we sequenced and assembled chloroplast (cp) genomes of the three species. The results revealed that the cp genome of H. bogdanii showed certain sequence variations compared with the cp genomes of the other two species (H. brevisubulatum and H. violaceum), and the latter two were characterized by a higher relative affinity. Parity rule 2 plot (PR2) analysis illuminated that most genes of all ten Hordeum species were concentrated in nucleotide T and G. Numerous single nucleotide polymorphism (SNP) and insertion/deletion (In/Del) events were detected in the three Hordeum species. A series of hotspots regions (tRNA-GGU ~ tRNA-GCA, tRNA-UGU ~ ndhJ, psbE ~ rps18, ndhF ~ tRNA-UAG, etc.) were identified by mVISTA procedures, and the five highly polymorphic genes (tRNA-UGC, tRNA-UAA, tRNA-UUU, tRNA-UAC, and ndhA) were proved by the nucleotide diversity (Pi). Although the distribution and existence of cp simple sequence repeats (cpSSRs) were predicted in the three Hordeum cp genomes, no rearrangement was found between them. A similar phenomenon has been found in the cp genome of the other seven Hordeum species, which has been published so far. In addition, evolutionary relationships were reappraised based on the currently reported cp genome of Hordeum L. This study offers a framework for gaining a better understanding of the evolutionary history of Hordeum species through the re-examination of their cp genomes, and by identifying highly polymorphic genes and hotspot regions that could provide important insights into the genetic diversity and differentiation of these species.
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Affiliation(s)
- Shuai Yuan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Cong Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Tianqi Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Junming Zhao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jinghan Peng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Weixia Kong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wei Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wenlong Gou
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Xiong Lei
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qingqing Yu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yao Ling
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
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Wan T, Qiao BX, Zhou J, Shao KS, Pan LY, An F, He XS, Liu T, Li PK, Cai YL. Evolutionary and phylogenetic analyses of 11 Cerasus species based on the complete chloroplast genome. FRONTIERS IN PLANT SCIENCE 2023; 14:1070600. [PMID: 36938043 PMCID: PMC10022824 DOI: 10.3389/fpls.2023.1070600] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The subgenus Cerasus, one of the most important groups in the genus Prunus sensu lato, comprises over 100 species; however, the taxonomic classification and phylogenetic relationships of Cerasus remain controversial. Therefore, it is necessary to reconstruct the phylogenetic tree for known Cerasus species. Here, we report the chloroplast (cp) genome sequences of 11 Cerasus species to provide insight into evolution of the plastome. The cp genomes of the 11 Cerasus species (157,571-158,830 bp) displayed a typical quadripartite circular structure. The plastomes contain 115 unique genes, including 80 protein-coding genes, four ribosomal RNAs, and 31 transfer RNAs. Twenty genes were found to be duplicated in inverted repeats as well as at the boundary. The conserved non-coding sequences showed significant divergence compared with the coding regions. We found 12 genes and 14 intergenic regions with higher nucleotide diversity and more polymorphic sites, including matK, rps16, rbcL, rps16-trnQ, petN-psbM, and trnL-trnF. During cp plastome evolution, the codon profile has been strongly biased toward the use of A/T at the third base, and leucine and isoleucine codons appear the most frequently. We identified strong purifying selection on the rpoA, cemA, atpA, and petB genes; whereas ccsA, rps19, matK, rpoC2, ycf2 and ndhI showed a signature of possible positive selection during the course of Cerasus evolution. In addition, we further analyzed the phylogenetic relationships of these species with 57 other congenic related species.Through reconstructing the Cerasus phylogeny tree, we found that true cherry is similar to the flora of China forming a distinct group, from which P. mahaleb was separated as an independent subclade. Microcerasus was genetically closer to Amygdalus, Armeniaca, and Prunus (sensu stricto) than to members of true cherry, whereas P. japonica and P. tomentosa were most closely related to P. triloba and P. pedunculata. However, P. tianshanica formed a clade with P. cerasus, P. fruticosa, P. cerasus × P. canescens 'Gisela 6', and P. avium as a true cherry group. These results provide new insights into the plastome evolution of Cerasus, along with potential molecular markers and candidate DNA barcodes for further phylogenetic and phylogeographic analyses of Cerasus species.
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Affiliation(s)
- Tian Wan
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
| | - Bai-xue Qiao
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
| | - Jing Zhou
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
| | - Ke-sen Shao
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
| | - Liu-yi Pan
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
| | - Feng An
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
| | - Xu-sheng He
- College of Natural Resources and Environment, Northwest Agriculture & Forestry University, Yangling, China
| | - Tao Liu
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
| | - Ping-ke Li
- Center of Experimental Station, Northwest Agriculture & Forestry University, Yangling, China
| | - Yu-liang Cai
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
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9
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Wu YM, Mu XY, Qin YH. The first complete chloroplast genome in Engelhardia sensu stricto, Engelhardia hainanensis Chen: genome characterization and its phylogenetic relationships within the family Juglandaceae. Mitochondrial DNA B Resour 2023; 8:479-483. [PMID: 37063241 PMCID: PMC10101671 DOI: 10.1080/23802359.2023.2196359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
Trees of Engelhardia are important components of subtropical and tropical forests in South-eastern Asia with great ecological and economic values. However, phylogenetic relationships within Engelhardioideae (Juglandaceae) remains obscure. In this study, we report the first complete chloroplast genome sequences of Engelhardia sensu stricto, Engelhardia hainanensis Chen, a rare species endemic in southern China. Its complete chloroplast genome is 161,574 bp in length, with a typical quadripartite structure that includes a large single-copy region of 91,158 bp, a small single-copy region of 18,790 bp, and its GC content is 35.8%. A total of 128 genes were identified, including 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Furthermore, a phylogenetic tree of Juglandaceae was constructed based the complete chloroplast genome sequence, which strongly support the three-subfamily classification system in Juglandaceae, and E. hainanensis was resolved sister to two Alfaropsis species. This study provides valuable genomic information for the species identification and phylogenetic study of Juglandaceae.
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Affiliation(s)
- Yuan-Mi Wu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, College of Ecology and Nature Conservation, Beijing Forestry University, Beijing, P. R. China
| | - Xian-Yun Mu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, College of Ecology and Nature Conservation, Beijing Forestry University, Beijing, P. R. China
- CONTACT Xian-Yun Mu College of Ecology and Nature Conservation, Beijing Forestry University, Beijing, P. R. China
| | - Yong-Hua Qin
- Guangxi Forestry Inventory and Planning Institute, Nanning, P. R. China
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10
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Liu H, He W, Zhang X, Jiang Z, Li Q, Xia C, Wang H. Characterization of the complete chloroplast genome of Veronica arvensis and its phylogenomic inference in plantaginaceae. Mitochondrial DNA B Resour 2022; 7:1928-1932. [DOI: 10.1080/23802359.2022.2139162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Huabing Liu
- China Tobacco Zhejiang Industry Co, Ltd, Hangzhou, China
| | - Wenmiao He
- China Tobacco Zhejiang Industry Co, Ltd, Hangzhou, China
| | - Xiaobing Zhang
- China Tobacco Zhejiang Industry Co, Ltd, Hangzhou, China
| | - Zhimin Jiang
- China Tobacco Zhejiang Industry Co, Ltd, Hangzhou, China
| | - Qi Li
- China Tobacco Zhejiang Industry Co, Ltd, Hangzhou, China
| | - Chen Xia
- China Tobacco Zhejiang Industry Co, Ltd, Hangzhou, China
| | - Hui Wang
- China Tobacco Zhejiang Industry Co, Ltd, Hangzhou, China
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11
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Zhou QY, Cai HX, Liu ZH, Yuan LX, Yang L, Yang T, Li B, Li P. Development of genomic resources for Wenchengia alternifolia (Lamiaceae) based on genome skimming data. PLANT DIVERSITY 2022; 44:542-551. [PMID: 36540711 PMCID: PMC9751079 DOI: 10.1016/j.pld.2021.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 08/27/2021] [Accepted: 09/28/2021] [Indexed: 06/17/2023]
Abstract
Wenchengia alternifolia (Lamiaceae), the sole species of the genus Wenchengia is extremely rare and is currently listed as Critically Endangered (CR) on the IUCN Red List. The species had long been considered endemic to Hainan Island, China and was once believed to be extinct until a small remnant population was rediscovered at the type locality in 2010. Four more populations were later found on Hainan and in Vietnam. In order to develop genomic resources for further studies on population genetics and conservation biology of this rare species, we identified infraspecific molecular markers in the present study, using genome skimming data of five individuals collected from two populations on Hainan Island and three populations in Vietnam respectively. The length of plastome of the five individuals varied from 152,961 bp to 150,204 bp, and exhibited a typical angiosperm quadripartite structure. Six plastid hotspot regions with the Pi > 0.01 (trnH-psbA, psbA-trnK, rpl22, ndhE, ndhG-ndhI and rps15-ycf1), 1621 polymorphic gSSRs, as well as 1657 candidate SNPs in 237 variant nuclear genes were identified, thereby providing important information for further genetic studies.
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Affiliation(s)
- Qi-Yue Zhou
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Hui-Xia Cai
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zi-Han Liu
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | | | - Lei Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Tuo Yang
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Bo Li
- Research Centre of Ecological Sciences, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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12
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Li Y, Jian Y, Mao Y, Meng F, Shao Z, Wang T, Zheng J, Wang Q, Liu L. "Omics" insights into plastid behavior toward improved carotenoid accumulation. FRONTIERS IN PLANT SCIENCE 2022; 13:1001756. [PMID: 36275568 PMCID: PMC9583013 DOI: 10.3389/fpls.2022.1001756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Plastids are a group of diverse organelles with conserved carotenoids synthesizing and sequestering functions in plants. They optimize the carotenoid composition and content in response to developmental transitions and environmental stimuli. In this review, we describe the turbulence and reforming of transcripts, proteins, and metabolic pathways for carotenoid metabolism and storage in various plastid types upon organogenesis and external influences, which have been studied using approaches including genomics, transcriptomics, proteomics, and metabonomics. Meanwhile, the coordination of plastid signaling and carotenoid metabolism including the effects of disturbed carotenoid biosynthesis on plastid morphology and function are also discussed. The "omics" insight extends our understanding of the interaction between plastids and carotenoids and provides significant implications for designing strategies for carotenoid-biofortified crops.
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Affiliation(s)
- Yuanyuan Li
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Yue Jian
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Yuanyu Mao
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Fanliang Meng
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Zhiyong Shao
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Tonglin Wang
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Jirong Zheng
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Qiaomei Wang
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Lihong Liu
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
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13
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Wang R, Gao J, Feng J, Yang Z, Qi Z, Li P, Fu C. Comparative and Phylogenetic Analyses of Complete Chloroplast Genomes of Scrophularia incisa Complex (Scrophulariaceae). Genes (Basel) 2022; 13:1691. [PMID: 36292576 PMCID: PMC9601301 DOI: 10.3390/genes13101691] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 10/14/2023] Open
Abstract
The Scrophularia incisa complex is a group of closely related desert and steppe subshrubs that includes S. incisa, S. kiriloviana and S. dentata, which are the only S. sect. Caninae components found in Northwest China. Based on earlier molecular evidence, the species boundaries and phylogenetic relationships within this complex remain poorly resolved. Here, we characterized seven complete chloroplast genomes encompassing the representatives of the three taxa in the complex and one closely related species, S. integrifolia, as well as three other species of Scrophularia. Comparative genomic analyses indicated that the genomic structure, gene order and content were highly conserved among these eleven plastomes. Highly variable plastid regions and simple sequence repeats (SSRs) were identified. The robust and consistent phylogenetic relationships of the S. incisa complex were firstly constructed based on a total of 26 plastid genomes from Scrophulariaceae. Within the monophyletic complex, a S. kiriloviana individual from Pamirs Plateau was identified as the earliest diverging clade, followed by S. dentata from Tibet, while the remaining individuals of S. kiriloviana from the Tianshan Mountains and S. incisa from Qinghai-Gansu were clustered into sister clades. Our results evidently demonstrate the capability of plastid genomes to improve phylogenetic resolution and species delimitation, particularly among closely related species, and will promote the understanding of plastome evolution in Scrophularia.
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Affiliation(s)
- Ruihong Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Jing Gao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, China
| | - Jieying Feng
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Zhaoping Yang
- Key Laboratory of Biological Resources and Conservation and Application, College of Life 9 Sciences, Tarim University, Alaer 843300, China
| | - Zhechen Qi
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chengxin Fu
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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14
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Wu X, Luo D, Zhang Y, Yang C, Crabbe MJC, Zhang T, Li G. Comparative Genomic and Phylogenetic Analysis of Chloroplast Genomes of Hawthorn (Crataegus spp.) in Southwest China. Front Genet 2022; 13:900357. [PMID: 35860470 PMCID: PMC9289535 DOI: 10.3389/fgene.2022.900357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/15/2022] [Indexed: 11/21/2022] Open
Abstract
The hawthorns (Crataegus spp.) are widely distributed and famous for their edible and medicinal values. There are ∼18 species and seven varieties of hawthorn in China distributed throughout the country. We now report the chloroplast genome sequences from C. scabrifolia, C. chungtienensis and C. oresbia, from the southwest of China and compare them with the previously released six species in Crataegus and four species in Rosaceae. The chloroplast genome structure of Crataegus is typical and can be divided into four parts. The genome sizes are between 159,654 and 159,898bp. The three newly sequenced chloroplast genomes encode 132 genes, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Comparative analysis of the chloroplast genomes revealed six divergent hotspot regions, including ndhA, rps16-trnQ-UUG, ndhF-rpl32, rps16-psbK, trnR-UCU-atpA and rpl32-trnL-UAG. According to the correlation and co-occurrence analysis of repeats with indels and SNPs, the relationship between them cannot be ignored. The phylogenetic tree constructed based on the complete chloroplast genome and intergenic region sequences indicated that C. scabrifolia has a different origin from C. chungtienensis and C. oresbia. We support the placement of C. hupehensis, C. cuneata, C. scabrifolia in C. subg. Crataegus and C. kansuensis, C. oresbia, C. kansuensis in C. subg. Sanguineae. In addition, based on the morphology, geographic distribution and phylogenetic relationships of C. chungtienensis and C. oresbia, we speculate that these two species may be the same species. In conclusion, this study has enriched the chloroplast genome resources of Crataegus and provided valuable information for the phylogeny and species identification of this genus.
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Affiliation(s)
- Xien Wu
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - Dengli Luo
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - Yingmin Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - Congwei Yang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - M. James C. Crabbe
- Wolfson College, Oxford University, Oxford, United Kingdom
- Institute of Biomedical and Environmental Science and Technology, School of Life Sciences, University of Bedfordshire, Luton, United Kingdom
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Ticao Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
- *Correspondence: Ticao Zhang, ; Guodong Li,
| | - Guodong Li
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
- *Correspondence: Ticao Zhang, ; Guodong Li,
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15
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Si H, Li R, Zhang Q, Liu L. Complete chloroplast genome of Plantago asiatica and its phylogenetic position in Plantaginaceae. Mitochondrial DNA B Resour 2022; 7:819-821. [PMID: 35573592 PMCID: PMC9103697 DOI: 10.1080/23802359.2022.2073838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Plantago asiatica, an herbaceous perennial species of Plantaginaceae, has been used as a traditional herbal medicine plant in China. In this study, the complete chloroplast (cp) genome of P. asiatica was sequenced and assembled using genome skimming data. The cp genome was 165,045 bp in length including the large single-copy (LSC, 82,964 bp) and small single-copy (SSC, 4,633 bp) regions separated by two copies of inverted region (IR, 38,724 bp). The cp genome encoded 113 unique genes, consisting of 79 protein-coding genes, 30 tRNA genes, and four rRNA genes, additionally with 27 duplicated genes in the IR regions. Phylogenetic analysis indicated that the representative species from Plantago was monophyletic and they were divided into four subgenera. P. asiatica belongs to the subgenus Plantago and was sister to P. rigida with high bootstrap value support.
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Affiliation(s)
- Hao Si
- School of Life Sciences, Key Laboratory of Plant Stress Biology, Henan University, Kaifeng, China
| | - Rui Li
- School of Life Sciences, Key Laboratory of Plant Stress Biology, Henan University, Kaifeng, China
| | - Qingde Zhang
- School of Life Sciences, Key Laboratory of Plant Stress Biology, Henan University, Kaifeng, China
| | - Luxian Liu
- School of Life Sciences, Key Laboratory of Plant Stress Biology, Henan University, Kaifeng, China
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16
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Yang R, Li R, Dong M, Liu L. Characterization of the complete chloroplast genome of Peltoboykinia tellimoides (Saxifragaceae). Mitochondrial DNA B Resour 2022; 7:741-743. [PMID: 35558180 PMCID: PMC9090422 DOI: 10.1080/23802359.2022.2070040] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 04/19/2022] [Indexed: 11/24/2022] Open
Abstract
Peltoboykinia tellimoides, which is distributed in Japan and China, is the type species of Peltoboykinia. In this study, we sequenced and assembled the complete chloroplast (cp) genome of P. tellimoides and reconstructed the phylogeny of Saxifragaceae based on the whole cp genome sequences. The cp genome of P. tellimoides was 156,274 bp in length, comprising a pair of inverted repeat regions (25,099 bp) separated by a large single copy region (88,109 bp) and a small single copy region (17,967 bp). The genome encoded 112 unique genes consisting of 78 different protein-coding genes, 30 transfer RNA and four ribosomal RNA genes, with 16 duplicated genes in the inverted repeats. Phylogenetic analysis indicated that P. tellimoides together with three Chrysosplenium species formed a high support clade, which was sister to Micranthes melanocentra.
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Affiliation(s)
- Ranran Yang
- Key laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Rui Li
- Key laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Meifang Dong
- Key laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Luxian Liu
- Key laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
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17
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Zhang S, Guo B, He S, He Y. Characterization of the complete chloroplast genome of Rumex dentatus L. (Polygonaceae). Mitochondrial DNA B Resour 2022; 7:546-547. [PMID: 35372690 PMCID: PMC8967193 DOI: 10.1080/23802359.2022.2054380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Rumex dentatus L. is a flowering plant with promising therapeutic effects. Here, we reported the complete chloroplast genome sequence of R. dentatus. The length of the complete genome is 159,103 bp, with a pair of inverted repeat regions (IRb/IRa, 30,628 bp) separated by a large single-copy (LSC, 84,848 bp) region and a small single-copy (SSC, 12,999 bp) region. The overall GC content of the genome was 37.6%, and the corresponding values in the LSC, SSC, and IR regions were 35.8%, 32.6%, and 41.1%, respectively. There are 129 genes, including 84 protein coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic tree showed that R. dentatus was most relative to the species of R. nepalensis and R. crispus.
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Affiliation(s)
- Suping Zhang
- School of Pharmacy, Henan University, Kaifeng, China
- Institutes of Traditional Chinese Medicine, Henan University, Kaifeng, China
| | - Bingao Guo
- School of Life Sciences, Henan University, Kaifeng, China
| | - Sheqi He
- School of Pharmacy, Henan University, Kaifeng, China
- Institutes of Traditional Chinese Medicine, Henan University, Kaifeng, China
| | - Yanxia He
- Institutes of Traditional Chinese Medicine, Henan University, Kaifeng, China
- School of Life Sciences, Henan University, Kaifeng, China
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18
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Han Y, Gao Y, Li Y, Zhai X, Zhou H, Ding Q, Ma L. Chloroplast Genes Are Involved in The Male-Sterility of K-Type CMS in Wheat. Genes (Basel) 2022; 13:genes13020310. [PMID: 35205355 PMCID: PMC8871828 DOI: 10.3390/genes13020310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/30/2022] [Accepted: 02/02/2022] [Indexed: 12/04/2022] Open
Abstract
The utilization of crop heterosis can greatly improve crop yield. The sterile line is vital for the heterosis utilization of wheat (Triticum aestivum L.). The chloroplast genomes of two sterile lines and one maintainer were sequenced using second-generation high-throughput technology and assembled. The nonsynonymous mutated genes among the three varieties were identified, the expressed difference was further analyzed by qPCR, and finally, the function of the differentially expressed genes was analyzed by the barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) method. A total of 16 genes containing 31 nonsynonymous mutations between K519A and 519B were identified. There were no base mutations in the protein-encoding genes between K519A and YS3038. The chloroplast genomes of 519B and K519A were closely related to the Triticum genus and Aegilops genus, respectively. The gene expression levels of the six selected genes with nonsynonymous mutation sites for K519A compared to 519B were mostly downregulated at the binucleate and trinucleate stages of pollen development. The seed setting rates of atpB-silenced or ndhH-silenced 519B plants by BSMV-VIGS method were significantly reduced. It can be concluded that atpB and the ndhH are likely to be involved in the reproductive transformation of 519B.
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Affiliation(s)
- Yucui Han
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China; (Y.H.); (Y.L.)
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (Y.G.); (X.Z.); (H.Z.)
| | - Yujie Gao
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (Y.G.); (X.Z.); (H.Z.)
| | - Yun Li
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China; (Y.H.); (Y.L.)
| | - Xiaoguang Zhai
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (Y.G.); (X.Z.); (H.Z.)
| | - Hao Zhou
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (Y.G.); (X.Z.); (H.Z.)
| | - Qin Ding
- College of Horticulture, Northwest A&F University, Xianyang 712100, China
- Correspondence: (Q.D.); (L.M.)
| | - Lingjian Ma
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (Y.G.); (X.Z.); (H.Z.)
- Correspondence: (Q.D.); (L.M.)
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19
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Han C, Ding R, Zong X, Zhang L, Chen X, Qu B. Structural characterization of Platanthera ussuriensis chloroplast genome and comparative analyses with other species of Orchidaceae. BMC Genomics 2022; 23:84. [PMID: 35086477 PMCID: PMC8796522 DOI: 10.1186/s12864-022-08319-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 01/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genus Tulotis has been classified into the genus Platanthera in the present taxonomic studies since the morphological characteristics of this genus is very similar to that of Platanthera. Platanthera ussuriensis, formerly named as Tulotis ussuriensis, is a small terrestrial orchid species and has been listed as wild plant under State protection (category II) in China. An improved understanding of the genomic information will enable future applications of conservation strategy as well as phylogenetic studies for this rare orchid species. The objective of this research was to characterize and compare the chloroplast genome of P. ussuriensis with other closely related species of Orchidaceae. RESULTS The chloroplast genome sequence of P. ussuriensis is 155,016 bp in length, which included a pair of inverted repeats (IRs) of 26,548 bp that separated a large single copy (LSC) region of 83,984 bp and a small single copy (SSC) region of 17,936 bp. The annotation contained a total of 132 genes, including 86 protein-coding genes, 38 tRNA genes and 8 rRNA genes. The simple sequence repeat (SSR) analysis showed that there were 104 SSRs in the chloroplast genome of P. ussuriensis. RNA editing sites recognition indicated 72 RNA editing events occurred, and all codon changes were C to T conversions. Comparative genomics showed that the chloroplast sequence of Platanthera related species were relatively conserved, while there were still some high variation regions that could be used as molecular markers. Moreover, Platanthera related species showed similar IR/SSC and IR/LSC borders. The phylogenetic analysis suggested that P. ussuriensis had a closer evolutionary relationship with P. japonica followed by the remaining Platanthera species. CONCLUSION Orchidaceae is a key group of biodiversity protection and also a hot spot group in the plant taxonomy and evolution studies due to their characteristics of high specialization and rapid evolution. This research determined the complete chloroplast genome of P. ussuriensis for the first time, and compared the sequence with other closely related orchid species. These results provide a foundation for future genomic and molecular evolution of the Orchidaceae species, and provide insights into the development of conservation strategy for Platanthera species.
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Affiliation(s)
- Chenyang Han
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110161, China
| | - Rui Ding
- College of Land and Environment, Shenyang Agricultural University, Shenyang, 110161, China
| | - Xiaoyan Zong
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110161, China
| | - Lijie Zhang
- College of Forestry, Shenyang Agricultural University, Shenyang, 110161, China
| | - Xuhui Chen
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110161, China.
| | - Bo Qu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110161, China
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20
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Comparative chloroplast genome analyses of cultivated spinach and two wild progenitors shed light on the phylogenetic relationships and variation. Sci Rep 2022; 12:856. [PMID: 35039603 PMCID: PMC8763918 DOI: 10.1038/s41598-022-04918-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/31/2021] [Indexed: 01/30/2023] Open
Abstract
Spinacia is a genus of important leafy vegetable crops worldwide and includes cultivated Spinacia oleracea and two wild progenitors, Spinacia turkestanica and Spinacia tetrandra. However, the chloroplast genomes of the two wild progenitors remain unpublished, limiting our knowledge of chloroplast genome evolution among these three Spinacia species. Here, we reported the complete chloroplast genomes of S. oleracea, S. turkestanica, and S. tetrandra obtained via Illumina sequencing. The three chloroplast genomes exhibited a typical quadripartite structure and were 150,739, 150,747, and 150,680 bp in size, respectively. Only three variants were identified between S. oleracea and S. turkestanica, whereas 690 variants were obtained between S. oleracea and S. tetrandra, strongly demonstrating the close relationship between S. turkestanica and S. oleracea. This was further supported by phylogenetic analysis. We reported a comprehensive variant dataset including 503 SNPs and 83 Indels using 85 Spinacia accessions containing 61 S. oleracea, 16 S. turkestanica, and eight S. tetrandra accessions. Thirteen S. oleracea accessions were derived through introgression from S. turkestanica that acts as the maternal parent. Together, these results provide a valuable resource for spinach breeding programs and improve our understanding of the phylogenetic relationships within Amaranthaceae.
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21
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Liu X, Li R, Wang S, Liu L. The complete chloroplast genome sequence of Zelkova sinica and phylogenetic implications in Rosales. Mitochondrial DNA B Resour 2021; 6:3154-3155. [PMID: 34746390 PMCID: PMC8567943 DOI: 10.1080/23802359.2021.1987168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Zelkova sinica is a popular landscape plant in China because of its wide adaptation, strong disease resistance, large crown and beautiful fall color. Here, we assembled the complete chloroplast (cp) genome of Z. sinica based on genome skimming data. The cp genome is 158,924 bp in length including two copies of inverted region (IR, 26,427 bp) separated by the large single copy (LSC, 87,318 bp) and small single copy (SSC, 18,752 bp) regions. It encodes 111 unique genes, containing 77 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, with 18 duplicated genes in the IR regions. Phylogenetic analysis shows that Z. sinica is sister to Z. schneideriana in Ulmaceae family.
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Affiliation(s)
- Xinyi Liu
- Key laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Rui Li
- Key laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Shuyun Wang
- School of Pharmacy, Henan University, Kaifeng, China
| | - Luxian Liu
- Key laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
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22
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The complete chloroplast genome and characteristics analysis of Musa basjoo Siebold. Mol Biol Rep 2021; 48:7113-7125. [PMID: 34541615 DOI: 10.1007/s11033-021-06702-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/07/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND An ornamental plant often seen in gardens and farmhouses, Musa basjoo Siebold can also be used as Chinese herbal medicine. Its pseudostem and leaves are diuretic; its root can be decocted together with ginger and licorice to cure gonorrhea and diabetes; the decoct soup of its pseudostem can help relieve heat, and the decoct soup of its dried flower can treat cerebral hemorrhage. There have not been many chloroplast genome studies on M. basjoo Siebold. METHODS AND RESULTS We characterized its complete chloroplast genome using Novaseq 6000 sequencing. This paper shows that the length of the chloroplast genome M. basjoo Siebold is 172,322 bp, with 36.45% GC content. M. basjoo Siebold includes a large single-copy region of 90,160 bp, a small single-copy region of 11,668 bp, and a pair of inverted repeats of 35,247 bp. Comparing the genomic structure and sequence data of closely related species, we have revealed the conserved gene order of the IR and LSC/SSC regions, which has provided a very inspiring discovery for future phylogenetic research. CONCLUSIONS Overall, this study has constructed an evolutionary tree of the genus Musa species with the complete chloroplast genome sequence for the first time. As can be seen, there is no obvious multi-branching in the genus, and M. basjoo Siebold and Musa itinerans are the closest relatives.
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23
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Paudel YP, Hu Z, Khatiwada JR, Fan L, Pradhan S, Liu B, Qin W. Chloroplast genome analysis of Chrysotila dentata. Gene 2021; 804:145871. [PMID: 34363887 DOI: 10.1016/j.gene.2021.145871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/20/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022]
Abstract
Chrysotila dentata is an ecologically important marine alga contributing to the coccolith formation. In this study, a complete chloroplast (cp DNA) genome of Chrysotila dentata was sequenced by using Illumina Hiseq and was analyzed with the help of a bioinformatics tool CPGAVAS2. The circular chloroplast genome of Chrysotila dentata has a size of 109,017 bp with two inverted repeats (IRs) regions (4513 bp each) which is a common feature in most land plants and algal species. The Chrysotila dentata cp genome consists of 61 identified protein-coding genes, 30 tRNA genes and 6 rRNAs with 21 microsatellites. The phylogenetic relationship with other select algal species revealed a close phylogeny of Chrysotila dentata with Phaeocystis antarctica. This is the first report of the cp genome analysis of genus Chrysotila and the results from this study will be helpful for understanding the genetic structure and function of chloroplast in other species of Chrysotila.
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Affiliation(s)
- Yagya Prasad Paudel
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, ON P7B 5E1, Canada
| | - Zixuan Hu
- Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, ON P7B 5E1, Canada
| | - Janak Raj Khatiwada
- Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, ON P7B 5E1, Canada
| | - Lu Fan
- School of Civil Engineering, Architecture and Environment, Hubei University of Technology, Wuhan 430068, China
| | - Shreeti Pradhan
- Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, ON P7B 5E1, Canada
| | - Benwen Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| | - Wensheng Qin
- Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, ON P7B 5E1, Canada.
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24
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Complete Chloroplast Genome Sequence of Fortunella venosa (Champ. ex Benth.) C.C.Huang (Rutaceae): Comparative Analysis, Phylogenetic Relationships, and Robust Support for Its Status as an Independent Species. FORESTS 2021. [DOI: 10.3390/f12080996] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Fortunella venosa (Rutaceae) is an endangered species endemic to China and its taxonomic status has been controversial. The genus Fortunella contains a variety of important economic plants with high value in food, medicine, and ornamental. However, the placement of Genus Fortunella into Genus Citrus has led to controversy on its taxonomy and Systematics. In this present research, the Chloroplast genome of F. venosa was sequenced using the second-generation sequencing, and its structure and phylogenetic relationship analyzed. The results showed that the Chloroplast genome size of F. venosa was 160,265 bp, with a typical angiosperm four-part ring structure containing a large single copy region (LSC) (87,597 bp), a small single copy region (SSC) (18,732 bp), and a pair of inverted repeat regions (IRa\IRb) (26,968 bp each). There are 134 predicted genes in Chloroplast genome, including 89 protein-coding genes, 8 rRNAs, and 37 tRNAs. The GC-content of the whole Chloroplast genome was 43%, with the IR regions having a higher GC content than the LSC and the SSC regions. There were no rearrangements present in the Chloroplast genome; however, the IR regions showed obvious contraction and expansion. A total of 108 simple sequence repeats (SSRs) were present in the entire chloroplast genome and the nucleotide polymorphism was high in LSC and SSC. In addition, there is a preference for codon usage with the non-coding regions being more conserved than the coding regions. Phylogenetic analysis showed that species of Fortunella are nested in the genus of Citrus and the independent species status of F. venosa is supported robustly, which is significantly different from F. japonica. These findings will help in the development of DNA barcodes that can be useful in the study of the systematics and evolution of the genus Fortunella and the family Rutaceae.
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25
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Comparative and phylogenetic analyses of the chloroplast genomes of species of Paeoniaceae. Sci Rep 2021; 11:14643. [PMID: 34282194 PMCID: PMC8289817 DOI: 10.1038/s41598-021-94137-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
Plants belonging to family Paeoniaceae are not only economically important ornamental plants but also medicinal plants used as an important source of traditional Chinese medicine. Owing to the complex network evolution and polyploidy evolution of this family, its systematics and taxonomy are controversial and require a detailed investigation. In this study, three complete chloroplast genomes of sect. Paeonia, one of the sections of Paeonia, were sequenced and then analysed together with 16 other published chloroplast genomes of Paeoniaceae species. The total lengths of the chloroplast genomes of these species were 152,153–154,405 bp. A total of 82–87 protein-coding genes, 31–40 tRNA genes and 8 rRNA genes were annotated. Bioinformatics analysis revealed 61–74 simple sequence repeats (SSRs) in the chloroplast genomes, most of which have A/T base preference. Codon usage analysis showed that A/U-ending codons were more positive than C/G-ending codons, and a slight bias in codon usage was observed in these species. A comparative analysis of these 19 species of Paeoniaceae was then conducted. Fourteen highly variable regions were selected for species relationship study. Phylogenetic analysis revealed that the species of sect. Paeonia gathered in one branch and then divided into different small branches. P. lactiflora, P. anomala, P. anomala subsp. veitchii and P. mairei clustered together. P. intermedia was related to P. obovata and P. obovata subsp. willmottiae. P. emodi was the sister to all other species in the sect. Paeonia.
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26
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Yuan W, Ma Y, He S, Chang D, He Y. Characterization of the complete chloroplast genome of Lonicera tatarica L. (Caprifoliaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1871-1872. [PMID: 34377785 PMCID: PMC8344791 DOI: 10.1080/23802359.2021.1934140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Lonicera tatarica L. is an excellent landscaping shrub with high ornamental value. Here, we report the complete chloroplast genome sequence of L. tatarica. The size of the chloroplast genome is 154,675 bp in length, including a large single copy region (LSC) of 88,361 bp, a small single copy region (SSC) of 18,750 bp, and a pair of inverted repeated regions of 23,782 bp. The L. tatarica chloroplast genome encodes 131 genes, including 85 protein-coding, 38 tRNA, and 8 rRNA genes. Phylogenetic analysis fully resolved L. tatarica in a clade with L. japonica, L. confusa, and L. maximowiczii. These data provide a useful resource when studying the genetic diversity of L. tatarica.
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Affiliation(s)
- Wangjun Yuan
- School of Pharmacy, Henan University, Kaifeng, China
| | - Yuanyuan Ma
- School of Pharmacy, Henan University, Kaifeng, China
| | - Sheqi He
- School of Pharmacy, Henan University, Kaifeng, China
| | - Dongwen Chang
- School of Life Sciences, Henan University, Kaifeng, China
| | - Yanxia He
- School of Life Sciences, Henan University, Kaifeng, China
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27
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Wu L, Cui Y, Wang Q, Xu Z, Wang Y, Lin Y, Song J, Yao H. Identification and phylogenetic analysis of five Crataegus species (Rosaceae) based on complete chloroplast genomes. PLANTA 2021; 254:14. [PMID: 34180013 DOI: 10.1007/s00425-021-03667-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/15/2021] [Indexed: 06/13/2023]
Abstract
The chloroplast genomes of the five Crataegus species were shown to have a conserved genome structure. Complete chloroplast genome sequences were more suitable than highly variable regions for the identification and phylogenetic analysis of Crataegus species. Hawthorn, which is commonly used as a traditional Chinese medicine, is one of the most popular sour fruits and has high economic value. Crataegus pinnatifida var. pinnatifida and C. pinnatifida var. major are frequently adulterated with other Crataegus species on the herbal medicine market. However, most Crataegus plants are difficult to identify using traditional morphological methods. Here, we compared five Crataegus chloroplast (CP) genomes comprising two newly sequenced (i.e., C. pinnatifida var. pinnatifida and C. pinnatifida var. major) and three previously published CP genomes. The CP genomes of the five Crataegus species had a conserved genome structure, gene content and codon usage. The total length of the CP genomes was 159,654-159,865 bp. A total of 129-130 genes, including 84-85 protein-coding genes, 37 tRNA genes and 8 rRNA genes, were annotated. Bioinformatics analysis revealed 96-103 simple sequence repeats (SSRs) and 48-70 long repeats in the five CP genomes. Combining the results of mVISTA and nucleotide diversity, five highly variable regions were screened for species identification and relationship studies. Maximum likelihood trees were constructed on the basis of complete CP genome sequences and highly variable regions. The results showed that the former had higher discriminatory power for Crataegus species, indicating that the complete CP genome could be used as a super-barcode to accurately authenticate the five Crataegus species.
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Affiliation(s)
- Liwei Wu
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China
| | - Yingxian Cui
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China
| | - Qing Wang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China
| | - Zhichao Xu
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China
| | - Yu Wang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Yulin Lin
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Jingyuan Song
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China
| | - Hui Yao
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China.
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China.
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28
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Yang YY, Qu XJ, Zhang R, Stull GW, Yi TS. Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture. Mol Phylogenet Evol 2021; 163:107232. [PMID: 34129935 DOI: 10.1016/j.ympev.2021.107232] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/21/2021] [Accepted: 06/10/2021] [Indexed: 11/17/2022]
Abstract
Plastid phylogenomic analyses have shed light on many recalcitrant relationships across the angiosperm Tree of Life and continue to play an important role in plant phylogenetics alongside nuclear data sets given the utility of plastomes for revealing ancient and recent introgression. Here we conduct a plastid phylogenomic study of Fagales, aimed at exploring contentious relationships (e.g., the placement of Myricaceae and some intergeneric relationships in Betulaceae, Juglandaceae, and Fagaceae) and dissecting conflicting phylogenetic signals across the plastome. Combining 102 newly sequenced samples with publically available plastomes, we analyzed a dataset including 256 species and 32 of the 34 total genera of Fagales, representing the largest plastome-based study of the order to date. We find strong support for a sister relationship between Myricaceae and Juglandaceae, as well as strongly supported conflicting signal for alternative generic relationships in Betulaceae and Juglandaceae. These conflicts highlight the sensitivity of plastid phylogenomic analyses to genic composition, perhaps due to the prevalence of uninformative loci and heterogeneity in signal across different regions of the plastome. Phylogenetic relationships were geographically structured in subfamily Quercoideae, with Quercus being non-monophyletic and its sections forming clades with co-distributed Old World or New World genera of Quercoideae. Compared against studies based on nuclear genes, these results suggest extensive introgression and chloroplast capture in the early diversification of Quercus and Quercoideae. This study provides a critical plastome perspective on Fagales phylogeny, setting the stage for future studies employing more extensive data from the nuclear genome.
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Affiliation(s)
- Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, Shangdong 250014, China
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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29
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Chen H, Wang Q. Regulatory mechanisms of lipid biosynthesis in microalgae. Biol Rev Camb Philos Soc 2021; 96:2373-2391. [PMID: 34101323 DOI: 10.1111/brv.12759] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 02/01/2023]
Abstract
Microalgal lipids are highly promising feedstocks for biofuel production. Microalgal lipids, especially triacylglycerol, and practical applications of these compounds have received increasing attention in recent years. For the commercial use of microalgal lipids to be feasible, many fundamental biological questions must be addressed based on detailed studies of algal biology, including how lipid biosynthesis occurs and is regulated. Here, we review the current understanding of microalgal lipid biosynthesis, with a focus on the underlying regulatory mechanisms. We also present possible solutions for overcoming various obstacles to understanding the basic biology of microalgal lipid biosynthesis and the practical application of microalgae-based lipids. This review will provide a theoretical reference for both algal researchers and decision makers regarding the future directions of microalgal research, particularly pertaining to microalgal-based lipid biosynthesis.
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Affiliation(s)
- Hui Chen
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Qiang Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
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30
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Huang X, Tan W, Li F, Liao R, Guo Z, Shi T, Gao Z. The chloroplast genome of Prunus zhengheensis: Genome comparative and phylogenetic relationships analysis. Gene 2021; 793:145751. [PMID: 34062257 DOI: 10.1016/j.gene.2021.145751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 05/06/2021] [Accepted: 05/27/2021] [Indexed: 12/25/2022]
Abstract
Prunus zhengheensis is a novel species originated in Fujian province, China. However, there is no further information available on its classification and molecular biology study. In this study, we first report the complete chloroplast (cp) genome sequence of P. zhengheensis. The cp genome of P. zhengheensis is 158,106 bp and GC content is 36.73%, is a circular structure composed of LSC (large single copy), SSC (small single copy), and IR (inverted repeat) regions, with the size of the three regions being 86,321 bp, 18,999 bp and 26,393 bp, respectively. The cp genome of P. zhengheensis contains 130 genes, and 242 SSRs are identified in the cp genome. The comparative analysis of cp genomes in eight Prunus plants demonstrates the subtle divergences occur in the protein-coding gene rps18, rps12, psbF, rpl33, matK, and rbcL, and that the KA/KS nucleotide substitution ratio of the ndhF of P. zhengheensis and P. armeniaca is 1.79636. The phylogenetic results indicate that the P. zhengheensis is closely related to P. mume, compared to other species of Prunus. Our research results provide the important genomic information for molecular phylogeny of P. zhengheensis.
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Affiliation(s)
- Xiao Huang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Wei Tan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Feng Li
- Jilin Academy of Agricultural Sciences, Jilin 136100, China.
| | - Ruyu Liao
- Fujian Academy of Agricultural Sciences, Fuzhou 350013, China.
| | - Zhongren Guo
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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31
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Tang Y, Zhao Y, Li C, Yang G, Peng J, Xu Z. New insights into the evolutionary characteristic between the New World and Old World Lupinus species using complete chloroplast genomes. ALL LIFE 2021. [DOI: 10.1080/26895293.2021.1926341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Yiwang Tang
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, People’s Republic of China
| | - Yunlin Zhao
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, People’s Republic of China
| | - Chaoyang Li
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, People’s Republic of China
| | - Guiyan Yang
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, People’s Republic of China
- College of Forestry, Northwest A & F University, Yangling, People’s Republic of China
| | - Jiao Peng
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, People’s Republic of China
| | - Zhenggang Xu
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, People’s Republic of China
- College of Forestry, Northwest A & F University, Yangling, People’s Republic of China
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32
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Xu G, Xu W. Complete chloroplast genomes of Chinese wild-growing Vitis species: molecular structures and comparative and adaptive radiation analysis. PROTOPLASMA 2021; 258:559-571. [PMID: 33230625 DOI: 10.1007/s00709-020-01585-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/11/2020] [Indexed: 06/11/2023]
Abstract
As a basalmost family of Vitaceae, Chinese wild Vitis species offer key insights into the demographic history of grapes. In this study, we obtained 10 complete chloroplast (cp) genomes from Chinese wild-growing Vitis species based on our whole genome re-sequencing data. These chloroplast genomes ranged from 160,838 to 232,020 bp in size and exhibited typical quadripartite structures. Comparative analyses revealed that inverted repeat (IR) regions are especially abundant and contribute to cp genome arrangements. Phylogenetic analysis of the whole Vitis cp genomes supported three clearly partitioned main origins, in keeping with their geographic distributions, among which East Asian species from China were found to be sister species with Eurasian Vitis species but exhibited significant divergence from the North American group. Two well-supported subgroups were observed within the Chinese wild-growing Vitis species. Among these species, Vitis piasezkii and Vitis betulifolia were closely related species, exhibiting a support rate of 100%. The molecular clock-based divergence time suggested that the earliest split subspecies was Vitis pseudoreticulata, which further indicated that the origin and initial gene pool are located in southern China (the habitat of V. pseudoreticulata is located in the region). Coincidentally, the divergence time was during the Pleistocene period (2.6-0.1 Ma). Due to glacial/interglacial temperature fluctuations, cold-adapted subspecies, e.g., Vitis amurensis, could re-colonize new habitats. Our results may help to elucidate the adaptive radiation of Chinese wild Vitis species in different environments.
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Affiliation(s)
- Guangya Xu
- School of Agronomy, Ningxia University, Yinchuan, 750021, Ningxia, People's Republic of China
| | - Weirong Xu
- School of Food & Wine, Ningxia University, Yinchuan, 750021, Ningxia, People's Republic of China.
- Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, Yinchuan, 750021, Ningxia, People's Republic of China.
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan, 750021, China.
- Chinese Wine Industry Technology Institute, Yinchuan, 750021, China.
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33
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Yuan W, Liu P, Zhang S, He Y. The complete chloroplast genome of Achyranthes bidentata Blume. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:782-783. [PMID: 33796647 PMCID: PMC7971321 DOI: 10.1080/23802359.2021.1882895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Achyranthes bidentata is a popular Chinese medicine, that has its place in the treatment of spasm, osteodynia of the lumbar region and knees. The complete chloroplast (cp) genome of A. bidentata was determined. The complete cp genome is 151,543 bp in length and includes a large single-copy (LSC) region of 83,922 bp, a small single-copy (SSC) region of 17,251 bp, and a pair of inverted repeat regions (IRs) of 25,185 bp. It encodes 131 genes, including 86 protein-coding genes, eight rRNAs, and 37 tRNAs. Phylogenetic analysis indicates that four samples of A. bidentata formed a clade with a 100% bootstrap value.
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Affiliation(s)
- Wangjun Yuan
- School of Pharmacy, Henan University, Kaifeng, China
| | - Peng Liu
- School of Pharmacy, Henan University, Kaifeng, China
| | - Suping Zhang
- School of Pharmacy, Henan University, Kaifeng, China
| | - Yanxia He
- School of Life Sciences, Henan University, Kaifeng, China
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34
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Zhang LQ, Zhang XY, Hu YW, Sun RS, Yu JL. Complete chloroplast genome of adonis amurensis (ranunculaceae), an important cardiac folk medicinal plant in east asia. Mitochondrial DNA B Resour 2021; 6:583-585. [PMID: 33628938 PMCID: PMC7889182 DOI: 10.1080/23802359.2021.1875916] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Adonis amurensis Regel et Radde is an important cardiac folk medicinal plant which endemic to Northeast Asia. We determined the first complete chloroplast genome of A. amurensis using genome skimming approach. The cp genome was 157,032 bp long, with a large single-copy region (LSC) of 86,218 bp and a small single-copy region (SSC) of 18,212 bp separated by a pair of inverted repeats (IRs) of 26,301 bp. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. We also reconstructed the phylogeny of Adonideae and Isopyreae using maximum likelihood (ML) method, including our data and previously reported cp genomes of related taxa. The phylogenetic analysis indicated that A. amurensis is close related with Adonis sutchuenensis.
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Affiliation(s)
- Li-Qiu Zhang
- School of Medicine and Pharmacy, Tonghua Normal University, Tonghua, China
| | - Xiao-Yan Zhang
- School of food science and Engineering, Tonghua Normal University, Tonghua, China
| | - Yan-Wu Hu
- School of Medicine and Pharmacy, Tonghua Normal University, Tonghua, China
| | - Ren-Shuang Sun
- School of Medicine and Pharmacy, Tonghua Normal University, Tonghua, China
| | - Jun-Lin Yu
- School of Medicine and Pharmacy, Tonghua Normal University, Tonghua, China
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35
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Li YL, Reed J, Xu YQ, Qu DH, Sun ZS. Complete chloroplast genome of Prunus fasciculata (Rosaceae), a species native to western North America. Mitochondrial DNA B Resour 2021; 6:480-482. [PMID: 33628896 PMCID: PMC7889079 DOI: 10.1080/23802359.2021.1872439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- Yue-Ling Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - James Reed
- California Botanic Garden, Claremont, CA, USA
| | - Yu-Qian Xu
- College of Life Sciences, Taizhou University, Taizhou, China
| | - Da-Hao Qu
- College of Life Sciences, Taizhou University, Taizhou, China
| | - Zhong-Shuai Sun
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
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36
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Liu L, Zhang Y, Li P. Development of genomic resources for the genus Celtis (Cannabaceae) based on genome skimming data. PLANT DIVERSITY 2021; 43:43-53. [PMID: 33778224 PMCID: PMC7987720 DOI: 10.1016/j.pld.2020.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 06/02/2023]
Abstract
Celtis is a Cannabaceae genus of 60-70 species of trees, or rarely shrubs, commonly known as hackberries. This woody genus consists of very valuable forest plants that provide important wildlife habitat for birds and mammals. Although previous studies have identified its phylogenetic position, interspecific relationships within Celtis remain unclear. In this study, we generated genome skimming data from five Celtis species to analyze phylogenetic relationships within the genus and develop genome resources. The plastomes of Celtis ranged in length from 158,989 bp to 159,082 bp, with a typical angiosperm quadripartite structure, and encoded a total of 132 genes with 20 duplicated in the IRs. Comparative analyses showed that plastome content and structure were relatively conserved. Whole plastomes showed no signs of gene loss, translocations, inversions, or genome rearrangement. Six plastid hotspot regions (trnH-psbA, psbA-trnK, trnG-trnR, psbC-trnS, cemA-petA and rps8-rpl14), 4097 polymorphic nuclear SSRs, as well as 62 low or single-copy gene fragments were identified within Celtis. Moreover, the phylogenetic relationships based on the complete plastome sequences strongly endorse the placement of C. biondii as sister to the ((((C. koraiensis, C. sinensis), C. tetrandra), C. julianae), C. cerasifera) clade. These findings and the genetic resources developed here will be conducive to further studies on the genus Celtis involving phylogeny, population genetics, and conservation biology.
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Affiliation(s)
- Luxian Liu
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475000, China
| | - Yonghua Zhang
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, 325035, China
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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37
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Wang XY, Liu LJ, Liu SL, Ye LX, He XK, Sun ZS. Complete chloroplast genome of Cerasus fengyangshanica (Rosaceae), a wild flowering cherry endemic to China. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:200-201. [PMID: 33537443 PMCID: PMC7832537 DOI: 10.1080/23802359.2020.1860723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Cerasus fengyangshanica is a wild flowering cherry endemic to Mount Fengyang, China. Here, we reported the complete chloroplast (cp) genome of C. fengyangshanica (GenBank accession number: MW160272). The cp genome was 157,964 bp long, with a large single-copy region (LSC) of 85,972 bp and a small single-copy region (SSC) of 19,086 bp separated by a pair of inverted repeats (IRs) of 26,453 bp. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. We also reconstructed the phylogeny of Prunus sensu lato using maximum likelihood (ML) method, including our data and previously reported cp genomes of related taxa. The phylogenetic analysis indicated that C. fengyangshanica is closely related with Prunus maximowiczii.
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Affiliation(s)
- Xiao-Yan Wang
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Ling-Juan Liu
- Administration of Fengyangshan-Baishanzu National Natural Reserve, Longquan, China
| | - Sheng-Long Liu
- Administration of Fengyangshan-Baishanzu National Natural Reserve, Longquan, China
| | - Li-Xin Ye
- Administration of Fengyangshan-Baishanzu National Natural Reserve, Longquan, China
| | - Xue-Kai He
- Administration of Fengyangshan-Baishanzu National Natural Reserve, Longquan, China
| | - Zhong-Shuai Sun
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
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38
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Guan Y, Wang P, Qie H, Huang Y, Yu W. The characterization and phylogenetic analysis of complete chloroplast genome in Morella cerifera (Myricaceae). Mitochondrial DNA B Resour 2021; 6:66-68. [PMID: 33521269 PMCID: PMC7819111 DOI: 10.1080/23802359.2020.1845997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The first complete chloroplast genome of Morella cerifera was obtained by illumina platform sequencing technology in this study. The size of genome is 158,943 base pairs, consist of a pair of IRs 26,043 bp in length, the LSC region of 88,167 bp and SSC region of 18,690 bp. The genome has 112 unique genes, among which 79 protein-coding genes, 29 tRNAs, and 4 rRNAs. Phylogenetic analysis revealed that M. cerifera clustered with M. rubra within Myricaceae.
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Affiliation(s)
- Yuanlin Guan
- Taihu Extension Center for Evergreen Fruit of Jiangsu Province, Suzhou, China
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Hefei, China
| | - Pengkai Wang
- Taihu Extension Center for Evergreen Fruit of Jiangsu Province, Suzhou, China
- Suzhou Polytechnic Institute of Agriculture, Suzhou, China
| | - Hongli Qie
- Taihu Extension Center for Evergreen Fruit of Jiangsu Province, Suzhou, China
| | - Yinghong Huang
- Taihu Extension Center for Evergreen Fruit of Jiangsu Province, Suzhou, China
| | - Wensheng Yu
- Taihu Extension Center for Evergreen Fruit of Jiangsu Province, Suzhou, China
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39
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Zhou X, Huang YB, Zhang ZC, Xu XY, Wang RH, Xu L, Qi ZC, Wei YK. The complete chloroplast genome of endangered Zhangjiajie sage Salvia daiguii Y. K. Wei & Y. B. Huang (Lamiaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3833-3834. [PMID: 33426293 PMCID: PMC7759251 DOI: 10.1080/23802359.2020.1840934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The complete chloroplast genome of Zhangjiajie sage, Salvia daiguii, was assembled in this study. The genome is 151,434 bp in length and contained 134 encoded genes in total, including 88 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The result of phylogenetic analysis based on 17 chloroplast genomes revealed that S. daiguii is clustered with Salvia miltiorrhiza in Lamiaceae.
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Affiliation(s)
- Xuan Zhou
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, PR China.,Shanghai Chenshan Plant Science Research Centre, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, PR China
| | - Yan-Bo Huang
- Shanghai Chenshan Plant Science Research Centre, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, PR China
| | - Zhi-Cheng Zhang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, PR China.,Shanghai Chenshan Plant Science Research Centre, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, PR China
| | - Xin-Yan Xu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, PR China.,Shanghai Chenshan Plant Science Research Centre, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, PR China
| | - Rui-Hong Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, PR China
| | - Ling Xu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, PR China
| | - Zhe-Chen Qi
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, PR China
| | - Yu-Kun Wei
- Shanghai Chenshan Plant Science Research Centre, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, PR China
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40
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Rono PC, Dong X, Yang JX, Mutie FM, Oulo MA, Malombe I, Kirika PM, Hu GW, Wang QF. Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships. Front Genet 2020; 11:560368. [PMID: 33362846 PMCID: PMC7756076 DOI: 10.3389/fgene.2020.560368] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/15/2020] [Indexed: 11/13/2022] Open
Abstract
The genus Alchemilla L., known for its medicinal and ornamental value, is widely distributed in the Holarctic regions with a few species found in Asia and Africa. Delimitation of species within Alchemilla is difficult due to hybridization, autonomous apomixes, and polyploidy, necessitating efficient molecular-based characterization. Herein, we report the initial complete chloroplast (cp) genomes of Alchemilla. The cp genomes of two African (Afromilla) species Alchemilla pedata and Alchemilla argyrophylla were sequenced, and phylogenetic and comparative analyses were conducted in the family Rosaceae. The cp genomes mapped a typical circular quadripartite structure of lengths 152,438 and 152,427 base pairs (bp) in A. pedata and A. argyrophylla, respectively. Alchemilla cp genomes were composed of a pair of inverted repeat regions (IRa/IRb) of length 25,923 and 25,915 bp, separating the small single copy (SSC) region of 17,980 and 17,981 bp and a large single copy (LSC) region of 82,612 and 82,616 bp in A. pedata and A. argyrophylla, respectively. The cp genomes encoded 114 unique genes including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Additionally, 88 and 95 simple sequence repeats (SSRs) and 37 and 40 tandem repeats were identified in A. pedata and A. argyrophylla, respectively. Significantly, the loss of group II intron in atpF gene in Alchemilla species was detected. Phylogenetic analysis based on 26 whole cp genome sequences and 78 protein-coding gene sequences of 27 Rosaceae species revealed a monophyletic clustering of Alchemilla nested within subfamily Rosoideae. Based on a protein-coding region, negative selective pressure (Ka/Ks < 1) was detected with an average Ka/Ks value of 0.1322 in A. argyrophylla and 0.1418 in A. pedata. The availability of complete cp genome in the genus Alchemilla will contribute to species delineation and further phylogenetic and evolutionary studies in the family Rosaceae.
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Affiliation(s)
- Peninah Cheptoo Rono
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jia-Xin Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Fredrick Munyao Mutie
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Millicent A Oulo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Itambo Malombe
- East African Herbarium, National Museums of Kenya, Nairobi, Kenya
| | - Paul M Kirika
- East African Herbarium, National Museums of Kenya, Nairobi, Kenya
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
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41
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Yang YX, Tian MH, Liu XH, Li YL, Sun ZS. Complete chloroplast genome of Prunus fruticosa and its implications for the phylogenetic position within Prunus sensulato (Rosaceae). Mitochondrial DNA B Resour 2020; 5:3624-3626. [PMID: 33367034 PMCID: PMC7594838 DOI: 10.1080/23802359.2020.1831993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Prunus fruticosa is a wild species of Prunus distributed across the central Eurasia. Here, we reported the complete chloroplast (cp) genome of P. fruticosa (GenBank accession number: MT916286). The cp genome was 158,217 bp long, with a large single-copy region (LSC) of 86,322 bp and a small single-copy region (SSC) of 19,153 bp separated by a pair of inverted repeats (IRs) of 26,371 bp. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. We also reconstructed the phylogeny of Prunus sensu lato using maximum likelihood (ML) method, including our data and previously reported cp genomes of related taxa. The phylogenetic analysis indicated that P. fruticosa is closely related with Prunus avium.
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Affiliation(s)
- Yu-Xin Yang
- College of Life Sciences, Taizhou University, Taizhou, China
| | - Mi-Hui Tian
- College of Life Sciences, Taizhou University, Taizhou, China
| | | | - Yue-Ling Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Zhong-Shuai Sun
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
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42
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Fang J, Lin A, Yuan X, Chen Y, He W, Huang J, Zhang X, Lin G, Zhang J, Xue T. The complete chloroplast genome of Isochrysis galbana and comparison with related haptophyte species. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101989] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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43
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Liu L, Du Y, Shen C, Li R, Lee J, Li P. The complete chloroplast genome of Papaver setigerum and comparative analyses in Papaveraceae. Genet Mol Biol 2020; 43:e20190272. [PMID: 32808964 PMCID: PMC7433754 DOI: 10.1590/1678-4685-gmb-2019-0272] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 05/08/2020] [Indexed: 11/22/2022] Open
Abstract
Papaver setigerum is an annual herb that is closely related to the opium poppy, P. somniferum. Genetic resources for P. setigerum are scarce. In the present study, we assembled the complete chloroplast (cp) genome of P. setigerum based on genome skimming data, and we conducted comparative cp genome analyses to study the evolutionary pattern in Papaveraceae. The cp genome of P. setigerum is 152,862 bp in length with a typical quadripartite structure. Comparative analyses revealed no gene rearrangement in the Papaveraceae family, although differences were evident in genome size, gene losses, as well as inverted repeats (IR) region expansion and contraction. The rps15 gene has been lost from the genomes of Meconopsis racemosa, Coreanomecon hylomeconoides, P. orientale, P. somniferum, and P. setigerum, and the ycf15 gene is found only in C. hylomeconoides. Moreover, 13 cpDNA markers, including psbA-trnH, rps16-trnQ, trnS-trnG, trnC-petN, trnE-trnT, trnL-trnF, trnF-ndhJ, petA-psbJ, ndhF-rpl32, rpl32-trnL, ccsA-ndhD, ndhE-ndhG, and rps15-ycf1, were identified with relatively high levels of variation within Papaver, which will be useful for species identification in this genus. Among those markers, psbA-trnH is the best one to distinguish P. somniferum and P. setigerum.
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Affiliation(s)
- Luxian Liu
- Henan University, School of Life Sciences, Key Laboratory of
Plant Stress Biology, Kaifeng, China
| | - Yingxue Du
- Henan University, School of Life Sciences, Key Laboratory of
Plant Stress Biology, Kaifeng, China
| | - Cheng Shen
- Zhejiang University, College of Life Sciences, The Key
Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of
Education, Hangzhou, China
| | - Rui Li
- Food inspection and Testing Institute of Henan Province,
Physical and Chemical Laboratory, Zhengzhou, China
| | - Joongku Lee
- Chungnam National University, Department of Environment and
Forest Resources, Daejeon, South Korea
| | - Pan Li
- Zhejiang University, College of Life Sciences, The Key
Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of
Education, Hangzhou, China
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44
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He Y, Ma Y, Li Z, Liu P, Yuan W. The complete chloroplast genome of Verbascum chinense (L.) Santapau. Mitochondrial DNA B Resour 2020; 5:3021-3022. [PMID: 33458041 PMCID: PMC7782814 DOI: 10.1080/23802359.2020.1797556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Verbascum chinense is a perennial plant in the Scrophulariaceae family that is traditionally used as sedative, astringent, febrifuge, and for skin eruptions. Here, we determined the complete chloroplast(cp) genome sequence for V. chinense using genome skimming sequencing. The cp genome was 153,618 bp and consisted of a large single copy (LSC) region (84,834 bp), a small single copy (SSC) region (17,884 bp), and two inverted repeats (IRs) (25,450 bp). It encodes 114 unique genes, including 80 protein-coding genes, four rRNAs, and 30 tRNAs. Phylogenetic analysis indicates that V. chinense exhibits a closer relationship with V. phoeniceum rather than Scrophularia.
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Affiliation(s)
- Yanxia He
- School of Life Sciences, Henan University, Kaifeng, China
| | - Yuanyuan Ma
- Institute of Chinese Materia Medica, Henan University, Kaifeng, China
| | - Zhengying Li
- School of Life Sciences, Henan University, Kaifeng, China
| | - Peng Liu
- Institute of Chinese Materia Medica, Henan University, Kaifeng, China
| | - Wangjun Yuan
- Institute of Chinese Materia Medica, Henan University, Kaifeng, China
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45
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Chen L, Liu Y, Chen J, Lin N, Xia M. The complete plastome and phylogeny of Barnardia japonica (Asparagaceae). Mitochondrial DNA B Resour 2020; 5:2640-2641. [PMID: 33457890 PMCID: PMC7782957 DOI: 10.1080/23802359.2020.1785350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Barnardia japonica is a perennial herb in Asparagaceae, which has important ornamental and medicinal value. Here, we sequenced and characterized the plastome of B. japonica from Sichuan, China. The plastome length of B. japonica was 156,111 bp, including an 84,333 bp LSC, a 18,272 bp SSC and two 26,753 bp IRs. A total of 132 genes were detected, including 20 duplicated genes and 112 unique genes. Phylogenetic analysis based on 32 taxa revealed the monophyly of B. japonica and its sister relationship to Albuca kirkii. In addition, our results will provide valuable information for the phylogeny of Asparagaceae.
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Affiliation(s)
- Li Chen
- Jinhua Polytechnic, Jinhua, China
| | - Ying Liu
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | | | - Na Lin
- Lishui Hospital of Traditional Chinese Medicine, Lishui, China
| | - Maoqin Xia
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
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46
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Li YL, Wei CY, Chen XY, Sun ZS. Characterization of the complete chloroplast genome sequence of the endangered species Platycrater arguta (Hydrangeaceae). Mitochondrial DNA B Resour 2020; 5:3394-3396. [PMID: 33458183 PMCID: PMC7782893 DOI: 10.1080/23802359.2020.1821816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- Yue-Ling Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, P. R. China
| | - Chun-Yan Wei
- College of Life Sciences, Taizhou University, Taizhou, P. R. China
| | - Xing-Yu Chen
- College of Life Sciences, Taizhou University, Taizhou, P. R. China
| | - Zhong-Shuai Sun
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, P. R. China
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47
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Zhang W, Liu P, Liu J, He Y. The complete chloroplast genome of Fraxinus hupehensis and phylogenic analysis of Lamiales. Mitochondrial DNA B Resour 2020; 5:3561-3562. [PMID: 33458241 PMCID: PMC7782264 DOI: 10.1080/23802359.2020.1829128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Fraxinus hupehensis is a national rare and Endangered tree in the Oleaceae family, that has high commercial value owing to its slow growth, interlaced roots, intricate tree shape, and easy to shape. Here, we determined the complete chloroplast (cp) genome sequence for F. hupehensis using genome skimming sequencing. The cp genome was 155,698 bp and consisted of a large single copy (LSC) region (86,498 bp), a small single copy (SSC) region (17,803 bp) and two inverted repeats (IRs) (25,694 bp). It encodes 131 genes, including 88 protein-coding genes, 8 rRNAs and 35 tRNAs. Phylogenetic analysis indicates that F. hupehensis was relatively closely related to F. chinensis compared to other species in the Oleaceae family.
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Affiliation(s)
- Weirui Zhang
- Eucommia Ulmoides Cultivation and Utilization of Henan Engineering Laboratory, Kaifeng, China
| | - Peng Liu
- Eucommia Ulmoides Cultivation and Utilization of Henan Engineering Laboratory, Kaifeng, China
| | - Jiahui Liu
- School of Life Sciences, Henan University, Kaifeng, China
| | - Yanxia He
- School of Life Sciences, Henan University, Kaifeng, China
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48
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Zhang Y, Zhang QY, Ran H, Cao Y. Characteristic of the complete chloroplast genome of Symphoricarpos sinensis, an important ornamental plant endemic to China. Mitochondrial DNA B Resour 2020; 5:3170-3171. [PMID: 33458099 PMCID: PMC7782690 DOI: 10.1080/23802359.2020.1807423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Symphoricarpos sinensis is an important ornamental plant in China. Due to the lack of efficient molecular markers, although recent studies supported that Symphoricarpos was phylogenetically closely related to Lonicera, Triosteum, Heptacodium, and Leycesteria, relationships among these taxa remained uncertain. To examine the phylogenetic position of Symphoricarpos within Caprifoliaceae, we characterized the complete chloroplast (cp) genome of S. sinensis. The results showed that S. sinensis shared a typical quadripartite structure as with most angiosperms. It was 155,738 bp in length, including two inverted repeat (IR) regions (24,010 bp), a small single-copy (SSC) region (18,942 bp) and a large single-copy (LSC) region (88,776 bp). Phylogenetic analysis demonstrated that Caprifoliaceae and Adoxaceae formed two distinct monophyletic clades, and S. sinensis was closely related to lonicera and Triosteum, albeit with low support. The whole cp genome of S. sinensis will be useful resources for future studies on phylogeny and conservation in Symphoricarpos.
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Affiliation(s)
- Yi Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Qing Yuan Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Hang Ran
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yanan Cao
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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49
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Cao MT, Wu JJ, Wang RH, Xu L, Qi ZC, Wei YK. The complete chloroplast genome of Russian sage Salvia yangii B. T. Drew (Lamiaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2590-2591. [PMID: 33457870 PMCID: PMC7782042 DOI: 10.1080/23802359.2020.1781581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The complete chloroplast genome of Russian sage Salvia yangii B. T. Drew was assembled in this study. The genome is 151,473 bp in length and contained 129 encoded genes in total, including 84 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The result of phylogenetic analysis based on 15 chloroplast genomes revealed that S. yangii is closely related to common sage (Salvia officinalis) in Lamiaceae.
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Affiliation(s)
- Meng-Ting Cao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Jun-Jie Wu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Rui-Hong Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Ling Xu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Zhe-Chen Qi
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yu-Kun Wei
- Shanghai Chenshan Plant Science Research Centre, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
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50
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Hong Z, Wu Z, Zhao K, Yang Z, Zhang N, Guo J, Tembrock LR, Xu D. Comparative Analyses of Five Complete Chloroplast Genomes from the Genus Pterocarpus (Fabacaeae). Int J Mol Sci 2020; 21:E3758. [PMID: 32466556 PMCID: PMC7312355 DOI: 10.3390/ijms21113758] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/20/2020] [Accepted: 05/24/2020] [Indexed: 12/14/2022] Open
Abstract
Pterocarpus is a genus of trees mainly distributed in tropical Asia, Africa, and South America. Some species of Pterocarpus are rosewood tree species, having important economic value for timber, and for some species, medicinal value as well. Up to now, information about this genus with regard to the genomic characteristics of the chloroplasts has been limited. Based on a combination of next-generation sequencing (Illumina Hiseq) and long-read sequencing (PacBio), the whole chloroplast genomes (cp genomes) of five species (rosewoods) in Pterocarpus (Pterocarpus macrocarpus, P. santalinus, P. indicus, P. pedatus, P. marsupium) have been assembled. The cp genomes of five species in Pterocarpus have similar structural characteristics, gene content, and sequence to other flowering plants. The cp genomes have a typical four-part structure, containing 110 unique genes (77 protein coding genes, 4 rRNAs, 29 tRNAs). Through comparative genomic analysis, abundant simple sequence repeat (SSR)loci (333-349) were detected in Pterocarpus, among which A /T single nucleotide repeats accounted for the highest proportion (72.8-76.4%). In the five cp genomes of Pterocarpus, eight hypervariable regions, including trnH-GUG_psbA, trnS-UGA_psbC, accD-psaI, ndhI-exon2_ndhI-exon1, ndhG_ndhi-exon2, rpoC2-exon2, ccsA, and trnfM-CAU, are proposed for use as DNA barcode regions. In the comparison of gene selection pressures (P. santalinus as the reference genome), purifying selection was inferred as the primary mode of selection in maintaining important biological functions. Phylogenetic analysis shows that Pterocarpus is a monophyletic group. The species P. tinctorius is resolved as early diverging in the genus. Pterocarpus was resolved as sister to the genus Tipuana.
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Affiliation(s)
- Zhou Hong
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China; (Z.H.); (K.Z.); (Z.Y.); (N.Z.); (J.G.)
| | - Zhiqiang Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China;
| | - Kunkun Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China; (Z.H.); (K.Z.); (Z.Y.); (N.Z.); (J.G.)
| | - Zengjiang Yang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China; (Z.H.); (K.Z.); (Z.Y.); (N.Z.); (J.G.)
| | - Ningnan Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China; (Z.H.); (K.Z.); (Z.Y.); (N.Z.); (J.G.)
| | - Junyu Guo
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China; (Z.H.); (K.Z.); (Z.Y.); (N.Z.); (J.G.)
| | - Luke R. Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA;
| | - Daping Xu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China; (Z.H.); (K.Z.); (Z.Y.); (N.Z.); (J.G.)
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