Genomes and Evolution
Chromosomes (History)
First detected by Wilhelm Hofmeister in 1848 during his studies of plant cell nuclei.
Anton Schneider, in 1873, observed the involvement of the “chromatic nuclear figure” (later identified as chromosomes) during mitosis in animal cells.
The chromosome theory of inheritance was proposed by Weismann in 1887, suggesting that chromosomes carry hereditary information.
The term “chromosome” was introduced by Waldeyer in 1888 to describe these structures.
Chromosome Parts
Telomeres: Ends of chromosomes.
These contain telomeric repetitive DNA sequences, which are not completely replicated in somatic cells, leading to cellular ageing and senescence. They protect the ends of chromosomes from degradation and fusion with neighboring chromosomes.
p-arm: Short arm of a chromosome.
The length and characteristics of the p-arm can vary between chromosomes and can be used in chromosome identification.
q-arm: Long arm of a chromosome.
Similar to the p-arm, the q-arm's features are important for chromosome identification and analysis.
Centromere: Chromosome locus where kinetochore fibers bind to chromatids, allowing for correct chromatid segregation in daughter cells.
It contains α-satellite DNA, which is crucial for centromere function and kinetochore assembly. The centromere ensures each daughter cell receives the correct number of chromosomes during cell division.
C-value paradox
Only ilda 1.5% of chromosomal material encodes proteins.
Whole-genome duplications can account for this, leading to an increase in non-coding DNA.
The C-value paradox refers to the observation that genome size does not correlate with organismal complexity. Some organisms with smaller genomes can be more complex than those with larger genomes due to differences in gene regulation, non-coding DNA functions, and other factors.
Chromosome Content
Genes: Protein-coding sequences that determine specific traits.
Repetitive DNA: Includes tandem repeats and interspersed repeats, contributing to genome size and structural organization.
Tandem repeats: Sequences repeated one after another (e.g., satellite DNA).
Interspersed repeats: Dispersed throughout the genome (e.g., SINEs and LINEs).
Regulatory DNA sequences: Control gene expression, including promoters, enhancers, and silencers.
Gene Structure
Prokaryotes: Simpler gene structure.
Operator: Region where repressor proteins bind to regulate transcription.
-10 Sequence (Pribnow box): A promoter sequence that facilitates RNA polymerase binding.
-35 Sequence: Another promoter sequence that helps in RNA polymerase recognition.
Flanking region: Adjacent sequences to the gene that may contain regulatory elements.
Spacer: Non-coding sequence between the -10 and -35 sequences.
Eukaryotes: More complex gene structure with introns and exons.
Flanking region: Contains various regulatory elements.
Exons (I, II, III): Protein-coding regions of the gene.
Introns (I, II): Non-coding regions that are spliced out during RNA processing.
GC Box: A regulatory sequence found in the promoter region.
GT/AG: Splicing signals at the intron-exon boundaries.
CAAT Box: Another regulatory sequence in the promoter region.
TATA Box: A core promoter sequence that determines the transcription start site.
Poly (A) tail: A sequence added to the 3' end of the mRNA to increase stability.
AATAA Box: Signal for the addition of the poly(A) tail.
Alternative Splicing
Alternative splicing is a process by which a single gene can code for multiple proteins by selectively including or excluding different exons. This increases the diversity of proteins that can be produced from a limited number of genes.
Genomes and Phenotypes
Genotype (DNA) -> Genome -> Genomics: Study of the entire DNA content of an organism.
RNA -> Transcriptome -> Transcriptomics: Study of all RNA molecules in a cell.
Protein -> Proteome -> Proteomics: Study of all proteins in a cell.
Metabolite -> Metabolome -> Metabolomics: Study of all small molecules in a cell.
Genes in Mammals
About 90% of genes are present (have orthologs) in all mammals, indicating a conserved core set of genes essential for mammalian biology.
Human and chimp share 99% of genes, highlighting close genetic similarity.
Phenotypic differences are due to the 1% difference, as well as variations in gene regulation and expression.
Genes could be duplicated, deleted, or heavily mutated, leading to phenotypic diversity.
Expansion of the β-defensin Cluster
Gene family Beta-defensin: An example of gene family expansion.
Cattle: 106 beta-defensin genes.
Human: 39 beta-defensin genes.
Mouse: 52 beta-defensin genes.
Interspersed DNA Repeats
Interspersed repeats do not form tandemly repeated blocks; instead, they are scattered throughout the genome.
They intermingle with other sequences, making up a significant part of the genome ( ilda 45% of the human genome, >50% in maize).
They are either transposable elements (e.g., LINEs, SINEs) or sequences derived from transposable elements. These elements can move around the genome and create copies of themselves.
Can copy and move genes, influencing genome evolution and gene expression.
Regulatory DNA Sequences
By location:
cis (close): Regulatory sequences located near the gene they control.
trans (on a different chromosome): Regulatory sequences located far from the gene they control, often encoding transcription factors.
By function:
enhancers: Increase gene expression.
silencers: Decrease gene expression.
insulators: Block the effects of enhancers or silencers, creating independent regulatory domains.
By conservation:
conserved: Regulatory sequences that are similar across different species, suggesting important functions.
non-conserved: Regulatory sequences unique to specific species, possibly involved in species-specific traits.
Ultra-Conserved (UC) Elements
481 elements that are conserved between human, fish, dog, and mice (Bejeranao et al., 2004). These elements often regulate genes involved in development and are critical for organismal function.
Genetic Marker
A genetic marker is a DNA sequence with a known location (physical or relative) on a chromosome. It is used to identify individuals or populations and to map genes.
The marker itself may be a part of a gene or may have no known function. Common types include SNPs, microsatellites, and RFLPs.
What is a Map?
A genetic (linkage) map is a representation of markers on a chromosome in linear order with distances between them expressed as percent of recombination (map units, centimorgans). It shows the relative positions of genetic markers based on recombination frequencies.
A physical map is a representation of physical positions of markers in a chromosome, usually measured in base pairs (bp), kilobases (kb), or megabases (Mb). It provides an absolute measure of distance along the chromosome.
Principles of Genetic Mapping
Genetic markers on the same chromosome are called 'syntenic' (on the same strand). They tend to be inherited together unless recombination occurs between them.
Synteny
Synteny: physical co-localisation of genes on the same chromosome in the same species. Conserved synteny refers to the preservation of gene order and content between different species, providing insights into genome evolution.
Principles of Genetic Mapping
To detect if markers are linked (syntenic) we should distinguish between maternal and paternal alleles of a genetic marker. Markers must be polymorphic in a mapping population, meaning they have different forms (alleles) that can be tracked.
Counting the number of offspring of different types and comparing them to the numbers assuming independent assortment using a chi-square test. This statistical test determines if the observed data significantly deviate from expected values under the null hypothesis of independent assortment.
A recombination frequency between two markers of 50% indicates independent assortment, meaning the genes are either on different chromosomes or far apart on the same chromosome.
Genetic (Linkage) Maps
Require special large mapping populations (>1000 individuals) to accurately estimate recombination frequencies.
Do not directly connect markers to chromosomes but instead create linkage groups, which are sets of markers that tend to be inherited together.
Genetic Maps
The distance between markers on a genetic map may not match physical distances on a chromosome due to variations in recombination rates along the chromosome. Regions with high recombination rates will appear farther apart on a genetic map compared to their physical distance.
It is often impossible to resolve the order of closely located markers (no recombination) because recombination events between them are too rare to be detected.
Genetic Mapping
Useful for detection of associations between markers and phenotypic traits within species. It helps identify regions of the genome that contribute to specific traits.
Not useful for comparative analysis between species because recombination frequencies can vary significantly between different species.
Linkage Maps for Agricultural Species
All are used to connect phenotypic traits to markers, which aids in marker-assisted selection and breeding.
Plants: Relatively easy to produce because construction of appropriate mapping populations is not a problem. Controlled crosses can generate large populations for mapping.
Animals: Construction of mapping populations is difficult and expensive. Until very recently, marker selection was complicated. Therefore, animal linkage maps often contain very few markers ( ilda 300 genome-wide), limiting their resolution.
Physical Maps
Cytogenetic maps: Based on chromosome banding patterns and in situ hybridization.
Genome sequences: Provide the most detailed physical map, with the exact order of nucleotides known.
Cytogenetic Maps
Detection position of known DNA fragment on a chromosome by in situ hybridization, which involves hybridizing a labeled DNA probe to chromosomes on a slide.
Commonly used variation Fluorescence In Situ Hybridization (FISH), which uses fluorescently labeled probes for detection.
FISH was first used to map genes in Drosophila (Langer-Safer et al, 1982), demonstrating its utility in chromosome mapping.
Genomic Diversity
Gene point mutation (change amino acids), leading to altered protein function.
Gene duplications/deletions (change number of copies), influencing gene dosage and expression.
Chromosomal rearrangements (regulation, copy numbers, etc), which can alter gene linkage and expression patterns.
Transposable (mobile) element activity (regulation, function), leading to insertions, deletions, and rearrangements in the genome.
Gene Mutations
Advantageous: Give a selective advantage and are passed on to offspring, increasing their frequency in the population.
Selectively Neutral Mutations: Have no effect and are kept; also known as Silent Mutations because they do not alter the amino acid sequence of the protein.
Deleterious: Harmful and result in the death of the cell or individual, normally prior to reproduction, thus decreasing their frequency in the population.
Gray-causing Mutation in Horses
Linkage (genetic) mapping to a 352 kb interval on chr 25, narrowing down the location of the mutation.
Genes: NR4A3, TXNDC4, INVS, STX17. These are candidate genes within the mapped interval.
PCR analysis detected a 4.6 kb insertion in intron no. 6 of STX17, identifying the causative mutation.
The duplication was detected in all Gray horses and in none of the non-Gray horses, confirming its association with the gray phenotype.
Regulatory mutation that affects expression of NR4A3 and STX17, indicating the insertion influences the expression of nearby genes.
White Coat Color in Dogs
Linkage mapping to a region containing the MITF gene (transcription factor), suggesting the involvement of this gene in pigmentation.
Two mutations were found:
Short Interspersed Repeat (SINE) insertion.
Variation in the MITF promoter, affecting gene expression.
Different combinations of the alleles lead to different phenotypes, demonstrating the complexity of genetic inheritance.
Chromosomal Rearrangements
Sulfites in Wine
keeps wine fresh, prevents oxidation, and inhibits microbial growth.
Longer shelf life, allowing wines to be stored and transported for extended periods.
Wines without sulfites must be stored at perfect conditions to prevent spoilage.
Comparison of Two Strains of Wine Yeasts
Reciprocal translocation, a type of chromosomal rearrangement where parts of two chromosomes are exchanged.
Adaptive Value of the Translocation in Yeasts
Enhanced expression of the gene enables wine yeast strains carrying the translocation to resist higher sulfite concentrations, providing a selective advantage in winemaking.
The Gene as a Unit of Heredity and Vector of Evolution
Genes are passed from one generation to another according to Mendelian principles. All offspring produced through sexual reproduction possess both differences and similarities to their parents, leading to genetic diversity.
Genetic changes that occur in populations and within species over time are the basis of evolution. Unlike individuals, populations continue over time, accumulating genetic changes.
Evolution of a species is dependent on changes in gene frequencies within or between populations over time. These changes can lead to adaptation to new environments.
Summary: One Health Relevance of Topics Discussed
Significance to animal health and welfare: Breeding out genetic conditions is important for livestock health, improving animal well-being and productivity.
Significance to public health:
The activity of mobile elements is the cause of some human genetic diseases, highlighting the importance of understanding their impact on the genome.
Screening human chromosomes and genomes for mutations is a basis for personal medicine, allowing for early detection and prevention of diseases.
Significance to environmental sustainability and ecosystem health: Genome sequencing of wild animals is used for conservation purposes, aiding in the management and protection of endangered species.