Genomics Exam #1 - Chp 2

C-value 

The DNA content of a single haploid nucleus

C-value enigma 

The more than sixty-thousand-fold variation in genome size across eukaryotes, with no correspondence to organismal complexity — and that the open question is which processes explain it 

G-value paradox 

The parallel failure of protein-coding gene number to track complexity 

Coding density 

The percentage of a genome that encodes protein 

Transposable element 

A DNA sequence that replicates or relocates itself within a genome 

DNA transposon vs. retrotransposon 

Cut-and-paste versus copy-and-paste through an RNA intermediate — and that only the second grows the genome 

LINE, SINE, LTR element 

The three retrotransposon classes, with the note that LINEs are autonomous and SINEs are not 

Polyploidy / whole-genome duplication 

Duplication of the entire gene complement, by hybridization or by failed chromosome separation 

Allopolyploid 

A polyploid formed by combining genomes from different species, as in bread wheat 

Genome streamlining 

Reduction driven by selection against the replicative cost of unnecessary DNA in very large populations 

Effective population size 

The population size that determines how strongly drift acts relative to selection

Muller's ratchet / drift-driven reduction 

Irreversible accumulation of slightly deleterious mutations in small, bottlenecked populations 

Junk DNA 

Sequence that is present but not maintained by selection — and that the term is contested 

Candidatus Carsonella ruddii (insect endosymbiont) 

• Genome Size:160 kb, 182 genes 

• Coding Density: ~95% 

• What it demonstrates: The far extreme of reduction; host dependence plus drift through transmission bottlenecks 

Prochlorococcus (ocean cyanobacterium) 

• Genome Size:~1.7 Mb 

• Coding Density:very high 

• What it demonstrates:Streamlining under enormous population size — though drift is also implicated 

Escherichia coli 

• Genome Size:4.6 Mb 

• Coding Density:~88% 

• What it demonstrates:The free-living bacterial baseline

Takifugu rubripes (pufferfish) 

• Genome Size: ~365 Mb, ~19,000 genes 

• Coding Density: high for a vertebrate 

• What it demonstrates: The same vertebrate gene set as humans in one-ninth the DNA 

Homo sapiens 

• Genome Size: 3.2 Gb, ~19,400 genes 

• Coding Density: ~1.5% 

• What it demonstrates: Ordinary in both size and gene count; ~46% transposable-element derived 

Caenorhabditis elegans 

• Genome Size: ~100 Mb, ~20,000 genes 

• Coding Density: moderate 

• What it demonstrates: The G-value paradox: human-like gene count, fewer than 1,000 somatic cells 

Triticum aestivum (bread wheat) 

• Genome Size: ~15 Gb, ~100,000 genes 

• Coding Density: low 

• What it demonstrates: The whole-genome-duplication route: an allohexaploid of three ancestral genomes 

Zea mays (maize) 

• Genome Size: ~2.3 Gb 

• Coding Density: low 

• What it demonstrates: ~85% repeat, mostly Gypsy and Copia LTR elements — a lineage-specific repeat flavor 

Lepidosiren paradoxa (South American lungfish) 

• Genome Size: ~91 Gb, ~31,000 genes 

• Coding Density: a tiny fraction 

• What it demonstrates: ~90% repeat from runaway LINE activity with weakened piRNA suppression 

Ambystoma mexicanum (axolotl) 

• Genome Size: ~32 Gb 

• Coding Density: very low 

• What it demonstrates: The nucleotypic effect made visible: large cells, slow development 

Allium cepa (onion) 

• Genome Size: ~16 Gb 

• Coding Density: low 

• What it demonstrates: Five times the human genome in a plant with no nervous system 

Tmesipteris oblanceolata (fork fern) 

• Genome Size: ~160 Gb 

• Coding Density: undetermined 

• What it demonstrates: The largest genome measured; no assembly exists, only a size measurement 

Birds and bats 

• Genome Size: under 2 Gb 

• Coding Density: relatively high 

• What it demonstrates: A metabolic ceiling on genome size in high-energy fliers