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Lecture 4:
The Genome The word and beyond
Course 485
Introduction to Genomics
AIMS
• Introduce the e origins of the words “genome” and “genomics”.
• Discuss the use and misuse of OME and OMIC terms.
• Introduce the general characteristics of viruses, prokaryotes, and eukaryotes.
• Highlight similarities and differences between different genomes
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COMMENTARY
'Ome Sweet 'Omics-- A Genealogical Treasury of Words By Joshua Lederberg and Alexa T. McCray
"So intricate and inscrutable a mystery is the origin of language that in 1866 the French Society of Linguistics formally banned further research on the subject."
--J. H. Dirckx, 1977. (Dx + Rx: A Physician's Guide to Medical Writing)
Genomics and Proteomics are the buzzwords of the dawning millennium. There is no counting of www.-ics.com and www.-ix.com sites to be found on the Web. That most of these terms, old and new, have been contrived as slogans to attract attention, does not diminish their likely substance, and they are embedded in the advancing edge of science and technology. Defying the French Linguists' caveat, we may yet ask, where do terms such as genome and genomics come from? What do the suffixes -ome and -omics, so abundant in today's vocabulary, signify?
The Oxford English Dictionary (OED) attributes genome to Hans Winkler, 1920; the full reference is his book Verbreitung und Ursache der Parthenogenesis im Pflanzen- und Tierreiche, (Verlag Fischer, Jena). At page 165, he writes (in rough translation): "I propose the expression Genom for the haploid chromosome set, which, together with the pertinent protoplasm, specifies the material foundations of the species ...." He discusses this in the context of hybrids that may comprise distinctive genomes from the respective parents, and are then heterogenomatisch. The term was used sporadically in the 1920s and 1930s--Theodosius Dobzhansky scorned it; he would have preferred a "non-committal expression like 'set of chromosomes.'" (1937--Genetics and the Origin of Species)
The OED also offers an etymology, that Winkler's Genom is an irregular formation from gen + some--from chromosome--and this is recopied in many other sources. OED scholarship can rarely be contested, but it has to be challenged here: the story is more interesting, though it must be conjectural for want of specific documentary evidence from Winkler or his contemporaries. As a botanist, Winkler must have been familiar with a host of -ome words like biome, rhizome, phyllome, thallome, tracheome--all of which predated 1920. They share in common, the concept of -ome signifying the collectivity of the units in the stem. Thus rhizome is the entire root system, or modifications thereof. Any zoologist would have known coelome, or system of cavities. Hence, genome would be understood to be the collectivity--dare we say the genre--of the genes.
Genomics was introduced 24 years ago by Victor McKusick and Frank Ruddle, as the catchword for the new journal of that name they had just founded. It has the same narrower connotation today, of emphasis on linear gene mapping and DNA sequencing. Hence we also see flanking extensions like functional genomics and structural genomics, to widen the horizon of genomic studies to what resembles the overall medley of genetics of yesteryear, albeit with all the power of high technology.
Our favorite sources on scientific terminology include Roland W. Brown's Composition of Scientific Words, 1954 (but often reprinted), and W.E. Flood's Scientific Words, 1961. Brown offers: "-ome: < Gr, -oma, signifying condition, having the nature of." Brown also remarks how "words, when they make their debut in scientific or literary society ... should be simple, euphonious, pure and mnemonically attractive." Genome does qualify on all counts.
Flood says: "-ma Gk. ... produces a noun often expressing the result of a verbal action ...." Thus drama, panorama, plasma, edema, cinema. He also cautions that starting from sarcoma, the medical profession has co-opted the -oma suffix to signify an overgrowth or neoplasm of any specified tissue.
http://genomebiology.com/2002/3/7/comment/1010.1
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CommentNo place like Ome!"#$%"&'(')#*+,%
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Published: 26 June 2002
Genome Biology 2002, 3(7):comment1010.1–1010.2
The electronic version of this article is the complete one and can befound online at http://genomebiology.com/2002/3/7/comment/1010
© BioMed Central Ltd (Print ISSN 1465-6906; Online ISSN 1465-6914)
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What is a gene, post-ENCODE?History and updated definitionMark B. Gerstein,1,2,3,9 Can Bruce,2,4 Joel S. Rozowsky,2 Deyou Zheng,2 Jiang Du,3
Jan O. Korbel,2,5 Olof Emanuelsson,6 Zhengdong D. Zhang,2 Sherman Weissman,7
and Michael Snyder2,8
1Program in Computational Biology & Bioinformatics, Yale University, New Haven, Connecticut 06511, USA; 2MolecularBiophysics & Biochemistry Department, Yale University, New Haven, Connecticut 06511, USA; 3Computer Science Department,Yale University, New Haven, Connecticut 06511, USA; 4Center for Medical Informatics, Yale University, New Haven, Connecticut06511, USA; 5European Molecular Biology Laboratory, 69117 Heidelberg, Germany; 6Stockholm Bioinformatics Center, AlbanovaUniversity Center, Stockholm University, SE-10691 Stockholm, Sweden; 7Genetics Department, Yale University, New Haven,Connecticut 06511, USA; 8Molecular, Cellular, & Developmental Biology Department, Yale University, New Haven, Connecticut06511, USA
While sequencing of the human genome surprised us with how many protein-coding genes there are, it did notfundamentally change our perspective on what a gene is. In contrast, the complex patterns of dispersed regulationand pervasive transcription uncovered by the ENCODE project, together with non-genic conservation and theabundance of noncoding RNA genes, have challenged the notion of the gene. To illustrate this, we review theevolution of operational definitions of a gene over the past century—from the abstract elements of heredity ofMendel and Morgan to the present-day ORFs enumerated in the sequence databanks. We then summarize thecurrent ENCODE findings and provide a computational metaphor for the complexity. Finally, we propose a tentativeupdate to the definition of a gene: A gene is a union of genomic sequences encoding a coherent set of potentiallyoverlapping functional products. Our definition sidesteps the complexities of regulation and transcription byremoving the former altogether from the definition and arguing that final, functional gene products (rather thanintermediate transcripts) should be used to group together entities associated with a single gene. It also manifestshow integral the concept of biological function is in defining genes.
IntroductionThe classical view of a gene as a discrete element in thegenome has been shaken by ENCODE
The ENCODE consortium recently completed its characterizationof 1% of the human genome by various high-throughput experi-mental and computational techniques designed to characterizefunctional elements (The ENCODE Project Consortium 2007).This project represents a major milestone in the characterizationof the human genome, and the current findings show a strikingpicture of complex molecular activity. While the landmark hu-man genome sequencing surprised many with the small number(relative to simpler organisms) of protein-coding genes that se-quence annotators could identify (∼21,000, according to the lat-est estimate [see www.ensembl.org]), ENCODE highlighted thenumber and complexity of the RNA transcripts that the genomeproduces. In this regard, ENCODE has changed our view of “whatis a gene” considerably more than the sequencing of the Hae-mophilus influenza and human genomes did (Fleisch-mann et al. 1995; Lander et al. 2001; Venter et al. 2001). Thediscrepancy between our previous protein-centric view of thegene and one that is revealed by the extensive transcriptionalactivity of the genome prompts us to reconsider now what a geneis. Here, we review how the concept of the gene has changed over
the past century, summarize the current thinking based on thelatest ENCODE findings, and propose a new updated gene defi-nition that takes these findings into account.
History of the gene, 1860 to just before ENCODE
Definition 1860s–1900s: Gene as a discrete unit of heredity
The concept of the “gene” has evolved and become more com-plex since it was first proposed (see timeline in Fig. 1, accom-panying poster). There are various definitions of the term, al-though common initial descriptions include the ability to deter-mine a particular characteristic of an organism and the heritabil-ity of this characteristic. In particular, the word gene was first usedby Wilhelm Johannsen in 1909, based on the concept developedby Gregor Mendel in 1866 (Mendel 1866). The word was a de-rivative of pangene, which was used by Hugo De Vries for entitiesinvolved in pangenesis, Darwin’s hypothetical mechanism of he-redity (Heimans 1962). Johnannsen called a gene the “specialconditions, foundations and determiners which are pres-ent [in the gametes] in unique, separate and thereby indepen-dent ways [by which] many characteristics of the organism arespecified” (Johannsen 1909, p. 124). The etymology of the termderives from the Greek genesis (“birth”) or genos (“origin”). Therelated word genetics was used by the geneticist William Batesonin 1905 (http://www.jic.ac.uk/corporate/about/bateson.htm).
Mendel showed that when breeding plants, some traits suchas height or flower color do not appear blended in their off-
9Corresponding author.E-mail [email protected]; fax (360) 838-7861.Article is online at http://www.genome.org/cgi/doi/10.1101/gr.6339607.Freely available online through the Genome Research Open Access option.
Perspective
17:669–681 ©2007 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/07; www.genome.org Genome Research 669www.genome.org
Cold Spring Harbor Laboratory Press on September 1, 2015 - Published by genome.cshlp.orgDownloaded from
Few references on the origins of the words “genome” and “genomics” and some implications
Beer, Bethesda, and Biology: How "Genomics" Came Into Being
Over the last decade, molecular ge-netics has spun off a lexicon of new words that scientists, including cancer researchers, now use to describe their work. One word that has become stan-dard fare at many cancer meetings is "genomics," meaning the study and comparison of genomes across species.
Where did the word genomics come from? It is the brainchild of Thomas H. Roderick, Ph.D., a geneticist at the Jackson Laboratory, Bar Harbor, Maine, who dreamed up the word in 1986 as the name of the then yet-to-be-published journal Genomics. In a recent inter-view, Roderick tells the News the story behind the word.
News: How did you come up with the word genomics?
Roderick: In 1986, I attended a good-sized international meeting in Bethesda to discuss the feasibility of mapping the entire human ge-nome. The meeting had adjourned for the day, and Frank Ruddle, Ph.D. [Yale University], and Vic-tor McKusick, M.D. [The Johns Hopkins University], convened a short submeeting involving about 50 people, including myself, to dis-cuss starting a new genome-ori-
Bethesda. It was called the McDonald's Raw Bar [which has since been tom down]. There might have been 10 of us that night who went there and sat around drinking beer- actually a lot of beer. It was great fun.
We kept moving on the name. Some of us really wanted to name the journal, Genome. But the Canadian Journal of Genetics and Cytology had already announced their intention to change its name to "Genome," with their first issue to appear in 1987, about the time the new journal ofMcKusick and Ruddle was supposed to appear. Several names were considered using "Genome" as
ented scientific journal. The jour- Dr. Thomas H. Roderick nal was to be a place to include se-quencing data and as well to include dis-covery of new genes, gene mapping, and new genetic technologies. At the end of the meeting, Frank and Victor charged us to come up with a name for the new journal.
It now was late in the evening. A few of us went out to a recommended bar near one of those big office buildings in
part of the title, but it was agreed they all were too cumbersome.
So, we sat around and talked. We were into our second or third pitcher, when I proposed the word "genomics." I don't know exactly how I came up with the word. I'm a geneticist, and it cer-tainly isn't far from the word "genetics." I've heard the word "genetics" since I
Journal of the National Cancer Institute, Vol. 90, No.2, January 21, 1998
was in high school, so it must have played a part in the name. In fact, I'm sure it did.
I said the word to Frank Ruddle. Frank recognized it as a name that en-compassed what we wanted to do. It wasn't just the objectives of the journal. It was GE-NOM-ICS. It was an activity, a new way of thinking about biology.
We adjourned that evening thinking genomics wasn't a bad name. But I didn't hear any more about it until Vic-tor and Frank decided that was what they wanted to name the journal. Frank told me later that Victor had done some scholarly study of the word to be certain it was etymologically appropriate.
News: When you proposed the term genomics, what was the defini-tion that was in your mind?
Roderick: Well, it certainly encom-passed what the journal wanted to cover. It encompassed se-quencing, mapping, and new technologies. But we felt it also had the comparative aspect of genomes of various species, their evolution, and how they related to each other. Although we didn't come up with the term "functional genomics," we thought of the genome as a functioning whole beyond just single genes or sequences spread around a chromosome.
News: Did you ever think when you left the raw bar in Bethesda that this name would
become such a big part of biology? Roderick: No. Victor and Frank
thought their proposed journal had an important set of objectives defining a specific timely mission. I thought we had a tentative name for a journal be-yond just sequencing and mapping.
-BobKuska
NEWS 93
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COMMENTARY Open Access
Badomics words and the power and peril ofthe ome-memeJonathan A Eisen1,2,3,4,5*
Abstract
Languages and cultures, like organisms, are constantly evolving. Words, like genes, can come and go – spreadingaround or going extinct. Here I discuss the spread of one small subset of words that are meant to convey“comprehensiveness” in some way: the “omes” and other words derived from “genome” or “genomics.” I focus on abad aspect of this spread the use of what I refer to as “badomics” words. I discuss why these should be consideredbad and how to distinguish badomics words from good ones.
Keywords: Genomics, Language, Memes, Omics, Badomics, Genome, Ome-ome, Language parasites
Main textThe rise of genome (the word)In 1920, “Verbreitung und Ursache der Parthenogenesisim Pflanzen- und Tierreiche”–a landmark book byGerman botanist Hans Winkler–was published [1]. Trans-lating the title into English yields “Spread and cause ofpathogenesis in plant and animal kingdoms”. An interest-ing book, no doubt (and one that is available to read on-line thanks to the Biodiversity Heritage Library [2]), but itis not a fascination with pathogenesis that has kept thebook in the limelight for almost 100 years. Instead, it isone passage on page 165 that is critical:
Ich schlage vor, für den haploidenChromosomensatz, der im Verein mit demzugehörigen Protoplasma die materielle Grundlageder systematischen Einheit darstellt den Ausdruck:das Genom zu verwenden und Kerne, Zellen undOrganismen, in denen ein gleichartiges Genom mehrals einmal in jedem Kern vorhanden ist,homogenomatisch zu nennen, solche dagegen, dieverschiedenartige Genome im Kern führen,heterogenomatisch.
For those not up on their German, the beginning hasbeen translated into English by Joshua Lederberg andAlexa McCray [3]:
I propose the expression Genom for the haploidchromosome set, which, together with the pertinentprotoplasm, specifies the material foundations of thespecies.
In other words, this was the birth of the term “genome”.
The spread of the ome-memeIf Winkler were alive today, he would be amazed and whathis simple coinage has become. Genomes and “genomics”(the study of genomes)–the concepts and the words–areeverywhere and have even spread widely into popular cul-ture. A side effect of this spread has been the proliferationof genomic terminology. In this issue of GigaScience,McDonald et al. [4] track one aspect of this spread in theemergence of new “ome” words. They describe the collec-tion of omics terms as the “ome-ome”. The main point oftheir analysis of the ome-ome is that, well, omics is every-where. And they use this as evidence for the need to de-velop more standards for, in essence, communicationamong the different omes (or, well, the tools that deal withthe different omes).The increasing size of the ome-ome suggests (to me at
least) that the drive to add “ome” or some variant of it tojust about anything is a meme (a spreading culturalpractice). Documenting and studying the spread of theome-meme has become an academic exercise of sorts.And, as with any academic area, they are different camps.Some have approached their analyses in a reserved–perhapseven objective–manner [3]. Yet others have seemed to bealmost cheering on the ominess (e.g., [5]). But the majorityhave been, well, less impressed (e.g., [6-9]).
Correspondence: [email protected] Center, University of California, Davis, CA, USA2Department of Evolution and Ecology, University of California, Davis, CA, USAFull list of author information is available at the end of the article
© 2012 Eisen; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative CommonsAttribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction inany medium, provided the original work is properly cited.
Eisen GigaScience 2012, 1:6http://www.gigasciencejournal.com/content/1/1/6
P E R S P E C T I V E S
Journal of Biomolecular Techniques18:277 © 2007 ABRF
FRAB
JOURNAL OF BIOMOLECULAR TECHNIQUES, VOLUME 18, ISSUE 5, DECEMBER 2007 277
These days omics is an au courant buzz word in life sci-ences, and my recent visit on Google.com listed 829 words with omics. The suffix -omics is used frequently
to describe something big, and refers to a field of study in life sciences that focuses on large-scale data/information to understand life summed up in “omes” and “omics” such as proteomics, genomics, metabolomics, etc. It is indeed inter-esting to discern that there is little history of how genomics and proteomics came into being, which started the era of omics.
The word genomics was first coined by Dr. Thomas H. Roderick, a geneticist at the Jackson Laboratory, Bar Harbor, ME, in 1986. During an international meeting in Bethesda on the feasibility of mapping the entire human genome, Frank Ruddle (Yale University), Victor McKusick (The Johns Hopkins University), and Tom Roderick (with some other colleagues) convened a short sub-meeting. They went to McDonald’s Raw Bar (which has now been torn down) to discuss starting a new journal. After a bit of beer that evening, the discussion led to a name for the yet-to-be-published journal, and Tom Roderick proposed the word genomics.1 The journal is now known as Genomics.
The word genome is believed to have a different origin. In an earlier commentary, Lederberg and McCray reported that Oxford English Dictionary attributes genome to Hans Win-kler.2 In the book Verbreitung und Ursache Der Parthenogenesis im Pflanzen- und Tierreiche, Winkler in 1920 used the word Genom in the context of haploid chromosome set. Anyway, the origin of chromosome is from the Greek stem. As we now know, genome refers to the complete genetic makeup of an organism; hence some scholars have made the inference that there exists some root, ome, of Greek origin, referring to wholeness or to completion, but no such root is known to exist in the literature. Lastly, many scholars in science believe that the suffix -ome has been derived from genome, a word which formed in parallel with chromosome.
Downstream of genomics, the word proteomics was first proposed much later by Marc Wilkins in 1995, to describe an entire organism’s protein complement. Marc at that time was a Ph.D. student in Keith Williams’s labo-ratory at Macquarie University in Sydney, Australia. The word proteomics arose out of Williams’s idea to screen and determine all the proteins produced by the DNA of an organism, rather than using the more conventional approach of sequencing DNA in order to determine the genes that produce proteins.2 Marc Wilkins first used the word proteomics as an alternative to the phrase “the protein complement of the genome.”
The other twist to “omics” may be associated with the “Om” (pronounced “Aum”), an ancient Sanskrit intona-tion, which, like music, transcends the barriers of age, race, culture, and even species. It is made up of three Sanskrit letters, aa, au, and ma, which, when combined together, make the sound “Aum” or “Om,” which signifies fullness, as in a divinity that encompasses the entire universe in its unlimitnedness. It is believed to be the basic sound of the world and to contain all other sounds, and is a mantra in itself. If repeated with the correct intonation, it can reso-nate throughout the body, so that the sound penetrates to the center of one’s being, the atman or soul. There is harmony, peace, and bliss in this simple but deeply philo-sophical sound.
Finally, there is now a word omicist—a scientist who studies omeomics, cataloging all the “omics” subfields, such as genomics, proteomics, and interactomics.
So we keep repeating “omics” mantras like metabolo-mics, metabonomics, metallomics, lipidomics, interactom-ics, transcriptomics, spliceomics, neuromics, physiomics, predictomics, and so on …
REFERENCESKuska B. Beer, Bethesda, and biology: How “genomics” came into
being. J Natl Cancer Inst 1998;90(2):93.Lederberg J, McCray AT. ’Ome Sweet ’Omics—A geneological Trea-
sure of words. Scientist 2001;15(7):8.Swinbanks D. Government backs proteome proposal. Nature
1995;378(6558):653.
The Wholeness in Suffix -omics, -omes, and the Word Om
Satya P. Yadav
Molecular Biotechnolog y Core Laboratory, The Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio
ADDRESS CORRESPONDENCE AND REPRINT REQUESTS TO: Satya P. Yadav, Molecular Biotechnology Core Laboratory, The Lerner Research Institute, Cleveland Clinic Foundation, Mail Code: FFb-12, 9500 Euclid Avenue, Cleveland, OH 44195 (phone: 216-445-7095; fax: 216-444-2998; email: [email protected]).
Few references on the origins of the words “genome” and “genomics” and some implications
The genome
• The word “genome” was first proposed by a the German botanist Hans Winckler (1920).
• He wrote:
“ I propose the word Genom for the haploid chromosome set, which, together with the
pertinent protoplasm, specifies the material foundation of the species”.
What inspired creating such a word?
The genome
• Combining gene + chromosome?
• Influenced by botany related terms such as rhizome (the entire root system)?
• Other more poetic explanations??
What is the genome?
Entire genetic material that make a species
• The word “genome” open the floodgates for thousands of OMEs!!!
OMEs are everywhere
Finally, a Sanskrit-speaking friend offers that "-OM signifies fullness, completeness as in divinity ..., it encompasses the entire universe in its unlimitedness." Ωµ, with its endless intonation, is then redolent with the Ω, the greatest and the very last character in the Greek alphabet. What could resonate more with today's -ome terms!
In physics, probably starting with Faraday's ion, cation, anion, the -on suffix has tended to signify an elementary particle, later materially focused on the photon, electron, proton, meson, etc., whereas -ome in biology has the opposite intellectual function, of directing attention to a holistic abstraction, an eventual goal, of which only a few parts may be initially at hand. The accompanying table illustrates a number of prevailing examples. It includes Lederberg's own recent coinage of microbiome, to signify the ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share our body space and have been all but ignored as determinants of health and disease.
The very neolexical process evokes some provocative analogies: our individual minds interact to constitute human culture, which we can relabel as the noöome, to take a leaf from Teilhard de Chardin.
Joshua Lederberg is professor-emeritus and Sackler Foundation Scholar at The Rockefeller University. He chairs the Editorial Advisory Board of The Scientist. He has played the neological game himself with entries like plasmid, exobiology, euphenics, and prototroph. Eugram (for what is now called E-mail) never caught on. Alexa T. McCray is the director of the Lister Hill National Center for Biomedical Communications. She is a linguist by training and inclination.
antigenome bacteriome basidiome biome cardiome caulome chondriome cladome coelome epigenome erythrome genome geome hadrome histome
immunogenome immunome haptenome karyome leptome microbiome mnemome mycetome neurome odontome osteome pharmacogenome phenome phyllome physiome
plastidome plerome proteinome proteome psychome regulome rhabdome rhizome stereome thallome tracheome transcriptome trichome vacuome
Listed above we present a lexicome of terms, suffixed by -ome, extracted from the MEDLINE database, the OED, and the Web of Science. Our aim was to select terms using the -ome suffix in the sense of this article. For the most part this excludes the suffixes -tome, -stome, -some, -drome. Some terms are best known as the -omics derivative. Today, we should assume that further derivations are no longer from Greek or Sanskrit, that the -ome idea is borrowed from the multitude of terms already ensconced into English or the scientific lingua franca. Most of these terms are already in print; almost all should be self-revealing; a few are conjectural. Guess which of these -omes were made up only just now; even for these, there may well be an -omics.com to match. The Scientist 15[7]:8, Apr. 2, 2001
Some of our OMEsSome times it seems anything can be OMEfied
What do you think about the OMEs you have encountered so far in your career?
Useful/useless?
Meaningful/meaningless?
Do you have an OME word in your mind?
Genomics
• Thomas H. Roderick (and others) in 1986 came up with the word “genomics”.
• The word was chosen as a name for a new journal.
• Became a buzzword and very cool.
• Tons of OMICS out there.
What is genomics?
genomics |jēˈnōmiks, -ˈnäm-, | pl.noun [ treated as sing. ] Biology the branch of molecular biology concerned with the structure, function, evolution, and mapping of genomes. ORIGIN 1980s: from genome‘the complete set of genes present in an organism’ + -ics.
Genome organization & representation
How is the genetic code organized?
Thousands/ millions/ billions of nucleotide basepairs
How are they organized into a genome?
Genome organization
Genome organization differ depending on:
• Genome chemical identity?
• Genome size
• Genome physical architecture
• Number of genome units
• Genome copy number
• taxonomic group (evolutionary history)
Genome chemical identity
The majority of life forms have a genetic material in the form of double stranded (ds)
DNA.
Which organisms exhibit variation in the identity of their genomes?
Genome chemical identity
Viruses have genomes in the form of:
• Single stranded DNA • Single stranded RNA • Double stranded DNA • Double stranded RNA
The simplicity of lower taxa is reflected in the genome size
BUT
in eukaryotes, the size of the genome is not related to organisms complexity
Genome size
Genome physical architecture
The genome physical architecture can be arranged in:
• Linear unit(s) • Circular unit(s)
What is the advantage and disadvantages of having a circular genome?
What are the advantages and disadvantages of having a linear genome?
Genome physical architecture
Genome physical architecture
Circular chromosomes:
• No ends (telomeres) • No fear of telomere
shortening • No need for end
protection. • Suitable for
reproduction by cell division.
Genome physical architecture
Linear chromosomes:
• Ends (telomeres) • Telomere shortening • Meiosis?
Genome physical architectureThe genome physical architecture can be
arranged in:
• One unit (a single chromosome) • Multiple units (multiple chromosomes)
Genome physical architectureBigger genomes are usually organized into
multiple chromosomes
What is the advantage and disadvantages of having a single unit (chromosomes) genome?
What is the advantage and disadvantages of having multiple units (chromosomes) genome?
Genome physical architecture
Genome physical architecture
• The number of copies of the genome within cells varies across taxa.
• What is the advantage of having multiple copies of the genome?
Genomes across taxa
Genomes evolved through time and genome organization evolved as well.
Genome organization
Why organizing the genome?
location location location! Space?
How can the genetic code in a small space?
Genome organization
The characteristics of the genomes of different life forms
Viruses Prokaryotes Eukaryotes
Viral genomes
• Genome can be: 1. single stranded DNA. 2. double stranded DNA. 3. single stranded RNA. 4. double stranded RNA.
• Genome can be linear or circular.
Viral genomes• One molecule or segmented genome (many pieces).
• Viruses with RNA genome are called retroviruses!
• Genome size 2 thousand basepairs (2Kb) – 2 million basepairs (2 Mb).
• No special organization of the genome.
Viral genomes
Gago S et. al., (2009). Extremely high mutation rate of a hammerhead viroid. Science 323 (5919):1308
Prokaryotic genomes
• Most genomes are: 1. Single molecule (some multiple). 2. One circular chromosome (some linear). 3. Double stranded DNA. 4. Some have small additional circular DNA that can replicate independently (plasmid).
• Genome is organized in a structure called (Nucleoid).
Prokaryotic genomes
Prokaryotic genomes organization
What are plasmids?
How big they are compared to the chromosome?
Are they independent or dependent on the chromosome?
How many copies in a single bacterium?
Eukaryotic genomes
Where is the eukaryotic genome located?
Eukaryotic genomes
Nuclear genome, mitochondrial genome, chloroplast genome
Mitochondrial genomeThe mitochondria has its own genetic material
What is the function of the mitochondria?
How many copies of the genetic material a mitochondria has?
Mitochondrial genome• The mitochondrial
genome is a small circular one.
• Genome organization is similar to prokaryotic genomes.
• Notice the number of genes in the mitochondrial genome and their functions
Chloroplast genomeChloroplast has its own genetic material
What is the function of the chloroplast?
How many copies of the genetic material a chloroplast has?
Chloroplast genome
• The chloroplast genome is a small circular one genome.
• Genome organization is similar to prokaryotic genomes.
Why the mitochondria and chloroplast have similar genomes to prokaryotes?
Endosymbiosis
The mitochondrial and chloroplast are a result of an endosymbiotic relationships between various prokaryotic cells.
Aerobic proteobacterium Cyanobacterium
How is the mitochondrial genome organized?
How is the chloroplast genome organized?
Do plants have mitochondrial genomes?
Nuclear genomeWhere is the nuclear genome located?
Nuclear genomes
• Characteristics eukaryotic nuclear genomes are:
1. Genome is a double stranded DNA.
2. Genome arranged in several linear packages called chromosomes through interactions with several proteins.
• The chromosomes in their most condensed form are called metaphase chromosomes.
• The entire genome represented by metaphase chromosomes is called karyotype.
• The number of sets of chromosomes in a given eukaryotic cell is referred to as the level of ploidy.
What is your level of ploidy?
Nuclear genomes
The genome packaged into chromosomes
Karyotype
The genome packaged into chromosomes
Eukaryotic nuclear chromosomes are linear with different chromosome copy numbers
How is the nuclear genome organized and packaged?
Do you remember from last lecture?
Eukaryotic genome packaging
To think about
How can we start exploring genomes?
Can we study the whole thing at once?
Expectations
• You enjoy knowing some of the history of the words.
• You understand the general characteristics of viral, prokaryotic and eukaryotic genomes.
Disclaimer
Figures, photos, and graphs in my lectures are collected using google searches. I do not claim to have
personally produced the material (except for some). I do cite only articles or books used. I thank all owners of
the visual aid that I use and apologize for not citing each individual item. If anybody finds the inclusion of their material in my lectures a violation of their copy
rights, please contact me via email.
