Nuclear Genome: C-Value and Genome Size

• Genomes are divided into different types.
  • Nuclear
  • Mitochondrion
  • Chloroplast
  • Endosymbionts/parasites/endophytic bacteria/etc.

Nuclear Genome

• C-value is the amount of DNA in a gamete.
• Genome size (bp) = (0.921 x 10^9) x DNA content (pg)
• The C-value enigma is that the amount of DNA does not always indicate complex organism.
• Genome sizes vary among diploid genomes
• Genome size and chromosome numbers for haploid cells vary from organism to organism
  • Yeast has a genome size of 12MB and a chromosome number of 16
  • Slime mold has a genome size of 70MB and a chromosome number of 7
  • Arabidopsis thaliana has a genome size of 125MB and a chromosome number of 5
  • Corn has a genome size of 5000MB and a chromosome number of 10
  • Onion has a genome size of 15000MB and a chromosome number of 8
  • Lily has a genome size of 50000MB and a chromosome number of 12
  • Nematode has a genome size of 97MB and a chromosome number of 6
  • Fruit fly has a genome size of 180Mb and a chromosome number of 4
  • Toad has a genome size of 3000MB and a chromosome number of 18
  • Lungfish has a genome size of 50000MB and a chromosome number of 17
  • Chicken has a genome size of 1200MB and a chromosome number of 39
  • Mouse has a genome size of 3000MB and a chromosome number of 20
  • Cow has a genome size of 3000MB and a chromosome number of 30
  • Dog has a genome size of 3000MB and a chromosome number of 39
  • Human has a genome size of 3000MB and a chromosome number of 23
• Plant genome size varies to extremes.
  • Paris japonica has 150,000 Mb
  • Genlisea margaretae has 63.4 Mb
• Extremely large genomes have been recorded, where the fern Tmesipteris oblanceolata has the largest genome recorded to date (2024).
  • The small fern, found only on a few Pacific islands, contains about 100 meters of DNA in every single cell.
  • Its genome is about 50x larger than the human genome (i.e 160.45 Gbp)
• There is a wide variety of genome sizes available in eukaryotes.
  • The genomes of T. oblanceolata are 50 times larger than the human genome.
  • Genome size variation among eukaryotes expands over 61,000-fold
• Chromosome numbers vary to extremes.
  • Slender goldenweed contains just 4 chromosomes
  • Adder’s-tongue fern contains 1262 chromosomes
• Ploidy is the sets of chromosome.
  • Basic number of chromosomes designated where 2n = 2x = 10
• Polyploidy results in more complex organisms.
  • Polyploidy is several sets of homeologous chromosomes.
  • Polyploidy = several sets of homologous chromosomes, e.g. bread wheat
• Redundancy and repetitiveness add to genome size and complexity.

Chloroplast Genome

• Chloroplast genome features include size, structure, and use in genetics and biotechnology.
• Circular, double-stranded, supercoiled DNA molecules
• cpDNA does not contain structural proteins
• GC content of cpDNA can differ greatly than nuclear and mtDNA, and can be separated from nuclear DNA via CsCl equilibrium density gradient centrifugation
• cpDNA is much larger than animal mtDNA, containing sizes from 80 – 600 kb
• cpDNA contains a significant portion of non coding DNA
• Number of copies of cpDNA vary between species
• Multiple copies occur per chloroplast, typically distributed among a number of nucleoid region.
• Universal genetic code is used in chloroplast protein synthesis

Mitochondrial Genome

• Mitochondrial genome features include size, structure, and use in genetics and medicine.
• Circular, double-stranded, supercoiled DNA molecules
• Linear mitochondrial genomes in some protozoa and fungi
• GC content of mtDNA differs greatly than nuclear DNA separated by cesium chloride (CsCI) equilibrium density gradient centrifugation
• No histones or similar proteins are associated with mtDNA
• Multiple genome copies within located multiple nucleoid regions
• Gene content is similar among mt genomes of different species.
• Mt genomes differ greatly in size
  • Human = ~16.5 kb
  • Yeast = ~80 kb
  • Plants = 100 kb – 2 Mb
• Main difference between plant, animal and fungal mt genomes: entire animal genome encodes for product while plant and fungal genomes also contain extra DNA that does not encode for products
• For some, genetic code differs from nuclear protein-coding genes
• Well-studied mtDNA disorders:
  • MERRF (myoclonic epilepsy with ragged red fibers) - multisystem disorder characterized by myoclonus (often the first symptom) and is followed by generalized epilepsy, ataxia, weakness, exercise intolerance, and dementia.
  • KSS (Kearns-Sayre syndrome) -progressive multisystem disorder defined by onset before age 20 years, pigmentary retinopathy, and progressive external ophthalmoplegia (PEO). Additional features include cerebellar ataxia, impaired intellect (intellectual disability, dementia, or both), sensorineural hearing loss, ptosis, oropharyngeal and esophageal dysfunction, exercise intolerance, muscle weakness, cardiac conduction block, and endocrinopathy.
  • Pearson syndrome is characterized by sideroblastic anemia and exocrine pancreas dysfunction and may be fatal in infancy without appropriate hematologic management
  • PEO (progressive external ophthalmoplegia) is characterized by ptosis, impaired eye movements due to paralysis of the extraocular muscles (ophthalmoplegia), oropharyngeal weakness, and variably severe proximal limb weakness with exercise intolerance
• Unlike nuclear DNA, which we inherit half from our mother and half from our father, mitochondrial DNA is passed on only by females.
  • When sperm fertilizes the egg, it leaves behind all its mitochondria: the developing fetus therefore inherits mitochondria only from the mother's egg.
• Human spermatozoa are devoid of intact mtDNA and lack mitochondrial transcription factor A (TFAM)
• TEAM (nucleoid protein) protect, maintain and transcribe mtDNA.
• During spermatogenesis, sperm cells express an isoform of TFAM, which retains the mitochondrial presequence, ordinarily removed upon mitochondrial import.
• Phosphorylation of the presequence prevents mitochondrial import and directs TFAM to the spermatozoon nucleus.
• TFAM relocalization from the mitochondria of spermatogonia to the spermatozoa nucleus directly correlates with the elimination of mtDNA, thereby explaining maternal inheritance in this species.
• mtDNA is widely applied to study human evolution because it is maternally inherited and nonrecombining.
• mtDNA - phylogenetic relationships between mt haplotypes correlates to maternal genealogical relationships
• mtDNA has a high mutation rate that that provides information on the most recent phase of human evolution over the past 150,000 years

Endosymbionts

• An endosymbiont or endobiont is any organism that lives within the body or cells of another organism, most often in a mutualistic relationship - Facultative - Hamiltonella defensa, Regiella insecticola, and Serratia symbiotica. - Obligate - Buchnera aphidicola
• Hemipterans are phloem feeders
• Phloem is a restricted diet
• Phloem is rich in sugars, but poor in amino acids
• Buchnera provide the aphid with essential amino acids
• Coevolution occurs when two or more species reciprocally affect each other's evolution through the process of natural selection (e.g. wheat and RWA)
• Progressive reduction in genome size leads to interdependency host.
• Buchnera aphidicola exhibit genome %GC content, genome total %GC content, genome size, and total gene content.
• Nuclear genes that transit a phenotype are encoded on chromosomes of both parents
• DNA is also passed down mitochondria and chloroplasts
• Mitochondrial and chloroplast genes usually show uniparental inheritance from generation to generation, i.e. all progeny (both male and female) have the phenotype of only one parent.
• In multicellular eukaryotes, the mother’s phenotype is expressed exclusively, a phenomenon called maternal inheritance.
• Maternal inheritance occurs because the amount of cytoplasm in the female greatly exceeds that in the male gamete. Therefore, the zygote receives most of the cytoplasm, containing the extranuclear genes, from the female and negligible from the male.