Genome organization

Prokarotic genome

Chromsomes and Mobile genetic elements, smaller than eukaryotes and varies greatly

Types of Mobile genetic element (MGEs)

Plasmids, integrative/conjugative elements (ICEs), Integrons, Transposons, Prokaryote virus/virus like genomes

small prokaryotic genomes

indicative of host dependencies, obligate parasites, lack metabolic capacities

large prokaryotuc genoms

6-8mil bp, usually free living microbes

Prokaryotic chromosomes

condensed into ovoid structure (Nucleoid), nucleoid anchor to cell membrane, usually circular (linear cannot be super, can consist of replicons (multipartite), some have multiple chromosomes, most monoploid but some polyploid (exceptions)

prokaryotic monoploidy

actually 1.some because always replicating, Template and daughter already starting next replication before finishing

Mobile (selfish) gentic element

DNA replicates independent of host chromosome, encodes gene for self perpetuating, encodes other accessory function (selective advantage to keep)

Plasmids

dsDNA, usually circualr, extrachromosomal, self replicating, in pro and eukaryotes, oftern carry adaptive gene(gives fitness advantage), contribute to horizontal gene transfer, vary host range, varu compatibilty and copy number, some can integrate into genome (stably maintained)

Plasmid host range

some only with single species - host encoded recognition, some between domains - plasmid encoded recognition

Plasmid copy number

amount of plasmid copy in cell, depend amount of accessory proteins, low is 5 -10 and high is hundereds

Plasmid compatibilty

ability for different plasmid to be in same cell, closely related incompatibkle becasue same regulatory element/enzymes - competes

Integrative and conjugative element (ICE) /conjugative transposons

encodes conjugation machinery, integrate into host chromosomes, transferred as ss or ds DNA, oftern modular - group genes of similar function

Integrons

piece of DNA encoding an interfase, dsDNA when integrated, can co-opt/build gene cassettes as operons, location specific recombination (ATT sites need at both locations), Mobile within cell (genomic rearrangement), not mobile on its own (need plasmid or ICE)

Transposons

encodes transposase, flanked with inverted repeats, differnet families - Compound (IS element flank) and Non compund (gene inserted in IS)

Prokaryotic viruses and virus like elements

no conserved/shared genes, diverse (2-10 per organsim) but poor understanding, RNA virus underexplored (DNA sampling), lambda phage intergrated but P1 phage exist - both cause phenotypic change

Borrelia burgdorferi (atypical prokayotic example)

0.9Mbp, linear genome, mulitple linear an dcircular plasmids, can have phages, usually polyploid

Eukaryotic genomes

more complex/less standard, organelles with own genomes, eukaryotic MGEs (virus and virus like element)

Eukaryotic genome components

nuclear genome (chromosomes) + organellar genome + MGEs + sometimes plasmids

Chromosome number

differe drastically, not associated with complexity

Primary endosymbiosis

early Asgardarchaeon in clos association (syntrophy) with early alphaproteobacterium, genomes look similar to thos organsim which they were derived

Mitochondria

derived alphaproteobacterium (rickettsiale), underwhen genome reduction (ony kept specialized genes), genes transferred to protoeukaryote nuclear genome (GC content and codon bias), usually single circular dsDNA, need precursors encoded on nuclear genome (piece of core machinery), 15-60Kbp

Chloroplast

derived cyanobacterium, underwhen genome reduction (only kept specialized genes), single circular dsDNA, need precursor encoded on nuclear genome (piece of core machinery), 120-130 genes (photosyntehes, transcription, translation), 110-220Kbp

Eukaryotic plsamids

mainly lower eukaryotes (fungi and algae) and higher plants, origins unclear, some derived from prokaryotic plasmids, often in organellar genomes

Eukaryotic virus

6 realm established only no Adnaviria

Marchantia polymorpha

8 autosome and 1 allosome, Mitochondrial and chloroplast genome, can house plasmid for transformation