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Milarska SE, Androsiuk P, Paukszto Ł, Jastrzębski JP, Maździarz M, Larson KW, Giełwanowska I. Complete chloroplast genomes of Cerastium alpinum, C. arcticum and C. nigrescens: genome structures, comparative and phylogenetic analysis. Sci Rep 2023; 13:18774. [PMID: 37907682 PMCID: PMC10618263 DOI: 10.1038/s41598-023-46017-y] [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: 06/07/2023] [Accepted: 10/26/2023] [Indexed: 11/02/2023] Open
Abstract
The genus Cerastium includes about 200 species that are mostly found in the temperate climates of the Northern Hemisphere. Here we report the complete chloroplast genomes of Cerastium alpinum, C. arcticum and C. nigrescens. The length of cp genomes ranged from 147,940 to 148,722 bp. Their quadripartite circular structure had the same gene organization and content, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Repeat sequences varied from 16 to 23 per species, with palindromic repeats being the most frequent. The number of identified SSRs ranged from 20 to 23 per species and they were mainly composed of mononucleotide repeats containing A/T units. Based on Ka/Ks ratio values, most genes were subjected to purifying selection. The newly sequenced chloroplast genomes were characterized by a high frequency of RNA editing, including both C to U and U to C conversion. The phylogenetic relationships within the genus Cerastium and family Caryophyllaceae were reconstructed based on the sequences of 71 protein-coding genes. The topology of the phylogenetic tree was consistent with the systematic position of the studied species. All representatives of the genus Cerastium were gathered in a single clade with C. glomeratum sharing the least similarity with the others.
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Affiliation(s)
- Sylwia E Milarska
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Piotr Androsiuk
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland.
| | - Łukasz Paukszto
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Pl. Łódzki 1, 10-721, Olsztyn, Poland
| | - Jan P Jastrzębski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Mateusz Maździarz
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Pl. Łódzki 1, 10-721, Olsztyn, Poland
| | - Keith W Larson
- Climate Impacts Research Centre, Umeå University, 90187, Umeå, Sweden
| | - Irena Giełwanowska
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
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Zhang W, Zhang Z, Liu B, Chen J, Zhao Y, Huang Y. Comparative analysis of 17 complete chloroplast genomes reveals intraspecific variation and relationships among Pseudostellaria heterophylla (Miq.) Pax populations. FRONTIERS IN PLANT SCIENCE 2023; 14:1163325. [PMID: 37426955 PMCID: PMC10325831 DOI: 10.3389/fpls.2023.1163325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/17/2023] [Indexed: 07/11/2023]
Abstract
Pseudostellaria heterophylla (Miq.) Pax is a well-known medicinal and ecologically important plant. Effectively distinguishing its different genetic resources is essential for its breeding. Plant chloroplast genomes can provide much more information than traditional molecular markers and provide higher-resolution genetic analyses to distinguish closely related planting materials. Here, seventeen P. heterophylla samples from Anhui, Fujian, Guizhou, Hebei, Hunan, Jiangsu, and Shandong provinces were collected, and a genome skimming strategy was employed to obtain their chloroplast genomes. The P. heterophylla chloroplast genomes ranged from 149,356 bp to 149,592 bp in length, and a total of 111 unique genes were annotated, including 77 protein-coding genes, 30 tRNA genes, and four rRNA genes. Codon usage analysis showed that leucine had the highest frequency, while UUU (encoding phenylalanine) and UGC (encoding cysteine) were identified as the most and least frequently used codons, respectively. A total of 75-84 SSRs, 16-21 short tandem repeats, and 27-32 long repeat structures were identified in these chloroplast genomes. Then, four primer pairs were revealed for identifying SSR polymorphisms. Palindromes are the dominant type, accounting for an average of 47.86% of all long repeat sequences. Gene orders were highly collinear, and IR regions were highly conserved. Genome alignment indicated that there were four intergenic regions (psaI-ycf4, ycf3-trnS, ndhC-trnV, and ndhI-ndhG) and three coding genes (ndhJ, ycf1, and rpl20) that were highly variable among different P. heterophylla samples. Moreover, 10 SNP/MNP sites with high polymorphism were selected for further study. Phylogenetic analysis showed that populations of Chinese were clustered into a monophyletic group, in which the non-flowering variety formed a separate subclade with high statistical support. In this study, the comparative analysis of complete chloroplast genomes revealed intraspecific variations in P. heterophylla and further supported the idea that chloroplast genomes could elucidate relatedness among closely related cultivation materials.
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Affiliation(s)
- Wujun Zhang
- Institute of Agricultural Bioresources, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Zhaolei Zhang
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Baocai Liu
- Institute of Agricultural Bioresources, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jingying Chen
- Institute of Agricultural Bioresources, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yunqing Zhao
- Institute of Agricultural Bioresources, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yingzhen Huang
- Institute of Agricultural Bioresources, Fujian Academy of Agricultural Sciences, Fuzhou, China
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Zhao H, Zhang Z, Li X, Tian Y, Zhao J, Liu J, Shi L. The complete chloroplast genome of Pseudostellaria davidii (franch.) Pax, 1934. Mitochondrial DNA B Resour 2023; 8:471-474. [PMID: 37025399 PMCID: PMC10071897 DOI: 10.1080/23802359.2023.2195514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
Pseudostellaria davidii (Franch.) Pax belongs to subseries distancs of Pseudostellaria (Caryophyllaceae), and is mainly distributed in north-eastern Asia. The complete chloroplast (cp) genome of P. davidii was assembled and annotated for the first time in this study. The cp genome of P. davidii is 149,732 bp in length with the GC content of 36.57%, and it consists of four subregions: a large single-copy (LSC) region of 81,156 bp, a small single-copy (SSC) region of 16,894 bp and two inverted repeats (IR) regions of 25,841 bp each. The cp genome of P. davidii encodes a total of 111 unique genes, which are 77 protein-coding genes, four rRNA genes, and 30 tRNA genes. The results of phylogenetic analysis strongly suggested that Pseudostellaria was a monophyletic group and P. davidii forms an independent sister clade to other species of Pseudostellaria.
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Affiliation(s)
- Hongye Zhao
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, P.R. China
| | - Zhaolei Zhang
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, P.R. China
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Xinyi Li
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, P.R. China
| | - Yu Tian
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, P.R. China
| | - Jingyi Zhao
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, P.R. China
| | - Jinxin Liu
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, P.R. China
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
- CONTACT Jinxin Liu
| | - Linchun Shi
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, P.R. China
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
- Linchun Shi Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, P.R. China
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Park J, Lee J, Park J. The investigation of intraspecific characteristics and comparative analyses of the complete mitochondrial genome of Stegobium paniceum (Linnaeus, 1758) (Coleoptera: Ptinidae) assembled from public NGS raw reads of the black truffle, Tuber melanosporum. Sci Prog 2022; 105:368504211072355. [PMID: 35040745 PMCID: PMC10358573 DOI: 10.1177/00368504211072355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Due to the rapid development of NGS technologies, a huge amount of NGS raw reads have been accumulated in public repositories, such as the Short Read Archive of NCBI. We successfully rescued the complete mitochondrial genome of Stegobium paniceum, a drug store beetle, from public NGS raw reads of truffle generated from the whole genome project. The circular mitogenome of S. paniceum is 15,474 bp long including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 803 bp. Intraspecific transfer RNAs structure and sequence variations were investigated and simple sequence repeats identified from three S. paniceum mitochondrial genomes were compared showing their diversities as fundamental data to utilize them in various aspects including developing efficient molecular markers in the family, Ptinidae. Phylogenetic analysis of 23 Bostrichoidea mitochondrial genomes presented better species identification based on phylogenetic analyses and the optimal options for constructing phylogenetic trees based on Bostrichoidea mitochondrial genomes. Our results present not only utilization of public NGS raw read sequences but also intraspecific features of S. paniceum mitochondrial genomes and comparative analysis of Bostrichoidea mitochondrial genomes in various aspects.
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Affiliation(s)
- Jongsun Park
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Jungmo Lee
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Jonghyun Park
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
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A Comparative Analyses of the Complete Mitochondrial Genomes of Fungal Endosymbionts in Sogatella furcifera, White-Backed Planthoppers. Int J Genomics 2021; 2021:6652508. [PMID: 34212028 PMCID: PMC8208876 DOI: 10.1155/2021/6652508] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/03/2021] [Accepted: 05/08/2021] [Indexed: 12/20/2022] Open
Abstract
Sogatella furcifera Horvath, commonly known as the white-backed planthoppers (WBPH), is an important pest in East Asian rice fields. Fungal endosymbiosis is widespread among planthoppers in the infraorder Fulgoromorpha and suborder Auchenorrhyncha. We successfully obtained complete mitogenome of five WBPH fungal endosymbionts, belonging to the Ophiocordycipitaceae family, from next-generation sequencing (NGS) reads obtained from S. furcifera samples. These five mitogenomes range in length from 55,390 bp to 55,406 bp, which is shorter than the mitogenome of the fungal endosymbiont found in Ricania speculum, black planthoppers. Twenty-eight protein-coding genes (PCGs), 12 tRNAs, and 2 rRNAs were found in the mitogenomes. Two single-nucleotide polymorphisms, two insertions, and three deletions were identified among the five mitogenomes, which were fewer in number than those of four species of Ophiocordycipitaceae, Ophiocordyceps sinensis, Hirsutella thompsonii, Hirsutella rhossiliensis, and Tolypocladium inflatum. Noticeably short lengths (up to 18 bp) of simple sequence repeats were identified in the five WBPH fungal endosymbiont mitogenomes. Phylogenetic analysis based on conserved PCGs across 25 Ophiocordycipitaceae mitogenomes revealed that the five mitogenomes were clustered with that of R. speculum, forming an independent clade. In addition to providing the full mitogenome sequences, obtaining complete mitogenomes of WBPH endosymbionts can provide insights into their phylogenetic positions without needing to isolate the mtDNA from the host. This advantage is of value to future studies involving fungal endosymbiont mitogenomes.
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Park J, Xi H, Kim Y. The Complete Chloroplast Genome of Arabidopsis thaliana Isolated in Korea (Brassicaceae): An Investigation of Intraspecific Variations of the Chloroplast Genome of Korean A. thaliana. Int J Genomics 2020; 2020:3236461. [PMID: 32964010 PMCID: PMC7492873 DOI: 10.1155/2020/3236461] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/02/2020] [Accepted: 08/17/2020] [Indexed: 01/18/2023] Open
Abstract
Arabidopsis thaliana (L.) Heynh. is a model organism of plant molecular biology. More than 1,700 whole genome sequences have been sequenced, but no Korean isolate genomes have been sequenced thus far despite the fact that many A. thaliana isolated in Japan and China have been sequenced. To understand the genetic background of Korean natural A. thaliana (named as 180404IB4), we presented its complete chloroplast genome, which is 154,464 bp long and has four subregions: 85,164 bp of large single copy (LSC) and 17,781 bp of small single copy (SSC) regions are separated by 26,257 bp of inverted repeat (IRs) regions including 130 genes (85 protein-coding genes, eight rRNAs, and 37 tRNAs). Fifty single nucleotide polymorphisms (SNPs) and 14 insertion and deletions (INDELs) are identified between 180404IB4 and Col0. In addition, 101 SSRs and 42 extendedSSRs were identified on the Korean A. thaliana chloroplast genome, indicating a similar number of SSRs on the rest five chloroplast genomes with a preference of sequence variations toward the SSR region. A nucleotide diversity analysis revealed two highly variable regions on A. thaliana chloroplast genomes. Phylogenetic trees with three more chloroplast genomes of East Asian natural isolates show that Korean and Chinese natural isolates are clustered together, whereas two Japanese isolates are not clustered, suggesting the need for additional investigations of the chloroplast genomes of East Asian isolates.
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Affiliation(s)
- Jongsun Park
- InfoBoss Inc., 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
| | - Hong Xi
- InfoBoss Inc., 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
| | - Yongsung Kim
- InfoBoss Inc., 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
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Xi H, Park J, Kim Y. The complete chloroplast genome sequence of rose-gold pussy willow, Salix gracilistyla Miq. (Salicaceae). Mitochondrial DNA B Resour 2019; 4:2118-2120. [PMID: 33365434 PMCID: PMC7687643 DOI: 10.1080/23802359.2019.1623115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 05/17/2019] [Indexed: 11/18/2022] Open
Abstract
To understand genetic background of Salix gracilistyla Miq., we presented its complete chloroplast genome which is 155,557 bp and has four sub regions: 84,530 bp of large single copy (LSC) and 16,218 bp of small single copy (SSC) regions are separated by 27,405 bp of inverted repeat (IR) regions including 130 genes (84 protein-coding gene, eight rRNAs, and 38 tRNAs). The overall GC content of the chloroplast genome is 36.7% and those in the LSC, SSC, and IR regions are 34.5%, 31.0%, and 41.9%, respectively. Phylogenetic trees show phylogenetic position of S. gracilistyla with low level of inter-species sequence variations.
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Affiliation(s)
- Hong Xi
- Infoboss Co., Ltd., Seoul, Korea
- InfoBoss Research Center, Seoul, Korea
| | - Jongsun Park
- Infoboss Co., Ltd., Seoul, Korea
- InfoBoss Research Center, Seoul, Korea
| | - Yongsung Kim
- Infoboss Co., Ltd., Seoul, Korea
- InfoBoss Research Center, Seoul, Korea
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