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Dai GZ, Song WY, Xu HF, Tu M, Yu C, Li ZK, Shang JL, Jin CL, Ding CS, Zuo LZ, Liu YR, Yan WW, Zang SS, Liu K, Zhang Z, Bock R, Qiu BS. Hypothetical chloroplast reading frame 51 encodes a photosystem I assembly factor in cyanobacteria. THE PLANT CELL 2024; 36:1844-1867. [PMID: 38146915 PMCID: PMC11062458 DOI: 10.1093/plcell/koad330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 09/29/2023] [Accepted: 12/20/2023] [Indexed: 12/27/2023]
Abstract
Hypothetical chloroplast open reading frames (ycfs) are putative genes in the plastid genomes of photosynthetic eukaryotes. Many ycfs are also conserved in the genomes of cyanobacteria, the presumptive ancestors of present-day chloroplasts. The functions of many ycfs are still unknown. Here, we generated knock-out mutants for ycf51 (sll1702) in the cyanobacterium Synechocystis sp. PCC 6803. The mutants showed reduced photoautotrophic growth due to impaired electron transport between photosystem II (PSII) and PSI. This phenotype results from greatly reduced PSI content in the ycf51 mutant. The ycf51 disruption had little effect on the transcription of genes encoding photosynthetic complex components and the stabilization of the PSI complex. In vitro and in vivo analyses demonstrated that Ycf51 cooperates with PSI assembly factor Ycf3 to mediate PSI assembly. Furthermore, Ycf51 interacts with the PSI subunit PsaC. Together with its specific localization in the thylakoid membrane and the stromal exposure of its hydrophilic region, our data suggest that Ycf51 is involved in PSI complex assembly. Ycf51 is conserved in all sequenced cyanobacteria, including the earliest branching cyanobacteria of the Gloeobacter genus, and is also present in the plastid genomes of glaucophytes. However, Ycf51 has been lost from other photosynthetic eukaryotic lineages. Thus, Ycf51 is a PSI assembly factor that has been functionally replaced during the evolution of oxygenic photosynthetic eukaryotes.
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Affiliation(s)
- Guo-Zheng Dai
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, PR China
| | - Wei-Yu Song
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, PR China
| | - Hai-Feng Xu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, PR China
| | - Miao Tu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, PR China
| | - Chen Yu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, PR China
| | - Zheng-Ke Li
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, PR China
| | - Jin-Long Shang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, PR China
| | - Chun-Lei Jin
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, PR China
| | - Chao-Shun Ding
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, PR China
| | - Ling-Zi Zuo
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, PR China
| | - Yan-Ru Liu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, PR China
| | - Wei-Wei Yan
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, PR China
| | - Sha-Sha Zang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, PR China
| | - Ke Liu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, PR China
| | - Zheng Zhang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, PR China
| | - Ralph Bock
- Department III, Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Bao-Sheng Qiu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, PR China
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Zhang A, Tian L, Zhu T, Li M, Sun M, Fang Y, Zhang Y, Lu C. Uncovering the photosystem I assembly pathway in land plants. NATURE PLANTS 2024; 10:645-660. [PMID: 38503963 DOI: 10.1038/s41477-024-01658-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 02/29/2024] [Indexed: 03/21/2024]
Abstract
Photosystem I (PSI) is one of two large pigment-protein complexes responsible for converting solar energy into chemical energy in all oxygenic photosynthetic organisms. The PSI supercomplex consists of the PSI core complex and peripheral light-harvesting complex I (LHCI) in eukaryotic photosynthetic organisms. However, how the PSI complex assembles in land plants is unknown. Here we describe PHOTOSYSTEM I BIOGENESIS FACTOR 8 (PBF8), a thylakoid-anchored protein in Arabidopsis thaliana that is required for PSI assembly. PBF8 regulates two key consecutive steps in this process, the building of two assembly intermediates comprising eight or nine subunits, by interacting with PSI core subunits. We identified putative PBF8 orthologues in charophytic algae and land plants but not in Cyanobacteria or Chlorophyta. Our data reveal the major PSI assembly pathway in land plants. Our findings suggest that novel assembly mechanisms evolved during plant terrestrialization to regulate PSI assembly, perhaps as a means to cope with terrestrial environments.
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Affiliation(s)
- Aihong Zhang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Lin Tian
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Tong Zhu
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Mengyu Li
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Mengwei Sun
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Ying Fang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Yi Zhang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China.
| | - Congming Lu
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China.
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Guo J, Yao Q, Dong J, Hou J, Jia P, Chen X, Li G, Zhao Q, Wang J, Liu F, Wang Z, Shan Y, Zhang T, Fu A, Wang F. Immunophilin FKB20-2 participates in oligomerization of Photosystem I in Chlamydomonas. PLANT PHYSIOLOGY 2024; 194:1631-1645. [PMID: 38039102 DOI: 10.1093/plphys/kiad645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 10/26/2023] [Accepted: 11/05/2023] [Indexed: 12/03/2023]
Abstract
PSI is a sophisticated photosynthesis protein complex that fuels the light reaction of photosynthesis in algae and vascular plants. While the structure and function of PSI have been studied extensively, the dynamic regulation on PSI oligomerization and high light response is less understood. In this work, we characterized a high light-responsive immunophilin gene FKB20-2 (FK506-binding protein 20-2) required for PSI oligomerization and high light tolerance in Chlamydomonas (Chlamydomonas reinhardtii). Biochemical assays and 77-K fluorescence measurement showed that loss of FKB20-2 led to the reduced accumulation of PSI core subunits and abnormal oligomerization of PSI complexes and, particularly, reduced PSI intermediate complexes in fkb20-2. It is noteworthy that the abnormal PSI oligomerization was observed in fkb20-2 even under dark and dim light growth conditions. Coimmunoprecipitation, MS, and yeast 2-hybrid assay revealed that FKB20-2 directly interacted with the low molecular weight PSI subunit PsaG, which might be involved in the dynamic regulation of PSI-light-harvesting complex I supercomplexes. Moreover, abnormal PSI oligomerization caused accelerated photodamage to PSII in fkb20-2 under high light stress. Together, we demonstrated that immunophilin FKB20-2 affects PSI oligomerization probably by interacting with PsaG and plays pivotal roles during Chlamydomonas tolerance to high light.
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Affiliation(s)
- Jia Guo
- College of Life Sciences, Northwest University, Xi'an 710069, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
| | - Qiang Yao
- College of Life Sciences, Northwest University, Xi'an 710069, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
| | - Jie Dong
- College of Life Sciences, Northwest University, Xi'an 710069, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
| | - Jinrong Hou
- College of Life Sciences, Northwest University, Xi'an 710069, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
| | - Pulian Jia
- College of Life Sciences, Northwest University, Xi'an 710069, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
| | - Xueying Chen
- College of Life Sciences, Northwest University, Xi'an 710069, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
| | - Guoyang Li
- College of Life Sciences, Northwest University, Xi'an 710069, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
| | - Qi Zhao
- College of Life Sciences, Northwest University, Xi'an 710069, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
- Shaanxi Key Laboratory for Carbon Neutral Technology, Xi'an 710069, China
| | - Jingyi Wang
- College of Life Sciences, Northwest University, Xi'an 710069, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
- Shaanxi Key Laboratory for Carbon Neutral Technology, Xi'an 710069, China
| | - Fang Liu
- College of Life Sciences, Northwest University, Xi'an 710069, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
| | - Ziyu Wang
- College of Life Sciences, Northwest University, Xi'an 710069, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
| | - Yuying Shan
- College of Life Sciences, Northwest University, Xi'an 710069, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
| | - Tengyue Zhang
- College of Life Sciences, Northwest University, Xi'an 710069, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
| | - Aigen Fu
- College of Life Sciences, Northwest University, Xi'an 710069, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
- Shaanxi Key Laboratory for Carbon Neutral Technology, Xi'an 710069, China
| | - Fei Wang
- College of Life Sciences, Northwest University, Xi'an 710069, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
- Shaanxi Key Laboratory for Carbon Neutral Technology, Xi'an 710069, China
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Islam MS, Chekhovskiy K, Saha MC. Dig up tall fescue plastid genomes for the identification of morphotype-specific DNA variants. BMC Genomics 2023; 24:586. [PMID: 37789301 PMCID: PMC10546690 DOI: 10.1186/s12864-023-09631-8] [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: 05/10/2023] [Accepted: 08/28/2023] [Indexed: 10/05/2023] Open
Abstract
BACKGROUND Tall fescue (Festuca arundinacea Schreb.) is an important cool-season perennial grass species. Hexaploid tall fescue has three distinct morphotypes used either as forage or turf purposes. Its chloroplast genome is conserved due to it being maternally inherited to the next generation progenies. To identify morphotype-specific DNA markers and the genetic variations, plastid genomes of all three tall fescue morphotypes, i.e., Continental cv. Texoma MaxQ II, Rhizomatous cv. Torpedo, and Mediterranean cv. Resolute, have been sequenced using Illumina MiSeq sequencing platform. RESULTS The plastid genomes of Continental-, Rhizomatous-, and Mediterranean tall fescue were assembled into circular master molecules of 135,283 bp, 135,336 bp, and 135,324 bp, respectively. The tall fescue plastid genome of all morphotypes contained 77 protein-coding, 20 tRNAs, four rRNAs, two pseudo protein-coding, and three hypothetical protein-coding genes. We identified 630 SNPs and 124 InDels between Continental and Mediterranean, 62 SNPs and 20 InDels between Continental and Rhizomatous, and 635 SNPs and 123 InDels between Rhizomatous and Mediterranean tall fescue. Only four InDels in four genes (ccsA, rps18, accD, and ndhH-p) were identified, which discriminated Continental and Rhizomatous plastid genomes from the Mediterranean plastid genome. Here, we identified and reported eight InDel markers (NRITCHL18, NRITCHL35, NRITCHL43, NRITCHL65, NRITCHL72, NRITCHL101, NRITCHL104, and NRITCHL110) from the intergenic regions that can successfully discriminate tall fescue morphotypes. Divergence time estimation revealed that Mediterranean tall fescue evolved approximately 7.09 Mya, whereas the divergence between Continental- and Rhizomatous tall fescue occurred about 0.6 Mya. CONCLUSIONS To our knowledge, this is the first report of the assembled plastid genomes of Rhizomatous and Mediterranean tall fescue. Our results will help to identify tall fescue morphotypes at the time of pre-breeding and will contribute to the development of lawn and forage types of commercial varieties.
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Affiliation(s)
- Md Shofiqul Islam
- Grass Genomics, Noble Research Institute LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA.
- Genetics Laboratory, Indiana Crop Improvement Association, 7700 Stockwell Road, Lafayette, IN, 47909, USA.
- Department of Agronomy, Purdue University, 915 Mitch Daniels Blvd, West Lafayette, IN, 47906, USA.
| | - Konstantin Chekhovskiy
- Grass Genomics, Noble Research Institute LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Malay C Saha
- Grass Genomics, Noble Research Institute LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
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Nellaepalli S, Lau AS, Jarvis RP. Chloroplast protein translocation pathways and ubiquitin-dependent regulation at a glance. J Cell Sci 2023; 136:jcs241125. [PMID: 37732520 PMCID: PMC10546890 DOI: 10.1242/jcs.241125] [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] [Indexed: 09/22/2023] Open
Abstract
Chloroplasts conduct photosynthesis and numerous metabolic and signalling processes that enable plant growth and development. Most of the ∼3000 proteins in chloroplasts are nucleus encoded and must be imported from the cytosol. Thus, the protein import machinery of the organelle (the TOC-TIC apparatus) is of fundamental importance for chloroplast biogenesis and operation. Cytosolic factors target chloroplast precursor proteins to the TOC-TIC apparatus, which drives protein import across the envelope membranes into the organelle, before various internal systems mediate downstream routing to different suborganellar compartments. The protein import system is proteolytically regulated by the ubiquitin-proteasome system (UPS), enabling centralized control over the organellar proteome. In addition, the UPS targets a range of chloroplast proteins directly. In this Cell Science at a Glance article and the accompanying poster, we present mechanistic details of these different chloroplast protein targeting and translocation events, and of the UPS systems that regulate chloroplast proteins.
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Affiliation(s)
- Sreedhar Nellaepalli
- Section of Molecular Plant Biology, Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Anne Sophie Lau
- Section of Molecular Plant Biology, Department of Biology, University of Oxford, Oxford OX1 3RB, UK
- Department of Plant Physiology, Faculty of Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - R. Paul Jarvis
- Section of Molecular Plant Biology, Department of Biology, University of Oxford, Oxford OX1 3RB, UK
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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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Castro AA, Nunes R, Carvalho LR, Targueta CP, Dos Santos Braga-Ferreira R, de Melo-Ximenes AA, Corvalán LCJ, Bertoni BW, Pereira AMS, de Campos Telles MP. Chloroplast genome characterization of Uncaria guianensis and Uncaria tomentosa and evolutive dynamics of the Cinchonoideae subfamily. Sci Rep 2023; 13:8390. [PMID: 37225737 DOI: 10.1038/s41598-023-34334-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 04/27/2023] [Indexed: 05/26/2023] Open
Abstract
Uncaria species are used in traditional medicine and are considered of high therapeutic value and economic importance. This work describes the assembly and annotation of the chloroplast genomes of U. guianensis and U. tomentosa, as well as a comparative analysis. The genomes were sequenced on MiSeq Illumina, assembled with NovoPlasty, and annotated using CHLOROBOX GeSeq. Addictionaly, comparative analysis were performed with six species from NCBI databases and primers were designed in Primer3 for hypervariable regions based on the consensus sequence of 16 species of the Rubiaceae family and validated on an in-silico PCR in OpenPrimeR. The genome size of U. guianensis and U. tomentosa was 155,505 bp and 156,390 bp, respectively. Both Species have 131 genes and GC content of 37.50%. The regions rpl32-ccsA, ycf1, and ndhF-ccsA showed the three highest values of nucleotide diversity within the species of the Rubiaceae family and within the Uncaria genus, these regions were trnH-psbA, psbM-trnY, and rps16-psbK. Our results indicates that the primer of the region ndhA had an amplification success for all species tested and can be promising for usage in the Rubiaceae family. The phylogenetic analysis recovered a congruent topology to APG IV. The gene content and the chloroplast genome structure of the analyzed species are conserved and most of the genes are under negative selection. We provide the cpDNA of Neotropical Uncaria species, an important genomic resource for evolutionary studies of the group.
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Affiliation(s)
- Andrezza Arantes Castro
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Rhewter Nunes
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil.
- Instituto Federal de Goiás - Campus Cidade de Goiás (IFG), Goiás, GO, 74600-000, Brazil.
| | - Larissa Resende Carvalho
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Cíntia Pelegrineti Targueta
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Ramilla Dos Santos Braga-Ferreira
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Amanda Alves de Melo-Ximenes
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Leonardo Carlos Jeronimo Corvalán
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | | | | | - Mariana Pires de Campos Telles
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
- Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás (PUC - GO), Goiânia, GO, 74605-050, Brazil
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8
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Ma D, Ding Q, Zhao Z, Han X, Zheng HL. Chloroplast genome analysis of three Acanthus species reveal the adaptation of mangrove to intertidal habitats. Gene 2023; 873:147479. [PMID: 37182557 DOI: 10.1016/j.gene.2023.147479] [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: 03/04/2023] [Revised: 04/24/2023] [Accepted: 05/08/2023] [Indexed: 05/16/2023]
Abstract
Acanthus is a distinctive genus that covers three species with different ecological niches including Acanthus mollis (arid terrestrial), Acanthus leucostachyus (damp forest) and Acanthus ilicifolius (coastal intertidal). It is an intriguing question how these species evolved from terrestrial to coastal intertidal. In the present study, we assembled chloroplast genomes of A. ilicifolius, A. leucostachyus and A. mollis, which exhibited typical quadripartite structures. The sizes were 150,758, 154,686 and 150,339 bp that comprised a large single copy (LSC, 82,963, 86,461 and 82,612 bp), a small single copy (SSC, 17,191, 17,511 and 17,019 bp), and a pair of inverted repeats (IRs, 25,302, 25,357 and 25,354 bp), respectively. Gene annotation revealed that A. ilicifolius, A. leucostachyus and A. mollis contained 113, 112 and 108 unique genes, each of which contained 79, 79 and 74 protein-coding genes, 30, 29 and 30 tRNAs, and 4 rRNA genes, respectively. Differential gene analysis revealed plenty of ndhs gene deletions in the terrestrial plant A. mollis. Nucleotide diversity analysis showed that the psbK, ycf1, ndhG, and rpl22 have the highest nucleotide variability. Compared to A. leucostachyus and A. mollis, seven genes in A. ilicifolius underwent positive selection. Among them, the atpF gene showed a strong positive selection throughout terrestrial to marine evolution and was important for adaptation to coastal intertidal habitats. Phylogenetic analysis indicated that A. ilicifolius has a closer genetic relationship with A. leucostachyus than A. mollis which further confirmed the evolutionary direction of Acanthus going from terrestrial to coastal intertidal zones.
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Affiliation(s)
- Dongna Ma
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Qiansu Ding
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Zhizhu Zhao
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Xiao Han
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Hai-Lei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China.
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9
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Yen LT, Kousar M, Park J. Comparative Analysis of Chloroplast Genome of Desmodium stryacifolium with Closely Related Legume Genome from the Phaseoloid Clade. Int J Mol Sci 2023; 24:ijms24076072. [PMID: 37047046 PMCID: PMC10094673 DOI: 10.3390/ijms24076072] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 04/14/2023] Open
Abstract
Desmodium styracifolium is a medicinal plant from the Desmodieae tribe, also known as Grona styracifolia. Its role in the treatment of urolithiasis, urinary infections, and cholelithiasis has previously been widely documented. The complete chloroplast genome sequence of D. Styracifolium is 149,155 bp in length with a GC content of 35.2%. It is composed of a large single copy (LSC) of 82,476 bp and a small single copy (SSC) of 18,439 bp, which are separated by a pair of inverted repeats (IR) of 24,120 bp each and has 128 genes. We performed a comparative analysis of the D. styracifolium cpDNA with the genome of previously investigated members of the Sesamoidea tribe and on the outgroup from its Phaseolinae sister tribe. The size of all seven cpDNAs ranged from 148,814 bp to 151,217 bp in length due to the contraction and expansion of the IR/SC boundaries. The gene orientation of the SSC region in D. styracifolium was inverted in comparison with the other six studied species. Furthermore, the sequence divergence of the IR regions was significantly lower than that of the LSC and the SSC, and five highly divergent regions, trnL-UAA-trnT-UGU, psaJ-ycf4, psbE-petL, rpl36-rps8, and rpl32-trnL-UGA, were identified that could be used as valuable molecular markers in future taxonomic studies and phylogenetic constructions.
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Affiliation(s)
- Le-Thi Yen
- Department of Fine Chemistry, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| | - Muniba Kousar
- Department of Fine Chemistry, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| | - Joonho Park
- Department of Fine Chemistry, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
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10
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Chanu NK, Mandal MK, Srivastava A, Mishra Y, Chaurasia N. Proteomics Reveals Damaging Effect of Alpha-Cypermethrin Exposure in a Non-Target Freshwater Microalga Chlorella sp. NC-MKM. Curr Microbiol 2023; 80:144. [PMID: 36943524 DOI: 10.1007/s00284-023-03179-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 01/02/2023] [Indexed: 03/23/2023]
Abstract
Alpha-cypermethrin, a pyrethroid pesticide, is frequently used on crops to prevent insect attacks. However, occasionally, due to drift, leaching, or with rainwater, it enters the aquatic environment and poses a serious threat to the growth of non-target aquatic organisms. In the current study, we were interested in investigating the damaging effect of alpha-cypermethrin on a local freshwater non-target green alga Chlorella sp. NC-MKM in terms of its protein levels. This was achieved by exposing Chlorella sp. NC-MKM to an EC50 concentration of alpha-cypermethrin for 1 day, followed by the two-dimensional (2-D) gel electrophoresis and MALDI-TOF MS. Fifty-three proteins, which had showed significant differential accumulation (> 1.5 fold, P < 0.05) after exposure to alpha-cypermethrin, were considered as differentially accumulated proteins (DAPs). These DAPs were further divided into several functional categories, and the expressions of each in control and treatment samples were compared. Comparison revealed that alpha-cypermethrin exposure affects the accumulation of proteins related with photosynthesis, stress response, carbohydrate metabolism, signal transduction and transporters, translation, transcription, cell division, lipid metabolism, amino acid and nucleotide biosynthesis, secondary metabolites production, and post-translational modification, and thus rendered the tested algal isolate sensitive toward this pesticide. The overall findings of this research thus offer a fundamental understanding of the possible mechanism of action of the insecticide alpha-cypermethrin on the microalga Chlorella sp. NC-MKM and also suggest potential biomarkers for the investigation of pesticide exposed microalgae.
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Affiliation(s)
- Ng Kunjarani Chanu
- Environmental Biotechnology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, 793022, Meghalaya, India
| | - Madan Kumar Mandal
- Environmental Biotechnology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, 793022, Meghalaya, India
| | - Akanksha Srivastava
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Yogesh Mishra
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Neha Chaurasia
- Environmental Biotechnology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, 793022, Meghalaya, India.
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11
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Jackson PJ, Hitchcock A, Brindley AA, Dickman MJ, Hunter CN. Absolute quantification of cellular levels of photosynthesis-related proteins in Synechocystis sp. PCC 6803. PHOTOSYNTHESIS RESEARCH 2023; 155:219-245. [PMID: 36542271 PMCID: PMC9958174 DOI: 10.1007/s11120-022-00990-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Quantifying cellular components is a basic and important step for understanding how a cell works, how it responds to environmental changes, and for re-engineering cells to produce valuable metabolites and increased biomass. We quantified proteins in the model cyanobacterium Synechocystis sp. PCC 6803 given the general importance of cyanobacteria for global photosynthesis, for synthetic biology and biotechnology research, and their ancestral relationship to the chloroplasts of plants. Four mass spectrometry methods were used to quantify cellular components involved in the biosynthesis of chlorophyll, carotenoid and bilin pigments, membrane assembly, the light reactions of photosynthesis, fixation of carbon dioxide and nitrogen, and hydrogen and sulfur metabolism. Components of biosynthetic pathways, such as those for chlorophyll or for photosystem II assembly, range between 1000 and 10,000 copies per cell, but can be tenfold higher for CO2 fixation enzymes. The most abundant subunits are those for photosystem I, with around 100,000 copies per cell, approximately 2 to fivefold higher than for photosystem II and ATP synthase, and 5-20 fold more than for the cytochrome b6f complex. Disparities between numbers of pathway enzymes, between components of electron transfer chains, and between subunits within complexes indicate possible control points for biosynthetic processes, bioenergetic reactions and for the assembly of multisubunit complexes.
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Affiliation(s)
- Philip J Jackson
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK.
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK.
| | - Andrew Hitchcock
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Amanda A Brindley
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | - C Neil Hunter
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
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12
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Wu T, Deng G, Yin Q, Chen S, Zhang Y, Wang B, Xiang L, Liu X. Characterization and molecular evolution analysis of Periploca forrestii inferred from its complete chloroplast genome sequence. Genome 2023; 66:34-50. [PMID: 36516428 DOI: 10.1139/gen-2022-0050] [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: 12/15/2022]
Abstract
Periploca forrestii, a medicinal plant of the family Apocynaceae, is known as an effective and widely used clinical prescription for the treatment of rheumatoid diseases. In this study, we de novo sequenced and assembled the completement chloroplast (cp) genome of P. forrestii based on combined Oxford Nanopore PromethION and Illumina data. The cp genome was 153 724 bp in length and had four subregions. Moreover, an 84 433 bp large single-copy and a 17 731 bp small single-copy were separated by 25 780 bp inverted repeats (IRs). The cp genome included 132 genes with 18 duplicates in the IRs. A total of 45 repeat structures and 183 simple sequence repeats were detected. Codon usage showed a bias toward A/T-ending codons. A comparative study of Apocynaceae revealed that an IR expansion occurred on P. forrestii. The Ka/Ks values of eight species of Apocynaceae suggested that positive selection was exerted on the psaI and ycf2 genes, which might reflect specific adaptions to the P. forrestii particular growth environment. Phylogenetic analysis indicated that Periplocoideae was a sister to Asclepiadoideae, forming a monophyletic group in the family Apocynaceae. This study provided an important P. forrestii genomic resource for future evolutionary studies and the phylogenetic reconstruction of the family Apocynaceae.
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Affiliation(s)
- Tianze Wu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Chinese Academy of Medical Sciences, Beijing 100700, China.,School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China
| | - Gang Deng
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Chinese Academy of Medical Sciences, Beijing 100700, China.,School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China
| | - Qinggang Yin
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Chinese Academy of Medical Sciences, Beijing 100700, China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Chinese Academy of Medical Sciences, Beijing 100700, China.,School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China
| | - Yongping Zhang
- National Engineering Technology Research Center for Miao Medicine, College of Pharmaceutical Sciences, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, Guizhou, China
| | - Bo Wang
- National Engineering Technology Research Center for Miao Medicine, College of Pharmaceutical Sciences, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, Guizhou, China
| | - Li Xiang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Chinese Academy of Medical Sciences, Beijing 100700, China
| | - Xia Liu
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China
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13
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The Complete Chloroplast Genome Sequence of Machilus chuanchienensis (Lauraceae): Genome Structure and Phylogenetic Analysis. Genes (Basel) 2022; 13:genes13122402. [PMID: 36553669 PMCID: PMC9778441 DOI: 10.3390/genes13122402] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Machilus chuanchienensis is an ecological tree distributed in southwestern China. It has a significant valuation with making Hawk tea using its leaves, an ethnic traditional tea-like beverage with a long history in Chinese tea culture. The whole chloroplast (cp) genome is an ideal model for the phylogenetic study of Lauraceae because of its simple structure and highly conserved features. There have been numerous reports of complete cp genome sequences in Lauraceae, but little is known about M. chuanchienensis. Here, the next-generation sequencing (NGS) was used to sequence the M. chuanchienensis cp genome. Then, a comprehensive comparative genome analysis was performed. The results revealed that the M. chuanchienensis's cp genome measured 152,748 base pairs (bp) with a GC content of 39.15% and coded 126 genes annotated, including comprising eight ribosomal RNA (rRNA), 36 transporter RNA (tRNA), and 82 protein-coding genes. In addition, the cp genome presented a typical quadripartite structure comprising a large single-copy (LSC; 93,811) region, a small single-copy (SSC; 18,803) region, and the inverted repeats (IRs; 20,067) region and contained 92 simple sequence repeat (SSR) locus in total. Phylogenetic relationships of 37 species indicated that M. chuanchienensis was a sister to M. balansae, M. melanophylla, and M. minutiflora. Further research on this crucial species may benefit significantly from these findings.
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14
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Xiang YL, Jin XJ, Shen C, Cheng XF, Shu L, Zhu RL. New insights into the phylogeny of the complex thalloid liverworts (Marchantiopsida) based on chloroplast genomes. Cladistics 2022; 38:649-662. [PMID: 35779275 DOI: 10.1111/cla.12513] [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: 02/20/2022] [Revised: 05/22/2022] [Accepted: 05/25/2022] [Indexed: 01/31/2023] Open
Abstract
Marchantiopsida (complex thalloid liverworts) are one of the earliest lineages of embryophytes (land plants), and well-known for their air pores and chambers, pegged rhizoids, and absence of organellular RNA editing sites. Despite their importance to an understanding of early embryophyte evolution, many key nodes within this class remain poorly resolved, owing to the paucity of genetic loci previously available for phylogenetic analyses. Here, we sequenced 54 plastomes, representing 28 genera, nearly all families, and all orders of Marchantiopsida. Based on these plastomes, we present a hypothesis of deep relationships within the class, and make the first investigations of gene contents and synteny. Overall, the Marchantiopsida plastomes were well-conserved, with the exception of the genus Cyathodium that has plastomes with higher GC content, fewer single sequence repeats (SSRs), and more structural variations, implying that this genus might possess RNA editing sites. Abundant repetitive elements and six highly divergent regions were identified as suitable for future infrafamilial taxonomic studies. The phylogenetic topology of Sphaerocarpales, Neohodgsoniales and Blasiales within Marchantiopsida was essentially congruent with previous studies but generally we obtained higher support values. Based on molecular evidence and previous morphological studies, we include Lunulariales in Marchantiales and suggest the retention of narrowed delimitation of monotypic families. The phylogenetic relationships within Marchantiales were better resolved, and 13 monophyletic families were recovered. Our analyses confirmed that the loss of intron 2 of ycf3 is a synapomorphy of Marchantiidae. Finally, we propose a new genus, Asterellopsis (Aytoniaceae), and present an updated classification of Marchantiopsida. The highly supported phylogenetic backbone provided here establishes a framework for future comparative and evolutionary studies of the complex thalloid liverworts.
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Affiliation(s)
- You-Liang Xiang
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Xin-Jie Jin
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China.,College of Life and Environmental Sciences, Wenzhou University, Wenzhou, 325035, China
| | - Chao Shen
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Xia-Fang Cheng
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Lei Shu
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Rui-Liang Zhu
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China.,Shanghai Institute of Eco-Chongming (SIEC), Shanghai, 200062, China.,Tiantong National Station of Forest Ecosystem, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, East China Normal University, Shanghai, 200241, China
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15
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Khan MS, Riaz R, Majid M, Mehmood K, Mustafa G, Joyia FA. The tobacco chloroplast YCF4 gene is essential for transcriptional gene regulation and plants photoautotrophic growth. FRONTIERS IN PLANT SCIENCE 2022; 13:1014236. [PMID: 36352880 PMCID: PMC9638951 DOI: 10.3389/fpls.2022.1014236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
A tobacco chloroplast hypothetical open reading frame 4 (YCF4) has been reported as a non-essential assembly factor for photosynthesis based on an incomplete knockout of YCF4, just 93 of 184 amino acids from the N-terminus were knocked out. On the other hand, we removed the complete sequence of YCF4 from tobacco chloroplasts and observed that ΔYCF4 plants were unable to survive photoautotrophically as their growth was hampered in the absence of an external carbon supply, clearly showing that the YCF4 is essential for photosynthesis. Initially, the aadA gene was introduced into the tobacco plastome replacing the complete YCF4 gene through homologous recombination events. The replacement of YCF4 with aadA was confirmed by PCR and Southern blot analysis in ΔYCF4 plants. Homoplasmic ΔYCF4 plants had a light green phenotype, and the leaves became pale yellow as the plants grew older. The structure of chloroplasts of ΔYCF4 mutants of light green phenotype was studied using a transmission electron microscope (TEM), and the micrographs demonstrated structural anomalies in the chloroplasts; including shape, size, and grana stacking compared to the wild-type plants. Further, transcriptome analysis revealed that the expression of PSI, PSII, and ribosomal genes remained unchanged in ∆YCF4 plants. On the other hand, transcriptome levels of rbcL (Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit), LHC (Light-Harvesting Complex), and ATP Synthase (atpB and atpL) decreased, indicating that the YCF4 has the function(s) in addition to assembling the photosynthetic complex. This was confirmed by in-silico protein-protein interactions of full-length YCF4 as well as 93 and 91 of 184 amino acids from N- and C-termini of the full-length protein, which revealed that the C-terminus (91 aa) of YCF4 is important in interacting with other chloroplast proteins. These findings provide genetic support for the plastid YCF4 gene's critical role in regulating the plastid gene expression and assembling the photosynthetic complex.
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Affiliation(s)
- Muhammad Sarwar Khan
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Rimsha Riaz
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Majid
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Kashif Mehmood
- Department of Molecular and Cellular Biology, Summerlee Science Complex, University of Guelph, Guelph, ON, Canada
| | - Ghulam Mustafa
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Faiz Ahmad Joyia
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
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16
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Comparative Genomics and Phylogenetic Analysis of the Chloroplast Genomes in Three Medicinal Salvia Species for Bioexploration. Int J Mol Sci 2022; 23:ijms232012080. [PMID: 36292964 PMCID: PMC9603726 DOI: 10.3390/ijms232012080] [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: 08/13/2022] [Revised: 09/08/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
To systematically determine their phylogenetic relationships and develop molecular markers for species discrimination of Salvia bowleyana, S. splendens, and S. officinalis, we sequenced their chloroplast genomes using the Illumina Hiseq 2500 platform. The chloroplast genomes length of S. bowleyana, S. splendens, and S. officinalis were 151,387 bp, 150,604 bp, and 151,163 bp, respectively. The six genes ndhB, rpl2, rpl23, rps7, rps12, and ycf2 were present in the IR regions. The chloroplast genomes of S. bowleyana, S. splendens, and S. officinalis contain 29 tandem repeats; 35, 29, 24 simple-sequence repeats, and 47, 49, 40 interspersed repeats, respectively. The three specific intergenic sequences (IGS) of rps16-trnQ-UUG, trnL-UAA-trnF-GAA, and trnM-CAU-atpE were found to discriminate the 23 Salvia species. A total of 91 intergenic spacer sequences were identified through genetic distance analysis. The two specific IGS regions (trnG-GCC-trnM-CAU and ycf3-trnS-GGA) have the highest K2p value identified in the three studied Salvia species. Furthermore, the phylogenetic tree showed that the 23 Salvia species formed a monophyletic group. Two pairs of genus-specific DNA barcode primers were found. The results will provide a solid foundation to understand the phylogenetic classification of the three Salvia species. Moreover, the specific intergenic regions can provide the probability to discriminate the Salvia species between the phenotype and the distinction of gene fragments.
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17
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AL-Juhani WS, Alharbi SA, Al Aboud NM, Aljohani AY. Complete chloroplast genome of the desert date (Balanites aegyptiaca (L.) Del. comparative analysis, and phylogenetic relationships among the members of Zygophyllaceae. BMC Genomics 2022; 23:626. [PMID: 36045328 PMCID: PMC9434970 DOI: 10.1186/s12864-022-08850-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 08/18/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Balanites aegyptiaca (L.) Delile, commonly known as desert date, is a thorny evergreen tree belonging to the family Zygophyllaceae and subfamily Tribuloideae that is widespread in arid and semiarid regions. This plant is an important source of food and medicines and plays an important role in conservation strategies for restoring degraded desert ecosystems.
Results
In the present study, we sequenced the complete plastome of B. aegyptiaca. The chloroplast genome was 155,800 bp, with a typical four-region structure: a large single copy (LSC) region of 86,562 bp, a small single copy (SSC) region of 18,102 bp, and inverted repeat regions (IRa and IRb) of 25,568 bp each. The GC content was 35.5%. The chloroplast genome of B. aegyptiaca contains 107 genes, 75 of which coding proteins, 28 coding tRNA, and 4 coding rRNA.
We did not observe a large loss in plastid genes or a reduction in the genome size in B. aegyptiaca, as found previously in some species belonging to the family Zygophyllaceae. However, we noticed a divergence in the location of certain genes at the IR-LSC and IR-SSC boundaries and loss of ndh genes relative to other species. Furthermore, the phylogenetic tree constructed from the complete chloroplast genome data broadly supported the taxonomic classification of B. aegyptiaca as belonging to the Zygophyllaceae family. The plastome of B. aegyptiaca was found to be rich in single sequence repeats (SSRs), with a total of 240 SSRs.
Conclusions
The genomic data available from this study could be useful for developing molecular markers to evaluate population structure, investigate genetic variation, and improve production programs for B. aegyptiaca. Furthermore, the current data will support future investigation of the evolution of the family Zygophyllaceae.
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18
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Xing J, Pan J, Yi H, Lv K, Gan Q, Wang M, Ge H, Huang X, Huang F, Wang Y, Rochaix JD, Yang W. The plastid-encoded protein Orf2971 is required for protein translocation and chloroplast quality control. THE PLANT CELL 2022; 34:3383-3399. [PMID: 35708659 PMCID: PMC9421593 DOI: 10.1093/plcell/koac180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Photosynthesis and the biosynthesis of many important metabolites occur in chloroplasts. In these semi-autonomous organelles, the chloroplast genome encodes approximately 100 proteins. The remaining chloroplast proteins, close to 3,000, are encoded by nuclear genes whose products are translated in the cytosol and imported into chloroplasts. However, there is still no consensus on the composition of the protein import machinery including its motor proteins and on how newly imported chloroplast proteins are refolded. In this study, we have examined the function of orf2971, the largest chloroplast gene of Chlamydomonas reinhardtii. The depletion of Orf2971 causes the accumulation of protein precursors, partial proteolysis and aggregation of proteins, increased expression of chaperones and proteases, and autophagy. Orf2971 interacts with the TIC (translocon at the inner chloroplast envelope) complex, catalyzes ATP (adenosine triphosphate) hydrolysis, and associates with chaperones and chaperonins. We propose that Orf2971 is intimately connected to the protein import machinery and plays an important role in chloroplast protein quality control.
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Affiliation(s)
| | | | - Heng Yi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Kang Lv
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qiuliang Gan
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Meimei Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Haitao Ge
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiahe Huang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Fang Huang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yingchun Wang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jean-David Rochaix
- Departments of Molecular Biology and Plant Biology, University of Geneva, Geneva, Switzerland
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19
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Gao P, Xia H, Li Q, Li Z, Zhai C, Weng L, Mi H, Yan S, Datla R, Wang H, Yang J. PALE-GREEN LEAF 1, a rice cpSRP54 protein, is essential for the assembly of the PSI-LHCI supercomplex. PLANT DIRECT 2022; 6:e436. [PMID: 35949951 PMCID: PMC9358330 DOI: 10.1002/pld3.436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/17/2022] [Accepted: 07/19/2022] [Indexed: 05/27/2023]
Abstract
Although photosynthetic multiprotein complexes have received major attention, our knowledge about the assembly of these proteins into functional complexes in plants is still limited. In the present study, we have identified a chlorophyll-deficient mutant, pale-green leaf 1 (pgl1), in rice that displays abnormally developed chloroplasts. Map-based cloning of this gene revealed that OsPGL1 encodes a chloroplast targeted protein homologous to the 54-kDa subunit of the signal recognition particle (cpSRP54). Immunoblot analysis revealed that the accumulation of the PSI core proteins PsaA and PsaB, subunits from the ATP synthase, cytochrome, and light-harvesting complex (LHC) is dramatically reduced in pgl1. Blue native gel analysis of thylakoid membrane proteins showed the existence of an extra band in the pgl1 mutant, which located between the dimeric PSII/PSI-LHCI and the monomeric PSII. Immunodetection after 2D separation indicated that the extra band consists of the proteins from the PSI core complex. Measurements of chlorophyll fluorescence at 77 K further confirmed that PSI, rather than PSII, was primarily impaired in the pgl1 mutant. These results suggest that OsPGL1 might act as a molecular chaperone that is required for the efficient assembly and specific integration of the peripheral LHCI proteins into the PSI core complex in rice.
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Affiliation(s)
- Peng Gao
- Saskatoon Research and Development CentreAgriculture and Agri‐food CanadaSaskatoonSKCanada
| | - Haoqiang Xia
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
| | - Qiang Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Zongzhu Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
| | - Chun Zhai
- Saskatoon Research and Development CentreAgriculture and Agri‐food CanadaSaskatoonSKCanada
| | - Lin Weng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
| | - Hualing Mi
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
| | - Song Yan
- Rice Research InstituteJiangxi Academy of Agricultural SciencesNanchangChina
| | - Raju Datla
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonSKCanada
| | - Hua Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Jun Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
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20
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Wang CK, Li XM, Dong F, Sun CH, Lu WL, Hu DG. Yang cycle enzyme DEP1: its moonlighting functions in PSI and ROS production during leaf senescence. MOLECULAR HORTICULTURE 2022; 2:10. [PMID: 37789483 PMCID: PMC10514949 DOI: 10.1186/s43897-022-00031-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/25/2022] [Indexed: 10/05/2023]
Abstract
Ethylene-mediated leaf senescence and the compromise of photosynthesis are closely associated but the underlying molecular mechanism is a mystery. Here we reported that apple DEHYDRATASE-ENOLASE-PHOSPHATASE-COMPLEX1 (MdDEP1), initially characterized to its enzymatic function in the recycling of the ethylene precursor SAM, plays a role in the regulation of photosystem I (PSI) activity, activating reactive oxygen species (ROS) homeostasis, and negatively regulating the leaf senescence. A series of Y2H, Pull-down, CO-IP and Cell-free degradation biochemical assays showed that MdDEP1 directly interacts with and dephosphorylates the nucleus-encoded thylakoid protein MdY3IP1, leading to the destabilization of MdY3IP1, reduction of the PSI activity, and the overproduction of ROS in plant cells. These findings elucidate a novel mechanism that the two pathways intersect at MdDEP1 due to its moonlighting role in destabilizing MdY3IP1, and synchronize ethylene-mediated leaf senescence and the compromise of photosynthesis.
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Affiliation(s)
- Chu-Kun Wang
- National Key Laboratory of Crop Biology; MOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Xiu-Ming Li
- National Key Laboratory of Crop Biology; MOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Fang Dong
- Shandong Institute of Pomology, Key Laboratory for Fruit Biotechnology Breeding of Shandong, Tai'an, 271000, Shandong, China
| | - Cui-Hui Sun
- National Key Laboratory of Crop Biology; MOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Wen-Li Lu
- National Key Laboratory of Crop Biology; MOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
| | - Da-Gang Hu
- National Key Laboratory of Crop Biology; MOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
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21
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Guo X, Wang Z, Cai D, Song L, Bai J. The chloroplast genome sequence and phylogenetic analysis of Apocynum venetum L. PLoS One 2022; 17:e0261710. [PMID: 35271574 PMCID: PMC8912179 DOI: 10.1371/journal.pone.0261710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 12/08/2021] [Indexed: 11/26/2022] Open
Abstract
Apocynum venetum L. (Apocynaceae) is valuable for its medicinal compounds and fiber content. Native A. venetum populations are threatened and require protection. Wild A. venetum resources are limited relative to market demand and a poor understanding of the composition of A. venetum at the molecular level. The chloroplast genome contains genetic markers for phylogenetic analysis, genetic diversity evaluation, and molecular identification. In this study, the entire genome of the A. venetum chloroplast was sequenced and analyzed. The A. venetum cp genome is 150,878 bp, with a pair of inverted repeat regions (IRA and IRB). Each inverted repeat region is 25,810 bp, which consist of large (LSC, 81,951 bp) and small (SSC, 17,307 bp) single copy areas. The genome-wide GC content was 38.35%, LSC made up 36.49%, SSC made up 32.41%, and IR made up 43.3%. The A. venetum chloroplast genome encodes 131 genes, including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. This study identified the unique characteristics of the A. venetum chloroplast genome, which will help formulate effective conservation and management strategies as well as molecular identification approaches for this important medicinal plant.
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Affiliation(s)
- Xiaonong Guo
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, China
- China-Malaysia National Joint Laboratory, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
- * E-mail:
| | - Zhuanxia Wang
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, China
- China-Malaysia National Joint Laboratory, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Deyu Cai
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, China
- China-Malaysia National Joint Laboratory, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Lei Song
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Jialin Bai
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, China
- China-Malaysia National Joint Laboratory, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
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22
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Wang N, Chen S, Xie L, Wang L, Feng Y, Lv T, Fang Y, Ding H. The complete chloroplast genomes of three Hamamelidaceae species: Comparative and phylogenetic analyses. Ecol Evol 2022; 12:e8637. [PMID: 35222983 PMCID: PMC8848467 DOI: 10.1002/ece3.8637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/10/2022] [Accepted: 01/27/2022] [Indexed: 11/07/2022] Open
Abstract
Hamamelidaceae is an important group that represents the origin and early evolution of angiosperms. Its plants have many uses, such as timber, medical, spice, and ornamental uses. In this study, the complete chloroplast genomes of Loropetalum chinense (R. Br.) Oliver, Corylopsis glandulifera Hemsl., and Corylopsis velutina Hand.‐Mazz. were sequenced using the Illumina NovaSeq 6000 platform. The sizes of the three chloroplast genomes were 159,402 bp (C. glandulifera), 159,414 bp (C. velutina), and 159,444 bp (L. chinense), respectively. These chloroplast genomes contained typical quadripartite structures with a pair of inverted repeat (IR) regions (26,283, 26,283, and 26,257 bp), a large single‐copy (LSC) region (88,134, 88,146, and 88,160 bp), and a small single‐copy (SSC) region (18,702, 18,702, and 18,770 bp). The chloroplast genomes encoded 132–133 genes, including 85–87 protein‐coding genes, 37–38 tRNA genes, and 8 rRNA genes. The coding regions were composed of 26,797, 26,574, and 26,415 codons, respectively, most of which ended in A/U. A total of 37–43 long repeats and 175–178 simple sequence repeats (SSRs) were identified, and the SSRs contained a higher number of A + T than G + C bases. The genome comparison showed that the IR regions were more conserved than the LSC or SSC regions, while the noncoding regions contained higher variability than the gene coding regions. Phylogenetic analyses revealed that species in the same genus tended to cluster together. Chunia Hung T. Chang, Mytilaria Lecomte, and Disanthus Maxim. may have diverged early and Corylopsis Siebold & Zucc. was closely related to Loropetalum R. Br. This study provides valuable information for further species identification, evolution, and phylogenetic studies of Hamamelidaceae plants.
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Affiliation(s)
- NingJie Wang
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - ShuiFei Chen
- Research Center for Nature Conservation and Biodiversity State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains State Environmental Protection Key Laboratory on Biosafety Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment Nanjing China
| | - Lei Xie
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - Lu Wang
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - YueYao Feng
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - Ting Lv
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - YanMing Fang
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - Hui Ding
- Research Center for Nature Conservation and Biodiversity State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains State Environmental Protection Key Laboratory on Biosafety Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment Nanjing China
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23
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Uthanumallian K, Iha C, Repetti SI, Chan CX, Bhattacharya D, Duchene S, Verbruggen H. Tightly Constrained Genome Reduction and Relaxation of Purifying Selection during Secondary Plastid Endosymbiosis. Mol Biol Evol 2022; 39:msab295. [PMID: 34613411 PMCID: PMC8763093 DOI: 10.1093/molbev/msab295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Endosymbiosis, the establishment of a former free-living prokaryotic or eukaryotic cell as an organelle inside a host cell, can dramatically alter the genomic architecture of the endosymbiont. Plastids or chloroplasts, the light-harvesting organelle of photosynthetic eukaryotes, are excellent models to study this phenomenon because plastid origin has occurred multiple times in evolution. Here, we investigate the genomic signature of molecular processes acting through secondary plastid endosymbiosis-the origination of a new plastid from a free-living eukaryotic alga. We used phylogenetic comparative methods to study gene loss and changes in selective regimes on plastid genomes, focusing on green algae that have given rise to three independent lineages with secondary plastids (euglenophytes, chlorarachniophytes, and Lepidodinium). Our results show an overall increase in gene loss associated with secondary endosymbiosis, but this loss is tightly constrained by the retention of genes essential for plastid function. The data show that secondary plastids have experienced temporary relaxation of purifying selection during secondary endosymbiosis. However, this process is tightly constrained, with selection relaxed only relative to the background in primary plastids. Purifying selection remains strong in absolute terms even during the endosymbiosis events. Selection intensity rebounds to pre-endosymbiosis levels following endosymbiosis events, demonstrating the changes in selection efficiency during different origin phases of secondary plastids. Independent endosymbiosis events in the euglenophytes, chlorarachniophytes, and Lepidodinium differ in their degree of relaxation of selection, highlighting the different evolutionary contexts of these events. This study reveals the selection-drift interplay during secondary endosymbiosis and evolutionary parallels during organellogenesis.
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Affiliation(s)
| | - Cintia Iha
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Sonja I Repetti
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | | | - Sebastian Duchene
- Deptartment of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
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24
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Saldaña CL, Rodriguez-Grados P, Chávez-Galarza JC, Feijoo S, Guerrero-Abad JC, Vásquez HV, Maicelo JL, Jhoncon JH, Arbizu CI. Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona ( Calycophyllum Spruceanum, Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species. Genes (Basel) 2022; 13:genes13010113. [PMID: 35052453 PMCID: PMC8774758 DOI: 10.3390/genes13010113] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 11/21/2022] Open
Abstract
Capirona (Calycophyllum spruceanum Benth.) belongs to subfamily Ixoroideae, one of the major lineages in the Rubiaceae family, and is an important timber tree. It originated in the Amazon Basin and has widespread distribution in Bolivia, Peru, Colombia, and Brazil. In this study, we obtained the first complete chloroplast (cp) genome of capirona from the department of Madre de Dios located in the Peruvian Amazon. High-quality genomic DNA was used to construct libraries. Pair-end clean reads were obtained by PE 150 library and the Illumina HiSeq 2500 platform. The complete cp genome of C. spruceanum has a 154,480 bp in length with typical quadripartite structure, containing a large single copy (LSC) region (84,813 bp) and a small single-copy (SSC) region (18,101 bp), separated by two inverted repeat (IR) regions (25,783 bp). The annotation of C. spruceanum cp genome predicted 87 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes, and one pseudogene. A total of 41 simple sequence repeats (SSR) of this cp genome were divided into mononucleotides (29), dinucleotides (5), trinucleotides (3), and tetranucleotides (4). Most of these repeats were distributed in the noncoding regions. Whole chloroplast genome comparison with the other six Ixoroideae species revealed that the small single copy and large single copy regions showed more divergence than inverted regions. Finally, phylogenetic analyses resolved that C. spruceanum is a sister species to Emmenopterys henryi and confirms its position within the subfamily Ixoroideae. This study reports for the first time the genome organization, gene content, and structural features of the chloroplast genome of C. spruceanum, providing valuable information for genetic and evolutionary studies in the genus Calycophyllum and beyond.
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Affiliation(s)
- Carla L. Saldaña
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru; (C.L.S.); (P.R.-G.); (J.C.C.-G.); (H.V.V.); (J.L.M.)
| | - Pedro Rodriguez-Grados
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru; (C.L.S.); (P.R.-G.); (J.C.C.-G.); (H.V.V.); (J.L.M.)
- Facultad de Ciencias, Universidad Nacional José Faustino Sánchez Carrión, Av. Mercedes Indacochea Nro. 609, Huacho 15136, Peru
| | - Julio C. Chávez-Galarza
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru; (C.L.S.); (P.R.-G.); (J.C.C.-G.); (H.V.V.); (J.L.M.)
| | - Shefferson Feijoo
- Estación Experimental Agraria San Bernardo, Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Carretera Cusco, Puerto Maldonado, Tambopata, Madre de Dios 17000, Peru;
| | - Juan Carlos Guerrero-Abad
- Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru;
| | - Héctor V. Vásquez
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru; (C.L.S.); (P.R.-G.); (J.C.C.-G.); (H.V.V.); (J.L.M.)
| | - Jorge L. Maicelo
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru; (C.L.S.); (P.R.-G.); (J.C.C.-G.); (H.V.V.); (J.L.M.)
| | - Jorge H. Jhoncon
- Centro de Investigación de Plantas Andinas y Nativas, Facultad de Ciencias, Universidad Nacional de Educación Enrique Guzmán y Valle, Av. Enrique Guzmán y Valle s/n, Lima 15472, Peru;
- Unidad de Investigación, Perú Maca SAC, Panamericana Sur KM. 37.2 Mz. D1. Lote 03A, Lima 15823, Peru
| | - Carlos I. Arbizu
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru; (C.L.S.); (P.R.-G.); (J.C.C.-G.); (H.V.V.); (J.L.M.)
- Correspondence:
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25
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Ma L, Zeng N, Cheng K, Li J, Wang K, Zhang C, Zhu H. Changes in fruit pigment accumulation, chloroplast development, and transcriptome analysis in the CRISPR/Cas9-mediated knockout of Stay-green 1 (slsgr1) mutant. FOOD QUALITY AND SAFETY 2021. [DOI: 10.1093/fqsafe/fyab029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The green-flesh (gf) mutant of the tomato fruit ripen to a muddy brown color and has been demonstrated previously to be a loss-of-function mutant. Here, we provide more evidence to support this view that SlSGR1 is involved in color change in ripening tomato fruits. Knocking out SlSGR1 expression using a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 genome editing strategy showed obviously a muddy brown color with significantly higher chlorophyll and carotenoid content compared with wild-type (WT) fruits. To further verify the role of SlSGR1 in fruit color change, we performed transcriptome deep sequencing (RNA-seq) analysis, where a total of 354 differentially expressed genes (124/230 downregulated/upregulated) were identified between WT and slsgr1. Additionally, the expression of numerous genes associated with photosynthesis and chloroplast function changed significantly when SlSGR1 was knocked out. Taken together, these results indicate that SlSGR1 is involved in color change in ripening fruit via chlorophyll degradation and carotenoid biosynthesis.
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26
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Wang J, Huang X, Ge H, Wang Y, Chen W, Zheng L, Huang C, Yang H, Li L, Sui N, Wang Y, Zhang Y, Lu D, Fang L, Xu W, Jiang Y, Huang F, Wang Y. The Quantitative Proteome Atlas of a Model Cyanobacterium. J Genet Genomics 2021; 49:96-108. [PMID: 34775074 DOI: 10.1016/j.jgg.2021.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 09/23/2021] [Accepted: 09/25/2021] [Indexed: 12/17/2022]
Abstract
Cyanobacteria are a group of oxygenic photosynthetic bacteria with great potentials in biotechnological applications and advantages as models for photosynthesis research. The subcellular locations of the majority of proteins in any cyanobacteria remain undetermined, representing a major challenge in using cyanobacteria for both basic and industrial researches. Here, using label free quantitative proteomics we mapped 2027 proteins of Synechocystis sp. PCC6803, a model cyanobacterium, to different subcellular compartments, and generated a proteome atlas with such information. The atlas leads to numerous unexpected but important findings, including the predominant localization of the histidine kinases Hik33 and Hik27 on the thylakoid but not the plasma membrane. Such information completely changes the concept regarding how the two kinases are activated. Together, the atlas provides subcellular localization information for nearly 60% proteome of a model cyanobacterium, and will serve as an important resource for the cyanobacterial research community.
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Affiliation(s)
- Jinlong Wang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Haitao Ge
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Wang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiyang Chen
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Limin Zheng
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengcheng Huang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haomeng Yang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Bejing 100093, China
| | - Lingyu Li
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Bejing 100093, China
| | - Na Sui
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Science, Shandong Normal University, Jinan 250014, China
| | - Yu Wang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanya Zhang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dandan Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Longfa Fang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - Yuqiang Jiang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Huang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Bejing 100093, China.
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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27
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Zhang L, Chen J, Zhang L, Wei Y, Li Y, Xu X, Wu H, Yang ZN, Huang J, Hu F, Huang W, Cui YL. The pentatricopeptide repeat protein EMB1270 interacts with CFM2 to splice specific group II introns in Arabidopsis chloroplasts. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1952-1966. [PMID: 34427970 DOI: 10.1111/jipb.13165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Chloroplast biogenesis requires the coordinated expression of chloroplast and nuclear genes. Here, we show that EMB1270, a plastid-localized pentatricopeptide repeat (PPR) protein, is required for chloroplast biogenesis in Arabidopsis thaliana. Knockout of EMB1270 led to embryo arrest, whereas a mild knockdown mutant of EMB1270 displayed a virescent phenotype. Almost no photosynthetic proteins accumulated in the albino emb1270 knockout mutant. By contrast, in the emb1270 knockdown mutant, the levels of ClpP1 and photosystem I (PSI) subunits were significantly reduced, whereas the levels of photosystem II (PSII) subunits were normal. Furthermore, the splicing efficiencies of the clpP1.2, ycf3.1, ndhA, and ndhB plastid introns were dramatically reduced in both emb1270 mutants. RNA immunoprecipitation revealed that EMB1270 associated with these introns in vivo. In an RNA electrophoretic mobility shift assay (REMSA), a truncated EMB1270 protein containing the 11 N-terminal PPR motifs bound to the predicted sequences of the clpP1.2, ycf3.1, and ndhA introns. In addition, EMB1270 specifically interacted with CRM Family Member 2 (CFM2). Given that CFM2 is known to be required for splicing the same plastid RNAs, our results suggest that EMB1270 associates with CFM2 to facilitate the splicing of specific group II introns in Arabidopsis.
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Affiliation(s)
- Li Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jingli Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Liqun Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Ying Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yajuan Li
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xinyun Xu
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Hui Wu
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zhong-Nan Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jirong Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Fenhong Hu
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Weihua Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yong-Lan Cui
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
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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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Xing Q, Bi G, Cao M, Belcour A, Aite M, Mo Z, Mao Y. Comparative Transcriptome Analysis Provides Insights into Response of Ulva compressa to Fluctuating Salinity Conditions. JOURNAL OF PHYCOLOGY 2021; 57:1295-1308. [PMID: 33715182 DOI: 10.1111/jpy.13167] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/18/2021] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
Ulva compressa, a green tide-forming species, can adapt to hypo-salinity conditions, such as estuaries and brackish lakes. To understand the underlying molecular mechanisms of hypo-salinity stress tolerance, transcriptome-wide gene expression profiles in U. compressa were created using digital gene expression profiles. The RNA-seq data were analyzed based on the comparison of differently expressed genes involved in specific pathways under hypo-salinity and recovery conditions. The up-regulation of genes in photosynthesis and glycolysis pathways may contribute to the recovery of photosynthesis and energy metabolism, which could provide sufficient energy for the tolerance under long-term hyposaline stress. Multiple strategies, such as ion transportation and osmolytes metabolism, were performed to maintain the osmotic homeostasis. Additionally, several long noncoding RNA were differently expressed during the stress, which could play important roles in the osmotolerance. Our work will serve as an essential foundation for the understanding of the tolerance mechanism of U. compressa under the fluctuating salinity conditions.
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Affiliation(s)
- Qikun Xing
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique deRoscoff (SBR), CNRS, Sorbonne Université, 29680, Roscoff, France
| | - Guiqi Bi
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Agricultural Synthetic Biology Center, Chinese Academy of Agricultural Sciences, Agricultural Genomes Institute at Shenzhen, Shenzhen, 518120, China
| | - Min Cao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Arnaud Belcour
- Inria, CNRS, IRISA, Equipe Dyliss, Univ Rennes, Rennes, France
| | - Méziane Aite
- Inria, CNRS, IRISA, Equipe Dyliss, Univ Rennes, Rennes, France
| | - Zhaolan Mo
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yunxiang Mao
- MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, 572022, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
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Liu S, Feng S, Huang Y, An W, Yang Z, Xie C, Zheng X. Characterization of the Complete Chloroplast Genome of Buddleja Lindleyana. J AOAC Int 2021; 105:202-210. [PMID: 33944934 DOI: 10.1093/jaoacint/qsab066] [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: 10/12/2020] [Revised: 03/25/2021] [Accepted: 04/12/2021] [Indexed: 11/13/2022]
Abstract
BACKGROUND Buddleja lindleyana Fort., which belongs to the Loganiaceae with a distribution throughout the tropics, is widely used as an ornamental plant in China. Buddleja contains several morphologically similar species, which need to be identified by molecular identification. But there is little molecular research on the genus Buddleja. OBJECTIVE Using molecular biology techniques to sequence and analyze the complete chloroplast (cp) genome of B. lindleyana. METHODS According to next-generation sequencing to sequence the genome data, a series of bioinformatics software were used to assembly and analysis the molecular structure of cp genome of B. lindleyana. RESULTS The complete cp genome of B. lindleyana is a circular 154,487-bp-long molecule with a GC content of 38.1%. It has a familiar quadripartite structure, including a large single-copy region (LSC; 85,489 bp), a small single-copy region (SSC; 17,898bp) and a pair of inverted repeats (IRs; 25,550 bp). A total of 133 genes were identified in the genome, including 86 protein-coding genes, 37 tRNA genes, 8 rRNA genes and 2 pseudogenes. CONCLUSIONS These results suggested that B. lindelyana cp genome could be used as a potential genomic resource to resolve the phylogenetic positions and relationships of Loganiaceae, and will offer valuable information for future research in the identification of Buddleja species and will conduce to genomic investigations of these species.
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Affiliation(s)
- Shanshan Liu
- National Engineering Research Center for Modernization of Traditional Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Shiyin Feng
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405
| | - Yuying Huang
- National Engineering Research Center for Modernization of Traditional Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Wenli An
- National Engineering Research Center for Modernization of Traditional Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Zerui Yang
- National Engineering Research Center for Modernization of Traditional Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Chunzhu Xie
- National Engineering Research Center for Modernization of Traditional Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Xiasheng Zheng
- National Engineering Research Center for Modernization of Traditional Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
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Nellaepalli S, Kim RG, Grossman AR, Takahashi Y. Interplay of four auxiliary factors is required for the assembly of photosystem I reaction center subcomplex. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1075-1086. [PMID: 33655619 DOI: 10.1111/tpj.15220] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/11/2021] [Accepted: 02/19/2021] [Indexed: 05/08/2023]
Abstract
The photosystem I (PSI) complex consisting of reaction center (RC) subunits, several peripheral subunits and many co-factors, is present in the thylakoid membranes of chloroplasts and cyanobacteria. The assembly of RC subunits (PsaA/B) that bind electron transfer co-factors and antenna pigments is an intricate process, and is mediated by several auxiliary factors such as Ycf3, Y3IP1/CGL59, Ycf4 and Ycf37/PYG7/CGL71. However, their precise molecular mechanisms in RC assembly remain to be addressed. Here we purified four PSI auxiliary factors by affinity chromatography, and characterized co-purified PSI assembly intermediates. We suggest that Ycf3 assists the initial assembly of newly synthesized PsaA/B subunits into an RC subcomplex, while Y3IP1 may be involved in transferring the RC subcomplex from Ycf3 to the Ycf4 module that stabilizes it. CGL71 may form an oligomer that transiently interacts with the PSI RC subcomplex, physically protecting it under oxic conditions until association with the peripheral PSI subunits occurs. Together, our results reveal the interplay among four auxiliary factors required for the stepwise assembly of the PSI RC.
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Affiliation(s)
- Sreedhar Nellaepalli
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan
| | - Rick G Kim
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Yuichiro Takahashi
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan
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Cheng YC, Houston R. Evaluation of the trnK-matK-trnK, ycf3, and accD-psal chloroplast regions to differentiate crop type and biogeographical origin of Cannabis sativa. Int J Legal Med 2021; 135:1235-1244. [PMID: 33604694 DOI: 10.1007/s00414-021-02518-x] [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: 08/29/2020] [Accepted: 01/27/2021] [Indexed: 10/22/2022]
Abstract
Cannabis sativa (marijuana and hemp) is one of the most controversial crops worldwide. In the USA, the state-specific legalization of marijuana and recently legalized hemp pose a problem for law enforcement. This study seeks to utilize chloroplast hSTRs, INDEL, and SNPs markers to develop genotyping methods to aid in the differentiation of legal hemp from illicit marijuana and also for tracking the flow of trafficked marijuana. Three polymorphic regions: trnK-matK-trnK, ycf3, and accD-psal, of the C. sativa chloroplast genome were evaluated in order to distinguish crop type and biogeographic origin. A total of nine polymorphic sites were genotyped from five distinct populations (hemp from the USA and Canada, marijuana from Chile and USA-Mexico, and medical marijuana from Chile) with a custom fragment and SNaPshotTM assay. The study also combined genotype results from the same sample set using 21 additional polymorphic markers from previous studies. The effectiveness of these multi-locus assays to distinguish sample groups was assessed using haplotype analysis, phylogenetic analysis, pairwise comparisons, and principal component analysis. Results indicated a clear separation of Canadian hemp using only the nine polymorphic sites developed in this study. The additional 21 markers were able to separate US hemp from both marijuana groups to a significant level (p < 0.05) when assessing average Fixation Indices (FST). This study demonstrated the applicability of these organelle markers for the determination of crop type and biogeographic origin of C. sativa. However, a more extensive database is needed to evaluate the true discriminatory power of these markers.
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Affiliation(s)
- Ya-Chih Cheng
- Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd, Huntsville, TX, 77340, USA
| | - Rachel Houston
- Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd, Huntsville, TX, 77340, USA.
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Puthiyaveetil S, McKenzie SD, Kayanja GE, Ibrahim IM. Transcription initiation as a control point in plastid gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194689. [PMID: 33561560 DOI: 10.1016/j.bbagrm.2021.194689] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/18/2022]
Abstract
The extensive processing and protein-assisted stabilization of transcripts have been taken as evidence for a viewpoint that the control of gene expression had shifted entirely in evolution from transcriptional in the bacterial endosymbiont to posttranscriptional in the plastid. This suggestion is however at odds with many observations on plastid gene transcription. Chloroplasts of flowering plants and mosses contain two or more RNA polymerases with distinct promoter preference and division of labor for the coordinated synthesis of plastid RNAs. Plant and algal plastids further possess multiple nonredundant sigma factors that function as transcription initiation factors. The controlled accumulation of plastid sigma factors and modification of their activity by sigma-binding proteins and phosphorylation constitute additional transcriptional regulatory strategies. Plant and algal plastids also contain dedicated one- or two-component transcriptional regulators. Transcription initiation thus continues to form a critical control point at which varied developmental and environmental signals intersect with plastid gene expression.
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Affiliation(s)
- Sujith Puthiyaveetil
- Department of Biochemistry and Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA.
| | - Steven D McKenzie
- Department of Biochemistry and Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Gilbert E Kayanja
- Department of Biochemistry and Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Iskander M Ibrahim
- Department of Biochemistry and Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
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Dong F, Lin Z, Lin J, Ming R, Zhang W. Chloroplast Genome of Rambutan and Comparative Analyses in Sapindaceae. PLANTS 2021; 10:plants10020283. [PMID: 33540810 PMCID: PMC7912957 DOI: 10.3390/plants10020283] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 02/03/2023]
Abstract
Rambutan (Nephelium lappaceum L.) is an important fruit tree that belongs to the family Sapindaceae and is widely cultivated in Southeast Asia. We sequenced its chloroplast genome for the first time and assembled 161,321 bp circular DNA. It is characterized by a typical quadripartite structure composed of a large (86,068 bp) and small (18,153 bp) single-copy region interspersed by two identical inverted repeats (IRs) (28,550 bp). We identified 132 genes including 78 protein-coding genes, 29 tRNA and 4 rRNA genes, with 21 genes duplicated in the IRs. Sixty-three simple sequence repeats (SSRs) and 98 repetitive sequences were detected. Twenty-nine codons showed biased usage and 49 potential RNA editing sites were predicted across 18 protein-coding genes in the rambutan chloroplast genome. In addition, coding gene sequence divergence analysis suggested that ccsA, clpP, rpoA, rps12, psbJ and rps19 were under positive selection, which might reflect specific adaptations of N. lappaceum to its particular living environment. Comparative chloroplast genome analyses from nine species in Sapindaceae revealed that a higher similarity was conserved in the IR regions than in the large single-copy (LSC) and small single-copy (SSC) regions. The phylogenetic analysis showed that N. lappaceum chloroplast genome has the closest relationship with that of Pometia tomentosa. The understanding of the chloroplast genomics of rambutan and comparative analysis of Sapindaceae species would provide insight into future research on the breeding of rambutan and Sapindaceae evolutionary studies.
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Affiliation(s)
- Fei Dong
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; or
| | - Zhicong Lin
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; or
| | - Jing Lin
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou 350002, China; or
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Correspondence: (R.M.); (W.Z.); Tel.: +1-217-333-1221 (R.M.); Tel.: +86-15-8006-2379 (W.Z.)
| | - Wenping Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou 350002, China; or
- Correspondence: (R.M.); (W.Z.); Tel.: +1-217-333-1221 (R.M.); Tel.: +86-15-8006-2379 (W.Z.)
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Nawkarkar P, Chugh S, Sharma S, Jain M, Kajla S, Kumar S. Characterization of the Chloroplast Genome Facilitated the Transformation of Parachlorella kessleri-I, A Potential Marine Alga for Biofuel Production. Curr Genomics 2021; 21:610-623. [PMID: 33414682 PMCID: PMC7770631 DOI: 10.2174/1389202921999201102164754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/28/2020] [Accepted: 08/27/2020] [Indexed: 11/22/2022] Open
Abstract
Introduction The microalga Parachlorella kessleri-I produces high biomass and lipid content that could be suitable for producing economically viable biofuel at a commercial scale. Sequencing the complete chloroplast genome is crucial for the construction of a species-specific chloroplast transformation vector. Methods In this study, the complete chloroplast genome sequence (cpDNA) of P. kessleri-I was assembled; annotated and genetic transformation of the chloroplast was optimized. For the chloroplast transformation, we have tested two antibiotic resistance makers, aminoglycoside adenine transferase (aadA) gene and Sh-ble gene conferring resistance to spectinomycin and zeocin, respectively. Transgene integration and homoplasty determination were confirmed using PCR, Southern blot and Droplet Digital PCR. Results The chloroplast genome (109,642 bp) exhibited a quadripartite structure with two reverse repeat regions (IRA and IRB), a long single copy (LSC), and a small single copy (SSC) region. The genome encodes 116 genes, with 80 protein-coding genes, 32 tRNAs and 4 rRNAs. The cpDNA provided essential information like codons, UTRs and flank sequences for homologous recombination to make a species-specific vector that facilitated the transformation of P. kessleri-I chloroplast. The transgenic algal colonies were retrieved on a TAP medium containing 400 mg. L-1 spectinomycin, but no transgenic was recovered on the zeocin-supplemented medium. PCR and Southern blot analysis ascertained the transgene integration into the chloroplast genome, via homologous recombination. The chloroplast genome copy number in wildtype and transgenic P. kessleri-I was determined using Droplet Digital PCR. Conclusion The optimization of stable chloroplast transformation in marine alga P. kessleri-I should open a gateway for directly engineering the strain for carbon concentration mechanisms to fix more CO2, improving the photosynthetic efficiency and reducing the overall biofuels production cost.
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Affiliation(s)
- Prachi Nawkarkar
- 1 International Centre for Genetic Engineering and Biotechnology, New Delhi110067, India; 2School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi110067, India; 3Tata Steel Limited, Research &
Development, P O Burmamines, Jamshedpur831007, India
| | - Sagrika Chugh
- 1 International Centre for Genetic Engineering and Biotechnology, New Delhi110067, India; 2School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi110067, India; 3Tata Steel Limited, Research &
Development, P O Burmamines, Jamshedpur831007, India
| | - Surbhi Sharma
- 1 International Centre for Genetic Engineering and Biotechnology, New Delhi110067, India; 2School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi110067, India; 3Tata Steel Limited, Research &
Development, P O Burmamines, Jamshedpur831007, India
| | - Mukesh Jain
- 1 International Centre for Genetic Engineering and Biotechnology, New Delhi110067, India; 2School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi110067, India; 3Tata Steel Limited, Research &
Development, P O Burmamines, Jamshedpur831007, India
| | - Sachin Kajla
- 1 International Centre for Genetic Engineering and Biotechnology, New Delhi110067, India; 2School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi110067, India; 3Tata Steel Limited, Research &
Development, P O Burmamines, Jamshedpur831007, India
| | - Shashi Kumar
- 1 International Centre for Genetic Engineering and Biotechnology, New Delhi110067, India; 2School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi110067, India; 3Tata Steel Limited, Research &
Development, P O Burmamines, Jamshedpur831007, India
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Jackson HO, Taunt HN, Mordaka PM, Smith AG, Purton S. The Algal Chloroplast as a Testbed for Synthetic Biology Designs Aimed at Radically Rewiring Plant Metabolism. FRONTIERS IN PLANT SCIENCE 2021; 12:708370. [PMID: 34630459 PMCID: PMC8497815 DOI: 10.3389/fpls.2021.708370] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/10/2021] [Indexed: 05/04/2023]
Abstract
Sustainable and economically viable support for an ever-increasing global population requires a paradigm shift in agricultural productivity, including the application of biotechnology to generate future crop plants. Current genetic engineering approaches aimed at enhancing the photosynthetic efficiency or composition of the harvested tissues involve relatively simple manipulations of endogenous metabolism. However, radical rewiring of central metabolism using new-to-nature pathways, so-called "synthetic metabolism", may be needed to really bring about significant step changes. In many cases, this will require re-programming the metabolism of the chloroplast, or other plastids in non-green tissues, through a combination of chloroplast and nuclear engineering. However, current technologies for sophisticated chloroplast engineering ("transplastomics") of plants are limited to just a handful of species. Moreover, the testing of metabolic rewiring in the chloroplast of plant models is often impractical given their obligate phototrophy, the extended time needed to create stable non-chimeric transplastomic lines, and the technical challenges associated with regeneration of whole plants. In contrast, the unicellular green alga, Chlamydomonas reinhardtii is a facultative heterotroph that allows for extensive modification of chloroplast function, including non-photosynthetic designs. Moreover, chloroplast engineering in C. reinhardtii is facile, with the ability to generate novel lines in a matter of weeks, and a well-defined molecular toolbox allows for rapid iterations of the "Design-Build-Test-Learn" (DBTL) cycle of modern synthetic biology approaches. The recent development of combinatorial DNA assembly pipelines for designing and building transgene clusters, simple methods for marker-free delivery of these clusters into the chloroplast genome, and the pre-existing wealth of knowledge regarding chloroplast gene expression and regulation in C. reinhardtii further adds to the versatility of transplastomics using this organism. Herein, we review the inherent advantages of the algal chloroplast as a simple and tractable testbed for metabolic engineering designs, which could then be implemented in higher plants.
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Affiliation(s)
- Harry O. Jackson
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Henry N. Taunt
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Pawel M. Mordaka
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Alison G. Smith
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Saul Purton
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
- *Correspondence: Saul Purton
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Macedo-Osorio KS, Martínez-Antonio A, Badillo-Corona JA. Pas de Trois: An Overview of Penta-, Tetra-, and Octo-Tricopeptide Repeat Proteins From Chlamydomonas reinhardtii and Their Role in Chloroplast Gene Expression. FRONTIERS IN PLANT SCIENCE 2021; 12:775366. [PMID: 34868174 PMCID: PMC8635915 DOI: 10.3389/fpls.2021.775366] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/26/2021] [Indexed: 05/05/2023]
Abstract
Penta-, Tetra-, and Octo-tricopeptide repeat (PPR, TPR, and OPR) proteins are nucleus-encoded proteins composed of tandem repeats of 35, 34, and 38-40 amino acids, respectively. They form helix-turn-helix structures that interact with mRNA or other proteins and participate in RNA stabilization, processing, maturation, and act as translation enhancers of chloroplast and mitochondrial mRNAs. These helical repeat proteins are unevenly present in plants and algae. While PPR proteins are more abundant in plants than in algae, OPR proteins are more abundant in algae. In Arabidopsis, maize, and rice there have been 450, 661, and 477 PPR proteins identified, respectively, which contrasts with only 14 PPR proteins identified in Chlamydomonas reinhardtii. Likewise, more than 120 OPR proteins members have been predicted from the nuclear genome of C. reinhardtii and only one has been identified in Arabidopsis thaliana. Due to their abundance in land plants, PPR proteins have been largely characterized making it possible to elucidate their RNA-binding code. This has even allowed researchers to generate engineered PPR proteins with defined affinity to a particular target, which has served as the basis to develop tools for gene expression in biotechnological applications. However, fine elucidation of the helical repeat proteins code in Chlamydomonas is a pending task. In this review, we summarize the current knowledge on the role PPR, TPR, and OPR proteins play in chloroplast gene expression in the green algae C. reinhardtii, pointing to relevant similarities and differences with their counterparts in plants. We also recapitulate on how these proteins have been engineered and shown to serve as mRNA regulatory factors for biotechnological applications in plants and how this could be used as a starting point for applications in algae.
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Affiliation(s)
- Karla S. Macedo-Osorio
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, México City, México
- Biological Engineering Laboratory, Genetic Engineering Department, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional-Unidad Irapuato, Irapuato, México
- División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana-Xochimilco, México City, México
- *Correspondence: Karla S. Macedo-Osorio,
| | - Agustino Martínez-Antonio
- Biological Engineering Laboratory, Genetic Engineering Department, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional-Unidad Irapuato, Irapuato, México
| | - Jesús A. Badillo-Corona
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, México City, México
- Jesús A. Badillo-Corona,
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Raman G, Park KT, Kim JH, Park S. Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications. BMC Genomics 2020; 21:855. [PMID: 33267775 PMCID: PMC7709266 DOI: 10.1186/s12864-020-07219-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/09/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The invasive species Xanthium spinosum has been used as a traditional Chinese medicine for many years. Unfortunately, no extensive molecular studies of this plant have been conducted. RESULTS Here, the complete chloroplast (cp) genome sequence of X. spinosum was assembled and analyzed. The cp genome of X. spinosum was 152,422 base pairs (bp) in length, with a quadripartite circular structure. The cp genome contained 115 unique genes, including 80 PCGs, 31 tRNA genes, and 4 rRNA genes. Comparative analyses revealed that X. spinosum contains a large number of repeats (999 repeats) and 701 SSRs in its cp genome. Fourteen divergences (Π > 0.03) were found in the intergenic spacer regions. Phylogenetic analyses revealed that Parthenium is a sister clade to both Xanthium and Ambrosia and an early-diverging lineage of subtribe Ambrosiinae, although this finding was supported with a very weak bootstrap value. CONCLUSION The identified hotspot regions could be used as molecular markers for resolving phylogenetic relationships and species identification in the genus Xanthium.
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Affiliation(s)
- Gurusamy Raman
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsangbuk-do, Republic of Korea, 38541
| | - Kyu Tae Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsangbuk-do, Republic of Korea, 38541
| | - Joo-Hwan Kim
- Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, Republic of Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsangbuk-do, Republic of Korea, 38541.
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Xu J, Shen X, Liao B, Xu J, Hou D. Comparing and phylogenetic analysis chloroplast genome of three Achyranthes species. Sci Rep 2020; 10:10818. [PMID: 32616875 PMCID: PMC7331806 DOI: 10.1038/s41598-020-67679-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/12/2020] [Indexed: 11/29/2022] Open
Abstract
In this study, the chloroplast genome sequencing of the Achyranthes longifolia, Achyranthes bidentata and Achyranthes aspera were performed by Next-generation sequencing technology. The results revealed that there were a length of 151,520 bp (A. longifolia), 151,284 bp (A. bidentata), 151,486 bp (A. aspera), respectively. These chloroplast genome have a highly conserved structure with a pair of inverted repeat (IR) regions (25,150 bp; 25,145 bp; 25,150 bp), a large single copy (LSC) regions (83,732 bp; 83,933 bp; 83,966 bp) and a small single copy (SSC) regions (17,252 bp; 17,263 bp; 17,254 bp) in A. bidentate, A. aspera and A. longifolia. There were 127 genes were annotated, which including 8 rRNA genes, 37 tRNA genes and 82 functional genes. The phylogenetic analysis strongly revealed that Achyranthes is monophyletic, and A. bidentata was the closest relationship with A. aspera and A. longifolia. A. bidentata and A. longifolia were clustered together, the three Achyranthes species had the same origin, then the gunes of Achyranthes is the closest relative to Alternanthera, and that forms a group with Alternanthera philoxeroides. The research laid a foundation and provided relevant basis for the identification of germplasm resources in the future.
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Affiliation(s)
- Jingya Xu
- Agricultural College, Henan University of Science and Technology, Luoyang, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-Di Herbs, Luoyang, China
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaofeng Shen
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing, China
| | - Baosheng Liao
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jiang Xu
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Dianyun Hou
- Agricultural College, Henan University of Science and Technology, Luoyang, China.
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-Di Herbs, Luoyang, China.
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Li CJ, Wang RN, Li DZ. Comparative analysis of plastid genomes within the Campanulaceae and phylogenetic implications. PLoS One 2020; 15:e0233167. [PMID: 32407424 PMCID: PMC7224561 DOI: 10.1371/journal.pone.0233167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/29/2020] [Indexed: 12/13/2022] Open
Abstract
The conflicts exist between the phylogeny of Campanulaceae based on nuclear ITS sequence and plastid markers, particularly in the subdivision of Cyanantheae (Campanulaceae). Besides, various and complicated plastid genome structures can be found in species of the Campanulaceae. However, limited availability of genomic information largely hinders the studies of molecular evolution and phylogeny of Campanulaceae. We reported the complete plastid genomes of three Cyanantheae species, compared them to eight published Campanulaceae plastomes, and shed light on a deeper understanding of the applicability of plastomes. We found that there were obvious differences among gene order, GC content, gene compositions and IR junctions of LSC/IRa. Almost all protein-coding genes and amino acid sequences showed obvious codon preferences. We identified 14 genes with highly positively selected sites and branch-site model displayed 96 sites under potentially positive selection on the three lineages of phylogenetic tree. Phylogenetic analyses showed that Cyananthus was more closely related to Codonopsis compared with Cyclocodon and also clearly illustrated the relationship among the Cyanantheae species. We also found six coding regions having high nucleotide divergence value. Hotpot regions were considered to be useful molecular markers for resolving phylogenetic relationships and species authentication of Campanulaceae.
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Affiliation(s)
- Chun-Jiao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ruo-Nan Wang
- College of Life Sciences, Northwest University, Xi'an, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
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Extensive survey of the ycf4 plastid gene throughout the IRLC legumes: Robust evidence of its locus and lineage specific accelerated rate of evolution, pseudogenization and gene loss in the tribe Fabeae. PLoS One 2020; 15:e0229846. [PMID: 32134967 PMCID: PMC7058334 DOI: 10.1371/journal.pone.0229846] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 02/15/2020] [Indexed: 12/12/2022] Open
Abstract
The genome organization and gene content of plastome (plastid genome) are highly conserved among most flowering plant species. Plastome variation (in size and gene order) is rare in photosynthetic species but size variation, rearrangements and gene/intron losses is attributed to groups of seed plants. Fabaceae (legume family), in particular the subfamily Papilionoideae and the inverted repeat lacking clade (IRLC), a largest legume lineage, display the most dramatic and structural change which providing an excellent model for understanding of mechanisms of genomic evolution. The IRLC comprises 52 genera and ca 4000 species divided into seven tribes. In present study, we have sampled several representatives from each tribe across the IRLC from various herbaria and field. The ycf4 gene, which plays a role in regulating and assembly of photosystem I, is more variable in the tribe Fabeae than in other tribes. In certain species of Lathyrus, Pisum and Vavilovia, all belonging to Fabeae, the gene is either absent or a pseudogene. Our study suggests that ycf4 gene has undergone positive selection. Furthermore, the rapid evolution of the gene is locus and lineage specific and is not a shared character of the IRLC in legumes.
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The Complete Plastid Genome of Rhododendron pulchrum and Comparative Genetic Analysis of Ericaceae Species. FORESTS 2020. [DOI: 10.3390/f11020158] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background and Objectives: Rhododendron pulchrum Sweet (R. pulchrum) belongs to the genus Rhododendron (Ericaceae), a valuable horticultural and medicinal plant species widely used in Western Europe and the US. Despite its importance, this is the first member to have its cpGenome sequenced. Materials and Methods: In this study, the complete cp genome of R. pulchrum was sequenced with NGS Illumina HiSeq2500, analyzed, and compared to eight species in the Ericaceae family. Results: Our study reveals that the cp genome of R. pulchrum is 136,249 bp in length, with an overall GC content of 35.98% and no inverted repeat regions. The R. pulchrum chloroplast genome encodes 73 genes, including 42 protein-coding genes, 29 tRNA genes, and two rRNA genes. The synonymous (Ks) and nonsynonymous (Ka) substitution rates were estimated and the Ka/Ks ratio of R. pulchrum plastid genes were categorized; the results indicated that most of the genes have undergone purifying selection. A total of 382 forward and 259 inverted long repeats, as well as 221 simple-sequence repeat loci (SSR) were detected in the R. pulchrum cp genome. Comparison between different Ericaceae cp genomes revealed significant differences in genome size, structure, and GC content. Conclusions: The phylogenetic relationships among eight Ericaceae species suggested that R. pulchrum is closely related to Vaccinium oldhamii Miq. and Vaccinium macrocarpon Aiton. This study provides a theoretical basis for species identification and future biological research of Rhododendron resources.
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Shi H, Yang M, Mo C, Xie W, Liu C, Wu B, Ma X. Complete chloroplast genomes of two Siraitia Merrill species: Comparative analysis, positive selection and novel molecular marker development. PLoS One 2019; 14:e0226865. [PMID: 31860647 PMCID: PMC6924677 DOI: 10.1371/journal.pone.0226865] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 12/05/2019] [Indexed: 11/18/2022] Open
Abstract
Siraitia grosvenorii fruit, known as Luo-Han-Guo, has been used as a traditional Chinese medicine for many years, and mogrosides are its primary active ingredients. Unfortunately, Siraitia siamensis, its wild relative, might be misused due to its indistinguishable appearance, not only threatening the reliability of the medication but also partly exacerbating wild resource scarcity. Therefore, high-resolution genetic markers must be developed to discriminate between these species. Here, the complete chloroplast genomes of S. grosvenorii and S. siamensis were assembled and analyzed for the first time; they were 158,757 and 159,190 bp in length, respectively, and possessed conserved quadripartite circular structures. Both contained 134 annotated genes, including 8 rRNA, 37 tRNA and 89 protein-coding genes. Twenty divergences (Pi > 0.03) were found in the intergenic regions. Nine protein-coding genes, accD, atpA, atpE, atpF, clpP, ndhF, psbH, rbcL, and rpoC2, underwent selection within Cucurbitaceae. Phylogenetic relationship analysis indicated that these two species originated from the same ancestor. Finally, four pairs of molecular markers were developed to distinguish the two species. The results of this study will be beneficial for taxonomic research, identification and conservation of Siraitia Merrill wild resources in the future.
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Affiliation(s)
- Hongwu Shi
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Meng Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Changming Mo
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, China
| | | | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bin Wu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- * E-mail: (BW); (XM)
| | - Xiaojun Ma
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- * E-mail: (BW); (XM)
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Cui Y, Zhou J, Chen X, Xu Z, Wang Y, Sun W, Song J, Yao H. Complete chloroplast genome and comparative analysis of three Lycium (Solanaceae) species with medicinal and edible properties. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Cecchin M, Marcolungo L, Rossato M, Girolomoni L, Cosentino E, Cuine S, Li‐Beisson Y, Delledonne M, Ballottari M. Chlorella vulgaris genome assembly and annotation reveals the molecular basis for metabolic acclimation to high light conditions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1289-1305. [PMID: 31437318 PMCID: PMC6972661 DOI: 10.1111/tpj.14508] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 05/05/2023]
Abstract
Chlorella vulgaris is a fast-growing fresh-water microalga cultivated on the industrial scale for applications ranging from food to biofuel production. To advance our understanding of its biology and to establish genetics tools for biotechnological manipulation, we sequenced the nuclear and organelle genomes of Chlorella vulgaris 211/11P by combining next generation sequencing and optical mapping of isolated DNA molecules. This hybrid approach allowed us to assemble the nuclear genome in 14 pseudo-molecules with an N50 of 2.8 Mb and 98.9% of scaffolded genome. The integration of RNA-seq data obtained at two different irradiances of growth (high light, HL versus low light, LL) enabled us to identify 10 724 nuclear genes, coding for 11 082 transcripts. Moreover, 121 and 48 genes, respectively, were found in the chloroplast and mitochondrial genome. Functional annotation and expression analysis of nuclear, chloroplast and mitochondrial genome sequences revealed particular features of Chlorella vulgaris. Evidence of horizontal gene transfers from chloroplast to mitochondrial genome was observed. Furthermore, comparative transcriptomic analyses of LL versus HL provided insights into the molecular basis for metabolic rearrangement under HL versus LL conditions leading to enhanced de novo fatty acid biosynthesis and triacylglycerol accumulation. The occurrence of a cytosolic fatty acid biosynthetic pathway could be predicted and its upregulation upon HL exposure was observed, consistent with the increased lipid amount under HL conditions. These data provide a rich genetic resource for future genome editing studies, and potential targets for biotechnological manipulation of Chlorella vulgaris or other microalgae species to improve biomass and lipid productivity.
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Affiliation(s)
- Michela Cecchin
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Luca Marcolungo
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Marzia Rossato
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Laura Girolomoni
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Emanuela Cosentino
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Stephan Cuine
- Institute of Biosciences and Biotechnologies of Aix‐Marseille, UMR7265Aix‐Marseille UniversityCEACNRSCEA CadaracheSaint‐Paul‐lez DuranceF‐13108France
| | - Yonghua Li‐Beisson
- Institute of Biosciences and Biotechnologies of Aix‐Marseille, UMR7265Aix‐Marseille UniversityCEACNRSCEA CadaracheSaint‐Paul‐lez DuranceF‐13108France
| | - Massimo Delledonne
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Matteo Ballottari
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
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Liu XF, Zhu GF, Li DM, Wang XJ. Complete chloroplast genome sequence and phylogenetic analysis of Spathiphyllum 'Parrish'. PLoS One 2019; 14:e0224038. [PMID: 31644545 PMCID: PMC6808432 DOI: 10.1371/journal.pone.0224038] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/03/2019] [Indexed: 11/18/2022] Open
Abstract
Spathiphyllum is a very important tropical plant used as a small, potted, ornamental plant in South China, with an annual output value of hundreds of millions of yuan. In this study, we sequenced and analyzed the complete nucleotide sequence of the Spathiphyllum 'Parrish' chloroplast genome. The whole chloroplast genome is 168,493 bp in length, and includes a pair of inverted repeat (IR) regions (IRa and IRb, each 31,600 bp), separated by a small single-copy (SSC, 15,799 bp) region and a large single-copy (LSC, 89,494 bp) region. Our annotation revealed that the S. 'Parrish' chloroplast genome contained 132 genes, including 87 protein coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. In the repeat structure analysis, we detected 281 simple sequence repeats (SSRs) which included mononucleotides (223), dinucleotides (28), trinucleotides (12), tetranucleotides (11), pentanucleotides (6), and hexanucleotides (1), in the S. 'Parrish' chloroplast genome. In addition, we identified 50 long repeats, comprising 18 forward repeats, 13 reverse repeats, 17 palindromic repeats, and 2 complementary repeats. Single nucleotide polymorphism (SNP) and insertion/deletion (indel) analyses of the chloroplast genome of the S. 'Parrish' relative S. cannifolium revealed 962 SNPs in S. 'Parrish'. There were 158 indels (90 insertions and 68 deletions) in the S. 'Parrish' chloroplast genome relative to the S. cannifolium chloroplast genome. Phylogenetic analysis of five species found S. 'Parrish' to be more closely related to S. kochii than to S. cannifolium. This study identified the characteristics of the S. 'Parrish' chloroplast genome, which will facilitate species identification and phylogenetic analysis within the genus Spathiphyllum.
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Affiliation(s)
- Xiao-Fei Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, College of Life Science, South China Normal University, Guangzhou, Guangdong, China
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Gen-Fa Zhu
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Dong-Mei Li
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Xiao-Jing Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, College of Life Science, South China Normal University, Guangzhou, Guangdong, China
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Ye X, Hu D, Guo Y, Sun R. Complete chloroplast genome of Castanopsis sclerophylla (Lindl.) Schott: Genome structure and comparative and phylogenetic analysis. PLoS One 2019; 14:e0212325. [PMID: 31361757 PMCID: PMC6667119 DOI: 10.1371/journal.pone.0212325] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 07/17/2019] [Indexed: 11/19/2022] Open
Abstract
Castanopsis sclerophylla (Lindl.) Schott is an important species of evergreen broad-leaved tree in subtropical areas and has high ecological and economic value. However, there are few studies on its chloroplast genome. In this study, the complete chloroplast genome sequence of C. sclerophylla was determined using the Illumina HiSeq 2500 platform. The complete chloroplast genome of C. sclerophylla is 160,497 bp long, including a pair of inverted repeat (IR) regions (25,675 bp) separated by a large single-copy (LSC) region of 90,255 bp and a small single-copy (SSC) region of 18,892 bp. The overall GC content of the chloroplast genome is 36.82%. A total of 131 genes were found; of these, 111 genes are unique and annotated, including 79 protein-coding genes, 27 transfer RNA genes (tRNAs), and four ribosomal RNA genes (rRNAs). Twenty-one genes were found to be duplicated in the IR regions. Comparative analysis indicated that IR contraction might be the reason for the smaller chloroplast genome of C. sclerophylla compared to three congeneric species. Sequence analysis indicated that the LSC and SSC regions are more divergent than IR regions within Castanopsis; furthermore, greater divergence was found in noncoding regions than in coding regions. The maximum likelihood phylogenetic analysis showed that four species of the genus Castanopsis form a monophyletic clade and that C. sclerophylla is closely related to Castanopsis hainanensis with strong bootstrap values. These results not only provide a basic understanding of Castanopsis chloroplast genomes, but also illuminate Castanopsis species evolution within the Fagaceae family. Furthermore, these findings will be valuable for future studies of genetic diversity and enhance our understanding of the phylogenetic evolution of Castanopsis.
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Affiliation(s)
- Xuemin Ye
- Jiangxi Provincial Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, China
| | - Dongnan Hu
- Jiangxi Provincial Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, China
| | - Yangping Guo
- Jiangxi Provincial Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, China
| | - Rongxi Sun
- Jiangxi Provincial Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, China
- * E-mail:
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Gazara RK, de Oliveira EAG, Rodrigues BC, Nunes da Fonseca R, Oliveira AEA, Venancio TM. Transcriptional landscape of soybean (Glycine max) embryonic axes during germination in the presence of paclobutrazol, a gibberellin biosynthesis inhibitor. Sci Rep 2019; 9:9601. [PMID: 31270425 PMCID: PMC6610145 DOI: 10.1038/s41598-019-45898-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/19/2019] [Indexed: 12/13/2022] Open
Abstract
Gibberellins (GA) are key positive regulators of seed germination. Although the GA effects on seed germination have been studied in a number of species, little is known about the transcriptional reprogramming modulated by GA during this phase in species other than Arabidopsis thaliana. Here we report the transcriptome analysis of soybean embryonic axes during germination in the presence of paclobutrazol (PBZ), a GA biosynthesis inhibitor. We found a number of differentially expressed cell wall metabolism genes, supporting their roles in cell expansion during germination. Several genes involved in the biosynthesis and signaling of other phytohormones were also modulated, indicating an intensive hormonal crosstalk at the embryonic axis. We have also found 26 photosynthesis genes that are up-regulated by PBZ at 24 hours after imbibition (HAI) and down-regulated at 36 HAI, which led us to suggest that this is part of a strategy to implement an autotrophic growth program in the absence of GA-driven mobilization of reserves. Finally, 30 transcription factors (mostly from the MYB, bHLH, and bZIP families) were down-regulated by PBZ and are likely downstream GA targets that will drive transcriptional changes during germination.
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Affiliation(s)
- Rajesh K Gazara
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Eduardo A G de Oliveira
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Bruno C Rodrigues
- Laboratório Integrado de Ciências Morfofuncionais, Núcleo em Ecologia e Desenvolvimento SócioAmbiental de Macaé (NUPEM), Macaé, Brazil
| | - Rodrigo Nunes da Fonseca
- Laboratório Integrado de Ciências Morfofuncionais, Núcleo em Ecologia e Desenvolvimento SócioAmbiental de Macaé (NUPEM), Macaé, Brazil
| | - Antônia Elenir A Oliveira
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil.
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Grossman A, Sanz-Luque E, Yi H, Yang W. Building the GreenCut2 suite of proteins to unmask photosynthetic function and regulation. Microbiology (Reading) 2019; 165:697-718. [DOI: 10.1099/mic.0.000788] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Arthur Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Emanuel Sanz-Luque
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Heng Yi
- Key Laboratory of Photobiology, Institute of Botany (CAS), Beijing, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Wenqiang Yang
- Key Laboratory of Photobiology, Institute of Botany (CAS), Beijing, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
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Ginigini J, Lecellier GJ, Nicolas M, Nour M, Hnawia E, Lebouvier N, Herbette G, Lockhart P, Raharivelomanana P. Chemodiversity of Calophyllum inophyllum L. oil bioactive components related to their specific geographical distribution in the South Pacific region. PeerJ 2019; 7:e6896. [PMID: 31198623 PMCID: PMC6535043 DOI: 10.7717/peerj.6896] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 04/02/2019] [Indexed: 11/27/2022] Open
Abstract
Background Different parts of the tree Calophyllum inophyllum L. (nuts, leaves, roots, bark, fruits, nut oil and resin) are used as traditional medicines and cosmetics in most of the Pacific Islands. The oil efficiency as a natural cure and in traditional cosmetics has been largely described throughout the South Pacific, which led us to investigate C. inophyllum’s chemical and genetic diversity. A correlative study of the nut resin and leaf DNA from three distinct archipelagos in the South Pacific was carried out in order to identify diversity patterns in C. inophyllum across the South Pacific. Methods Calophyllum inophyllum plants were sampled from French Polynesia, New Caledonia and Fiji. We extracted tamanu oil (nut oil) resin for chemo-diversity studies and sampled leaf tissues for genetic studies. We applied an analysis method designed for small quantities (at a microscale level), and used High Performance Liquid Chromatography (HPLC) to establish the chemo-diversity of tamanu oil resin. In-house standards were co-eluted for qualitative determination. Genetic diversity was assessed using chloroplast barcoding markers (the Acetyl-CoA carboxylase (accD) gene and the psaA-ycf3 intergenic spacer region). Results Our HPLC analysis revealed 11 previously known tamanu oil constituents, with variability among plant samples. We also isolated and characterized two new neoflavonoids from tamanu oil resin namely, tamanolide E1 and E2 which are diastereoisomers. Although genetic analysis revealed low genetic variation, our multivariate analysis (PCA) of the tamanu oil resin chemical profiles revealed differentiation among geographic regions. Conclusion We showed here that chromatographic analysis using formalized in-house standards of oil resin compounds for co-elution studies against oil resin samples could identify patterns of variation among samples of C. inophyllum, and discriminate samples from different geographical origins.
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Affiliation(s)
- Joape Ginigini
- Pacific Natural Products Research Centre, Institute of Applied Sciences, University of the South Pacific, Suva, Fiji
| | - Gaël J Lecellier
- Départment de Biologie, Université de Versailles Saint-Quentin-en-Yvelines, Versailles, France
| | - Mael Nicolas
- ISEA EA7484, University of Caledonia, Noumea, New Caledonia
| | - Mohammed Nour
- ISEA EA7484, University of Caledonia, Noumea, New Caledonia
| | - Edouard Hnawia
- ISEA EA7484, University of Caledonia, Noumea, New Caledonia
| | | | - Gaëtan Herbette
- Spectropole, Campus de St Jérôme, Aix-Marseille Univ, CNRS, Centrale Marseille, FSCM, Marseille, France
| | - Peter Lockhart
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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