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Genome, Plastid

Genome and Plastid: Explore the Essential Building Blocks of Life.
Genomes encompass the complete genetic material of an organism, encoding the instructions for its development and function.
Plastids, such as chloroplasts, are organelles found in plant and algal cells that play crucial roles in photosynthesis and other metabolic processes.
Understand the intricate relationships between genome and plastid, and harness the power of PubCompare.ai to streamline your research on these fundamental biological entities.

Most cited protocols related to «Genome, Plastid»

1
Annotating Organelle rrn5 Genes
Annotated mitochondrial and plastid rrn5 genes (alternatively designated rrf in plastid genomes) were retrieved from GenBank (complete mitochondrial and plastid genome sections: http://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?taxid=2759&opt=organelle and http://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?taxid=2759&opt=plastid, version 22 July 2014). The Chondrus crispus mitochondrial rrn5 (NCBI Gene ID 7020988) was removed from the downloaded sequences, because the authors’ gene assignment has been disputed (17 ). Similarly, the Bryopsis hypnoides plastid rrn5 (Gene ID 8463250) was removed due to the evidently incorrect gene annotation [both Basic Local Alignment Search Tool (BLAST) and CM searches identify a different locus in the plastid genome as bona fide rrn5]. Mitochondrial and plastid gene sequences were aligned separately with MUSCLE v3.6 (18 (link)) and incorporated into the Genetic Data Environment (GDE) sequence editor (19 (link)). Multiple alignments were then inspected by eye and manually adjusted in a few regions to improve primary sequence plus secondary structure fit, the latter assisted by minimum energy secondary structure predictions with RNAalifold (20 (link)). The verified annotated sequences include 108 mtDNA-encoded and 500 ptDNA-encoded rrn5 genes (Supplementary Table S1; marked by ‘+’ in the ‘Annotation’ column). These data sets, referred to as the mt-gene test set and the pt-gene test set, were used for developing and testing CMs. For building the models, sequence alignments of test set rrn5 sequences served as input for the Cmbuild and Cmcalibrate programs of Infernal v1.1, after masking columns that are not reliably aligned (15 (link)). The Cmbuild option ‘- -hand’ ensures that only the confidently aligned sequence positions are used for building mitochondrion- and plastid-specific CMs (referred to as mt-5S and pt-5S models, respectively). Use of the tree weighting option ‘- -wgsc’ (21 (link)) increases the chance of detecting sequences in an organismal group that is less well represented in the seed alignment. With these two basic CMs, we searched for rrn5 genes in individual organelle genome sequences by employing Cmsearch with default settings, i.e. local alignment, an inclusion (significance) E-value threshold of 10−02 and a reporting E-value threshold of 10.
Organelle rrn5 sequences discovered and validated in the course of our analyses (see below) were included in an additional CM (mtAT-5S) based on a wide taxonomic sampling and a focus on derived and A+T-rich 5S rRNAs that are less effectively identified with the basic mt-5S model. A fourth model has been developed (mtPerm-5S) based on the permuted 5S rRNAs encoded by mtDNAs from brown algae and potentially several other stramenopiles. All models will be made available (together with the seed sequence alignments) in the Rfam database. They will be also included in our automated organelle genome annotation tool MFannot (http://megasun.bch.umontreal.ca/cgi-bin/mfannot/mfannotInterface.pl).
Valach M., Burger G., Gray M.W, & Lang B.F. (2014). Widespread occurrence of organelle genome-encoded 5S rRNAs including permuted molecules. Nucleic Acids Research, 42(22), 13764-13777.
Publication 2014
3-O-(methylthiomethyl)apiitol tetraacetate Brown Algae Chondrus crispus DNA, Mitochondrial Gene Annotation Genes Genetic Testing Genome Genome, Plastid Mitochondria Mitochondrial Inheritance Muscle Tissue Organelles Plastids Reproduction RNA, Ribosomal, 5S Sequence Alignment Stramenopiles Trees
2
Viridiplantae Plastid Genome Sequences
Protein-coding data, including nucleotides and their corresponding amino acid sequences, for all Viridiplantae taxa that had complete or nearly complete plastid genome sequences were downloaded from GenBank on February 28, 2012. If there were multiple genome sequences from the same taxon, we included the sequence with the most data. Our sampling included most major lineages of Viridiplantae. A complete list of taxa and GenBank accession numbers is available in Additional file 1.
Taxonomic names (Additional file 1) follow various references. Four classes of chlorophytic algae (Chlorophyta) are recognized following a traditional classification [26 ,76 (link)]. Classes of streptophytic algae and orders for both chlorophytic and streptophytic algae follow Leliaert et al. [76 (link)]. Names for the three main bryophyte clades follow recent classifications: mosses (Bryophyta[144 ]), hornworts (Anthocerotophyta[145 (link)]), and liverworts (Marchantiophyta[146 (link)]). Major clades of tracheophytes follow Cantino et al. [147 ] and Soltis et al. [103 (link)]. Familial and ordinal names within major clades of land plants follow these references: Bryophyta[144 ]; Anthocerotophyta[145 (link)]; Marchantiophyta[146 (link)]; lycophytes (Lycopodiophyta) and ferns (Monilophyta) [148 ]; gymnosperms (Acrogymnospermae[149 ]); and angiosperms (Angiospermae[150 ]). All scientific names are italicized to distinguish common names from scientific names [147 ,151 ].
Ruhfel B.R., Gitzendanner M.A., Soltis P.S., Soltis D.E, & Burleigh J.G. (2014). From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evolutionary Biology, 14, 23.
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Publication 2014
Amino Acid Sequence Anthocerotophyta Chlorophyta Cycadopsida Embryophyta Ferns Genome Genome, Plastid Green Plants Liverworts Magnoliopsida Mosses Nucleotides Proteins Tracheophyta
3
Tobacco Plastid Transformation Vector Construction
A tobacco plastid transformation vector was constructed based on the iVEC technology (Figure 1A). The vector mediates integration of the expression cassettes into the intergenic spacer region between the trnfM and trnG genes of the tobacco plastid genome. For vector assembly, we first amplified five DNA fragments which have pairwise homologous end sequences by Pfu DNA polymerase using a standard PCR protocol (95°C 3 min; 95°C 30 s, 55°C 30 s, 72°C 3 min, 30 cycles; 72°C 7 min). The two DNA fragments providing the flanking regions for homologous recombination, LHRR (containing psaB, rps14 and trnfM, 1,940 bp) and RHRR (containing psbZ and trnG, 723 bp), were amplified from tobacco genomic DNA by PCR using primer pairs LHRR-F/LHRR-R and RHRR-F/RHRR-R, respectively. The primer sequences are listed in Table 1. Two additional DNA fragments were generated by PCR amplification with primer pairs aadA-F/aadA-R and gfp-F/gfp-R using aadA and gfp expression cassettes as templates that had been chemically synthesized (GeneCreate, China). The selectable marker gene aadA is driven by the Chlamydomonas reinhardtii psbA promoter (CrPpsbA), and followed by the 3′UTR from the C. reinhardtii rbcL gene (CrTrbcL). The cassette (1,647 bp) is flanked by two loxP sites to facilitate marker gene excision by Cre-mediated site-specific recombination (Corneille et al., 2001 (link); Zhou et al., 2008 (link)). The reporter gene gfp is controlled by the tobacco plastid rRNA operon promoter combined with the 5′UTR from gene10 of bacteriophage T7 (NtPrrn:T7g10) (Kuroda and Maliga, 2001 (link)), and the 3′UTR from the E. coli ribosomal RNA operon rrnB (TrrnB). NcoI and XbaI restriction sites were introduced at the 5′ and 3′ end, respectively, of the gfp gene (1,282 bp). The fifth DNA fragment (SK, 2,916 bp) was the vector backbone fragment from pBluescript II SK (+) without the multiple cloning site (MCS) amplified using primers pBS-F/pBS-R (Table 1). The five DNA fragments comprising the four DNA insert pieces (LHRR, 133 ng; RHRR, 50 ng; aadA expression cassette, 113 ng; gfp expression cassette, 88 ng) and the linear vector backbone fragment (100 ng) were mixed in a stoichiometric ratio of 2:2:2:2:1, and then co-transformed into E. coli (XL10-Gold, Agilent technologies) chemically competent cells (>2 × 108 cfu/μg assayed on pUC19). Positive clones were identified by selection for both ampicillin and spectinomycin resistance and further confirmed by their green fluorescence and by DNA sequencing.
Wu Y., You L., Li S., Ma M., Wu M., Ma L., Bock R., Chang L, & Zhang J. (2017). In vivo Assembly in Escherichia coli of Transformation Vectors for Plastid Genome Engineering. Frontiers in Plant Science, 8, 1454.
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Publication 2017
Ampicillin Bacteriophage T7 Cells Chlamydomonas reinhardtii Clone Cells Cloning Vectors Escherichia coli Fluorescence Genes Genes, Reporter Genetic Markers Genome Genome, Plastid Gold Homologous Recombination Intergenic Region Nicotiana Oligonucleotide Primers Operon Pfu DNA polymerase Plastids Recombination, Genetic rRNA Operon rRNA Promoter Spectinomycin Vertebral Column
4
Phylogenetic Relationships among Mediterranean Oaks
Our analysis included 59 individuals of the four Mediterranean Quercus Group Ilex species (File S1) covering their entire range in North Africa and western Eurasia. Additionally, 22 individuals of 16 Asian species of Group Ilex were analysed. The final dataset also included all species of the western North American Group Protobalanus (five species, 10 individuals), 16 species of Group Quercus (20 individuals, from North America and Eurasia), five species of the East Asian Group Cyclobalanopsis (11 individuals), seven species of the American Group Lobatae (eight individuals), and six species of Group Cerris (seven individuals). The outgroup set was represented by one sample each of the monotypic genera Notholithocarpus and Chrysolepis (western North America) and one species each of Castanea and Castanopsis (NCBI GenBank accessions HQ336406 (complete plastid genome of C. mollissima), JN044213, JF941179, FJ185053). Based on their genetic (plastid) signatures these genera are the closest relatives of Quercus within the Fagaceae (Manos, Cannon & Oh, 2008 ). For voucher information and accession numbers see File S1. The molecular analyses included three plastid DNA regions: a part of the rbcL gene, the trnH-psbA intergenic spacer and a portion of the trnK/matK region (3′ intron and partial gene). These markers were chosen based on the variability displayed in previous analyses (e.g., Manos, Zhou & Cannon, 2001 (link); Okaura et al., 2007 (link); Simeone et al., 2013 (link)) and the high number of their sequences available on GenBank. Primer sequences for the three regions were obtained from Kress & Erickson (2007) (link), Shaw et al. (2005) (link) and Piredda et al. (2011) (link), respectively. DNA extractions and PCR protocols were the same as in Piredda et al. (2011) (link). Sequencing of both DNA strands was performedat Macrogen (http://www.macrogen.com), using the forward and reverse PCR primers,; electropherograms were edited with CHROMAS 2.3 (http://www.technelysium.com.au) and checked visually.
Simeone M.C., Grimm G.W., Papini A., Vessella F., Cardoni S., Tordoni E., Piredda R., Franc A, & Denk T. (2016). Plastome data reveal multiple geographic origins of Quercus Group Ilex. PeerJ, 4, e1897.
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Publication 2016
Asian Americans East Asian People Fagaceae Genes Genes, vif Genome, Plastid Ilex Introns MATK protein, human North American People Oligonucleotide Primers Plastids Quercus Quercus ilex Reproduction
5
Plastid Genome Sequencing and Annotation
Cultivation of the algae and DNA isolation followed standard protocols. Sequencing of total DNA preparations employed the 454 and Illumina platforms. Initial assemblies of the reads were searched to identify scaffolds corresponding to the plastid genome and the final assembly of the plastid genome sequences was achieved by manual gap filling and polishing. MFannot (http://megasun.bch.umontreal.ca/cgi-bin/mfannot/mfannotInterface.pl) was used for obtaining an initial automated annotation of the assembled plastid genome sequences, which was checked and improved manually. Details on the cultivation, DNA isolation, sequencing, assembly, and annotation are provided in Supplementary methods. Annotated plastid genome sequences from T. minutus and Ochromonas sp. CCMP1393 are deposited in the GenBank database (accession numbers KJ624065 and KJ877675, respectively).
Ševčíková T., Horák A., Klimeš V., Zbránková V., Demir-Hilton E., Sudek S., Jenkins J., Schmutz J., Přibyl P., Fousek J., Vlček Č., Lang B.F., Oborník M., Worden A.Z, & Eliáš M. (2015). Updating algal evolutionary relationships through plastid genome sequencing: did alveolate plastids emerge through endosymbiosis of an ochrophyte?. Scientific Reports, 5, 10134.
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Publication 2015
Genome, Plastid isolation Ochromonas

Most recents protocols related to «Genome, Plastid»

1
Plastid Genome Annotation and Visualization
The clean data were assembled using GetOrganelle v. 1.7.1 [71 (link)], The complete circular assembly graph was checked and further extracted using Bandage v. 0.8.1 [72 (link)]. The finished plastid genomes were annotated by DOGMA [73 (link)], and GeSeq [74 (link)], and then manually adjusted by Geneious v. 9.1.7 [75 (link)]. Gene start and stop codons were determined via comparison with the A. maritima (NC_045093) and A. annua (NC_034683) genomes. The annotated plastid genomes were submitted to GenBank (Table 1) and Organellar Genome Draw (OGDRAW) [76 (link)] was used to illustrate a circular genome map.
Jin G., Li W., Song F., Yang L., Wen Z, & Feng Y. (2023). Comparative analysis of complete Artemisia subgenus Seriphidium (Asteraceae: Anthemideae) chloroplast genomes: insights into structural divergence and phylogenetic relationships. BMC Plant Biology, 23, 136.
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Publication 2023
Bandage Codon, Terminator Genes Genome Genome, Plastid Organelles
2
Comprehensive Plastid Genome Sequencing of the Palm Family
Plastomes of 210 accessions representing 182 species and 111 genera of Arecaceae were newly sequenced for this project, and detailed information about these accessions and voucher specimens is provided in Additional file 1 (Table S1). We further added complete or nearly complete plastid genome sequences from NCBI (https://www.ncbi.nlm.nih.gov/), corresponding to 76 accessions representing 71 species and 63 genera of the palm family (45 of these genera were duplicate with those newly sequenced here) (Additional file 1: Table S1). Most of these were derived from the phylogenomic studies conducted by Barrett et al. [47 (link)] and Comer et al. [48 (link)]. In addition, another 49 palm accessions representing 49 genera that have at least five plastid DNA regions in NCBI (www.ncbi.nlm.nih.gov) were also included (Additional file 2: Table S2), most of which were from Baker et al. [24 (link)]. In total, the final taxon sampling included 335 palm accessions representing 276 species and 178 genera, accounting for 98.3% of all currently circumscribed palm genera, and representing all the subtribes, tribes, and subfamilies [40 (link)]. Three palm genera, viz. Jailoloa Heatubun & W.J. Baker, Sabinaria R. Bernal & Galeano, and Wallaceodoxa Heatubun & W.J. Baker, which are recently described genera [40 (link)], were not sampled here because of the lack of DNA material or published plastid sequence data, but their phylogenetic positions within the family were resolved previously in analyses based mainly on nuclear data [60 , 79 (link), 85 (link), 86 (link)]. Additionally, complete plastome sequences of four genera of the family Dasypogonaceae and ten genera representing the other ten monocot orders (Additional file 1: Table S1) were selected as outgroups based on the phylogenetic framework provided by Givnish et al. [87 (link)] and Li et al. [52 (link)].
Yao G., Zhang Y.Q., Barrett C., Xue B., Bellot S., Baker W.J, & Ge X.J. (2023). A plastid phylogenomic framework for the palm family (Arecaceae). BMC Biology, 21, 50.
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Publication 2023
Arecaceae Genome, Plastid Plastids Tribes
3
Plastid Genome Sequencing and Annotation
Total genomic DNAs were extracted from silica-dried leaves following the CTAB protocol of Doyle and Doyle [88 ]. DNAs were sheared to approximately 500-bp fragments through ultrasonic treatment and used to construct short-insert libraries following the manufacturer’s protocol (NEBNext® Ultra II™DNA Library Prep Kit for Illumina®) and sequenced from both ends on the Illumina HiSeq 2500 platform at Beijing Genomics Institute (BGI, Shenzhen, China) to generate 2 × 150-bp sequencing reads. Approximately 3 GB of raw data was generated for each sample. Plastid reads were assembled using the software GetOrganelle [89 (link)] with parameter settings as follows: “-t 30 -R 15 -k 75, 85, 95, 105 -F embplant_pt,” using the plastid genomes of Nypa fruticans Wurmb (GenBank accession number: NC_029958) and Veitchia arecina Becc. (NC_029950) as references. All the plastid genes were then annotated using the software PGA [90 (link)], with the annotated plastome of Amborella trichopoda Baill. (NC_005086) as a reference, following the recommendation of Qu et al. [90 (link)]. GenBank accession numbers of the complete or nearly complete plastome newly sequenced here as well as those obtained from NCBI are listed in Additional file 1 (Table S1), and the GenBank accession numbers corresponding to the sequences from the 49 accessions with few plastid DNA regions available are listed in Additional file 2 (Table S2).
Yao G., Zhang Y.Q., Barrett C., Xue B., Bellot S., Baker W.J, & Ge X.J. (2023). A plastid phylogenomic framework for the palm family (Arecaceae). BMC Biology, 21, 50.
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Publication 2023
Cetrimonium Bromide DNA Library Genes Genome Genome, Plastid Plastids Silicon Dioxide Ultrasonics
4
Comprehensive Plastome Analysis of Alismatidae
A total of 38 species representing all 12 accepted families in Alismatidae were incorporated into this study. These included 1) 13 species belonging to five families newly sequenced in this study; 2) 21 plastomes from eight families downloaded from GenBank, 3) the sequenced data of the remaining four species, Amphibolis antarctica (SRR19106495), Najas marina (ERR5529706), Posidonia australis (SRR19106496) and Zannichellia palustris (ERR5554861), retrieved from the SRA database (Table S1). Three additional plastomes from Araceae, Tofieldiaceae, and Acoraceae were included as outgroups. The field sampling followed the ethics and legality of the local government and was permitted by the government.
Total genomic DNA extraction, DNA fragmentation and preparation of sequencing libraries of all 13 newly sampled species followed the description by Li et al. [31 (link)]. Genome skimming per sample was conducted on the Illumina HiSeq 2000 platform in Novogene (Tianjin, China), with 150 bp paired-end reads. Newly sequenced reads of 13 species and four SRA sequenced reads were filtered with Fastp v.0.20.1 [45 (link)] using default settings. Complete plastomes were de novo assembled using the software GetOrganelle v.1.7.1 [46 (link)] with default parameters. Plastid Genome Annotator (PGA [47 (link)]) and the online tool Geseq [48 (link)] were utilized for the annotation of assembled plastomes. The annotations for protein-coding genes (PCGs) were checked and adjusted manually according to published plastomes of Alismatales. All newly generated plastomes were deposited in the China National GeneBank DataBase (CNGBdb, https://db.cngb.org/; Table S1).
Li Z.Z., Lehtonen S, & Chen J.M. (2023). The dynamic history of plastome structure across aquatic subclass Alismatidae. BMC Plant Biology, 23, 125.
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Publication 2023
Acoraceae Alismatales Araceae DNA Fragmentation Genes Genome Genome, Plastid Naja Posidonia Protein Annotation
5
Sequencing and Analysis of Isoetes orientalis Chloroplast Genome
In the present study, fresh leaf material was obtained from the collection sites of Andaihou Village, Songyang County, Lishui City, China (119.273422 E, 28.271808 N) (Figure 1) and dried with silica. Specimens (voucher no.: Yufeng Gu Fern08748) were deposited at the Herbarium of the National Orchid Conservation Center (NOCC). Silica-dried material was sent to Shanghai Majorbio Bio-pharm Technology Co., Ltd. (Shanghai, China) for DNA extraction and sequencing, performed on an Illumina HiSeq X Ten platform (Illumina, San Diego, CA). The plastid genome was assembled using GetOrganelle v1.7.5 (Jin et al. 2018 ) using default parameters, and the results viewed and edited by Bandage v0.8.1 (Wick et al. 2015 (link)). The assembled chloroplast genome was annotated by Geneious Prime 2021.0.3 (https://www.geneious.com) (Kearse et al. 2012 (link)) with I. nuttallii as a reference at 90% similarity.
We drew the chloroplast complete genome map of this quillwort species (Figure 2) in OGDRAW – Draw Organelle Genome Maps (https://chlorobox.mpimp-golm.mpg.de/OGDraw.html). To find the phylogenetic position of I. orientalis, molecular phylogenetic analysis was carried out with 15 published, complete chloroplast genomes of Isoetes downloaded from GenBank.
Coding sequences (CDS) were extracted from the annotated sequences, then they were aligned using mauveAligner in Geneious Prime 2021.0.3. By employing a progressive algorithm and assuming collinearity, poorly aligned regions were excluded from the complete plastome dataset using Gblocks v0.91b in PhyloSuite v1.2.2 (Zhang et al. 2020 (link)). Using nucleotide as the type of sequence, up to half gap positions were allowed, and other parameters were set as default settings. For phylogenomic analysis, the resulting alignment was subjected to ML analyses performed using IQ-TREE v. 1.6.12 (Lam-Tung et al. 2015 (link)) with 10,000 bootstrap replicates. The best-fitting model was selected by ModelFinder (Kalyaanamoorthy et al. 2017 (link)) and implemented in IQ-TREE.
Li Y., Chen X., Lin X., Gu Y., Liu B, & Zhang R. (2023). Complete chloroplast genome of Isoetes orientalis (Isoetaceae), an endangered quillwort from China. Mitochondrial DNA. Part B, Resources, 8(3), 342-346.
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Publication 2023
Aleurites Bandage Base Sequence Chloroplasts Exons Genome, Chloroplast Genome, Plastid Organelles Pichia kudriavzevii Plant Leaves Silicon Dioxide Trees

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More about "Genome, Plastid"

Genomes and Plastids: Unraveling the Building Blocks of Life Genomes, the complete genetic blueprints of organisms, hold the key to understanding life's fundamental processes.
These intricate molecular structures encode the instructions for an organism's development and function, unlocking a world of biological wonders.
Closely tied to genomes are plastids, organelles found in plant and algal cells that play crucial roles in photosynthesis and other metabolic activities.
Exploring the interplay between genomes and plastids is a thrilling frontier of biological research.
Techniques like high-throughput sequencing platforms, such as the HiSeq 2500, HiSeq X Ten, HiSeq 2000, and NovaSeq 6000, allow researchers to delve deep into the genetic landscapes of diverse organisms.
Complementary tools like the CLC Genomics Workbench and Lasergene 7.1 software enable streamlined analysis and interpretation of these genomic datasets.
Extracting high-quality DNA from plant and algal samples is crucial for downstream genomic and plastid studies.
The DNeasy Plant Mini Kit is a popular choice for efficient DNA purification, while instruments like the ChemiDocTM MP System provide reliable quantification and quality assessment.
By harnessing the power of AI-driven platforms like PubCompare.ai, researchers can navigate the expansive body of scientific literature, locate relevant protocols, and identify the optimal experimental approaches for their genome and plastid analysis needs.
This seamless integration of cutting-edge technologies empowers researchers to make groundbreaking discoveries and advance our understanding of these fundamental building blocks of life.