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A chloroplast is a type of membrane-bound organelle known as a plastid that conducts photosynthesis mostly in plant and algal cells. The photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in the energy-storage molecules ATP and NADPH while freeing oxygen from water in the cells. The ATP and NADPH is then used to make organic molecules from carbon dioxide in a process known as the Calvin cycle. Chloroplasts carry out a number of other functions, including fatty acid synthesis, amino acid synthesis, and the immune response in plants. The number of chloroplasts per cell varies from one, in unicellular algae, up to 100 in plants like Arabidopsis and wheat.
Symbiogenesis is the leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms. The theory holds that mitochondria, plastids such as chloroplasts, and possibly other organelles of eukaryotic cells are descended from formerly free-living prokaryotes taken one inside the other in endosymbiosis. Mitochondria appear to be phylogenetically related to Rickettsiales bacteria, while chloroplasts are thought to be related to cyanobacteria.
The plastid is a membrane-bound organelle found in the cells of plants, algae, and some other eukaryotic organisms. They are considered to be intracellular endosymbiotic cyanobacteria. Examples include chloroplasts, chromoplasts, and leucoplasts.
Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). HGT is an important factor in the evolution of many organisms. HGT is influencing scientific understanding of higher order evolution while more significantly shifting perspectives on bacterial evolution.
Internal transcribed spacer (ITS) is the spacer DNA situated between the small-subunit ribosomal RNA (rRNA) and large-subunit rRNA genes in the chromosome or the corresponding transcribed region in the polycistronic rRNA precursor transcript.
Extrachromosomal DNA is any DNA that is found off the chromosomes, either inside or outside the nucleus of a cell. Most DNA in an individual genome is found in chromosomes contained in the nucleus. Multiple forms of extrachromosomal DNA exist, and, while some of these serve important biological functions, they can also play a role in diseases such as cancer.
The Archaeplastida are a major group of eukaryotes, comprising the photoautotrophic red algae (Rhodophyta), green algae, land plants, and the minor group glaucophytes. It also includes the non-photosynthetic lineage Rhodelphidia, a predatorial (eukaryotrophic) flagellate that is sister to the Rhodophyta, and probably the microscopic picozoans. The Archaeplastida have chloroplasts that are surrounded by two membranes, suggesting that they were acquired directly through a single endosymbiosis event by feeding on a cyanobacterium. All other groups which have chloroplasts, besides the amoeboid genus Paulinella, have chloroplasts surrounded by three or four membranes, suggesting they were acquired secondarily from red or green algae. Unlike red and green algae, glaucophytes have never been involved in secondary endosymbiosis events.
The Rafflesiaceae are a family of rare parasitic plants comprising 36 species in 3 genera found in the tropical forests of east and southeast Asia, including Rafflesia arnoldii, which has the largest flowers of all plants. The plants are endoparasites of vines in the genus Tetrastigma (Vitaceae) and lack stems, leaves, roots, and any photosynthetic tissue. They rely entirely on their host plants for both water and nutrients, and only then emerge as flowers from the roots or lower stems of the host plants.
Extranuclear inheritance or cytoplasmic inheritance is the transmission of genes that occur outside the nucleus. It is found in most eukaryotes and is commonly known to occur in cytoplasmic organelles such as mitochondria and chloroplasts or from cellular parasites like viruses or bacteria.
Plant evolution is the subset of evolutionary phenomena that concern plants. Evolutionary phenomena are characteristics of populations that are described by averages, medians, distributions, and other statistical methods. This distinguishes plant evolution from plant development, a branch of developmental biology which concerns the changes that individuals go through in their lives. The study of plant evolution attempts to explain how the present diversity of plants arose over geologic time. It includes the study of genetic change and the consequent variation that often results in speciation, one of the most important types of radiation into taxonomic groups called clades. A description of radiation is called a phylogeny and is often represented by type of diagram called a phylogenetic tree.
Mesangiospermae is a clade of flowering plants (angiosperms), informally called "mesangiosperms". They are one of two main groups of angiosperms. It is a name created under the rules of the PhyloCode system of phylogenetic nomenclature. There are about 350,000 species of mesangiosperms. The mesangiosperms contain about 99.95% of the flowering plants, assuming that there are about 175 species not in this group and about 350,000 that are. While such a clade with a similar circumscription exists in the APG III system, it was not given a name.
Chromera velia, also known as a "chromerid", is a unicellular photosynthetic organism in the superphylum Alveolata. It is of interest in the study of apicomplexan parasites, specifically their evolution and accordingly, their unique vulnerabilities to drugs.
Chloroplast DNA (cpDNA) is the DNA located in chloroplasts, which are photosynthetic organelles located within the cells of some eukaryotic organisms. Chloroplasts, like other types of plastid, contain a genome separate from that in the cell nucleus. The existence of chloroplast DNA was identified biochemically in 1959, and confirmed by electron microscopy in 1962. The discoveries that the chloroplast contains ribosomes and performs protein synthesis revealed that the chloroplast is genetically semi-autonomous. The first complete chloroplast genome sequences were published in 1986, Nicotiana tabacum (tobacco) by Sugiura and colleagues and Marchantia polymorpha (liverwort) by Ozeki et al. Since then, a great number of chloroplast DNAs from various species have been sequenced.
The inverted repeat-lacking clade(IRLC) is a monophyletic clade of the flowering plant subfamily Faboideae (or Papilionaceae). Faboideae includes the majority of agriculturally-cultivated legumes. The name of this clade is informal and is not assumed to have any particular taxonomic rank like the names authorized by the ICBN or the ICPN. The clade is characterized by the loss of one of the two 25-kb inverted repeats in the plastid genome that are found in most land plants. It is consistently resolved in molecular phylogenies. The clade is predicted to have diverged from the other legume lineages 39.0±2.4 million years ago (in the Eocene). It includes several large, temperate genera such as AstragalusL., HedysarumL., MedicagoL., OxytropisDC., SwainsonaSalisb., and TrifoliumL..
Meso-Papilionoideae is a monophyletic clade of the flowering plant subfamily Faboideae that includes the majority of papilionoid legumes. This clade is consistently resolved in molecular phylogenies. It contains many agronomically important genera, including Arachis (peanut), Cicer (chickpea), Glycine (soybean), Medicago (alfalfa), Phaseolus, Trifolium (clover), Vicia (vetch), and Vigna.
In phylogenetic nomenclature, the Pentapetalae are a large group of eudicots that were informally referred to as the "core eudicots" in some papers on angiosperm phylogenetics. They comprise an extremely large and diverse group that accounting about 65% of the species richness of the angiosperms, with wide variability in habit, morphology, chemistry, geographic distribution, and other attributes. Classical systematics, based solely on morphological information, was not able to recognize this group. In fact, the circumscription of the Pentapetalae as a clade is based on strong evidence obtained from DNA molecular analysis data.
A linear chromosome is a chromosome which is linear in shape, and contains terminal ends. In most eukaryotic cells, DNA is arranged in multiple linear chromosomes. In contrast, most prokaryotic cells generally contain a singular circular chromosome.
A plastid is a membrane-bound organelle found in plants, algae and other eukaryotic organisms that contribute to the production of pigment molecules. Most plastids are photosynthetic, thus leading to color production and energy storage or production. There are many types of plastids in plants alone, but all plastids can be separated based on the number of times they have undergone endosymbiotic events. Currently there are three types of plastids; primary, secondary and tertiary. Endosymbiosis is reputed to have led to the evolution of eukaryotic organisms today, although the timeline is highly debated.
Genome skimming is a sequencing approach that uses low-pass, shallow sequencing of a genome, to generate fragments of DNA, known as genome skims. These genome skims contain information about the high-copy fraction of the genome. The high-copy fraction of the genome consists of the ribosomal DNA, plastid genome (plastome), mitochondrial genome (mitogenome), and nuclear repeats such as microsatellites and transposable elements. It employs high-throughput, next generation sequencing technology to generate these skims. Although these skims are merely 'the tip of the genomic iceberg', phylogenomic analysis of them can still provide insights on evolutionary history and biodiversity at a lower cost and larger scale than traditional methods. Due to the small amount of DNA required for genome skimming, its methodology can be applied in other fields other than genomics. Tasks like this include determining the traceability of products in the food industry, enforcing international regulations regarding biodiversity and biological resources, and forensics.
References
- 1 2 "The McClintock Prize for Plant Genetics and Genome Studies". www.maizegdb.org.
- 1 2 3 4 5 6 7 Jeffrey D. Palmer publications indexed by Google Scholar
- 1 2 3 4 "Evolution Tree - Jeffrey D. Palmer". academictree.org.
- 1 2 Wolfe, K. H.; Morden, C. W.; Palmer, J. D. (1992). "Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant". Proceedings of the National Academy of Sciences. 89 (22): 10648–10652. Bibcode:1992PNAS...8910648W. doi: 10.1073/pnas.89.22.10648 . ISSN 0027-8424. PMC 50398 . PMID 1332054.
- 1 2 3 Chase, Mark W.; Soltis, Douglas E.; Olmstead, Richard G.; Morgan, David; Les, Donald H.; Mishler, Brent D.; Duvall, Melvin R.; et al. (1993). "Phylogenetics of Seed Plants: An Analysis of Nucleotide Sequences from the Plastid Gene rbcL" (PDF). Annals of the Missouri Botanical Garden . 80 (3): 528. doi:10.2307/2399846. hdl: 1969.1/179875 . ISSN 0026-6493. JSTOR 2399846.
- 1 2 Palmer, Jeffrey D.; Jansen, Robert K.; Michaels, Helen J.; Chase, Mark W.; Manhart, James R. (1988). "Chloroplast DNA Variation and Plant Phylogeny". Annals of the Missouri Botanical Garden. 75 (4): 1180. doi:10.2307/2399279. ISSN 0026-6493. JSTOR 2399279.
- ↑ Palmer, Jeffrey Donald (1982). Chloroplast DNA evolution : molecular and phylogenetic studies (PhD thesis). Stanford University. OCLC 38642864. ProQuest 303254176.
- ↑ Jeffrey D. Palmer publications indexed by the Scopus bibliographic database. (subscription required)
- ↑ Palmer, Jeffrey D.; Herbon, Laura A. (1988). "Plant mitochondrial DNA evolved rapidly in structure, but slowly in sequence" (PDF). Journal of Molecular Evolution . 28 (1–2): 87–97. Bibcode:1988JMolE..28...87P. doi:10.1007/BF02143500. hdl: 2027.42/48042 . ISSN 0022-2844. PMID 3148746. S2CID 2593930.
- 1 2 Keeling, Patrick J.; Palmer, Jeffrey D. (2008). "Horizontal gene transfer in eukaryotic evolution". Nature Reviews Genetics . 9 (8): 605–618. doi:10.1038/nrg2386. ISSN 1471-0056. PMID 18591983. S2CID 213613.
- ↑ "Jeffrey Palmer". Department of Biology.
- ↑ Richardson, Aaron O.; Palmer, Jeffrey D. (2007). "Horizontal Gene Transfer in Plants". Journal of Experimental Botany . 58 (1): 1–9. doi: 10.1093/jxb/erl148 . PMID 17030541.
- ↑ Bruns, Thomas Dickinson (1987). Molecular systematic studies of suillus and related taxa of the boletaceae using mitochondrial DNA (PhD thesis). University of Michigan. OCLC 68298947. ProQuest 303591973.(subscription required)
- ↑ "Thomas D. BRUNS". Our Environment at Berkeley.
- ↑ "Jeffrey Palmer". www.nasonline.org.
- ↑ "Overview: Membership". www.nasonline.org.
- ↑ "Academy Member Connection". www.amacad.org.
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