chapter 9

What is whole-genome shotgun sequencing?

What is whole-genome shotgun sequencing?

It’s a sequencing approach involving high-quality, semi-automated sequencing from both ends of random DNA fragments. DNA is sheared, size-selected, and cloned into vectors, creating long and short inserts, which help in assembling overlapping sequences for the entire genome.

What are paired-end reads, and why are they essential?

Paired-end reads sequence from both ends of long inserts. This approach improves assembly efficiency as pairs have known spacing and orientation, which helps in reconstructing sequences containing repetitive elements.

What was significant about the sequencing infrastructure used by Celera?

Celera used powerful computing infrastructure with 4-processor SMPs and 16-processor NUMA machines, totaling around 20,000 CPU hours, to run its genome assembly operations.

What is the C-value paradox?

An observation that genome size does not correlate with organism complexity, as some less complex organisms have larger genomes than humans.

What are SNPs, and why are they significant in human genomics?

SNPs (Single Nucleotide Polymorphisms) are variations at a single nucleotide position in the genome. They play a key role in genetic diversity and can influence traits and disease susceptibility.

What is the Cot curve?

A method to analyze genome complexity by measuring DNA reassociation rates. More complex genomes reassociate slower due to unique sequences.

What is a transposable element?

A "jumping gene" that can move within the genome, potentially causing mutations or altering gene function.

What is the difference between LINEs and SINEs?

Long Interspersed Nuclear Elements (LINEs) are long repeated sequences with retrotransposition capability, while Short Interspersed Nuclear Elements (SINEs) are shorter and require LINEs for transposition.

What are YACs and BACs used for?

Yeast Artificial Chromosomes (YACs) and Bacterial Artificial Chromosomes (BACs) are used to clone large DNA fragments in genomic studies and sequencing.

Who discovered transposable elements?

Barbara McClintock discovered transposable elements, or "jumping genes," in the 1950s while studying corn.

What is the function of base excision repair?

It repairs DNA by removing damaged bases and replacing them, maintaining genome integrity.

What are molecular markers?

Markers like microsatellites or STRs (short tandem repeats) used to identify specific DNA sequences for mapping and genetic analysis.

What is spectral karyotyping (SKY)?

A technique using fluorescent dyes to visualize chromosomes in different colors, useful for identifying chromosomal abnormalities.

What is the Human Genome Project (HGP)?

An international effort begun in 1990 to sequence the entire human genome, which contains approximately 3.3 billion base pairs.

What is the purpose of DNA ligase in repair?

DNA ligase seals breaks in the DNA backbone, completing the repair of single-strand damage.

What is alternative splicing?

A process where a single gene can produce multiple protein products, increasing protein diversity in organisms.

What is a reference genome?

A previously sequenced genome used as a template for comparing newly sequenced genomes to accelerate assembly and analysis.

What is comparative genomics?

The study of comparing genomes across species to learn about evolutionary relationships and gene functions.

What are ESTs (Expressed Sequence Tags)?

Markers derived from cDNA sequences that identify gene-expressed regions in the genome, useful in locating genes.

What is the C0t curve used for?

Analyzing genome size and complexity by measuring the reassociation rates of DNA sequences in a given genome.

What are CpG islands?

Regions with a high frequency of CG dinucleotides, often found near gene promoters and involved in gene regulation.

What is the role of G-banding in genetics?

A chromosomal staining technique that divides chromosomes into bands, helping to identify structural changes.

What is a clone contig map?

A set of ordered, partially overlapping DNA clones covering a chromosome or genome segment, forming a basis for sequencing.

What is physical mapping?

Creating a map of genetic markers by directly analyzing genomic DNA, rather than through recombination, to determine the physical locations of genes.

What is the proteome?

The full set of proteins expressed by a genome, with vertebrates displaying greater complexity due to alternative splicing and unique protein motifs.

What is a genetic linkage map?

A map showing the positions of genes or markers based on recombination frequencies, used in studying inheritance and traits.

What is the function of a polyribosome?

A complex of multiple ribosomes translating the same mRNA, allowing simultaneous protein synthesis.

What is primer walking?

A sequencing technique where new primers are designed from each successive DNA sequence read, enabling systematic sequencing of long DNA fragments.

What is a restriction map?

A map showing the locations of restriction enzyme sites on DNA, used to analyze the physical structure of genomes.

What was the impact of automated sample preparation in sequencing?

Automation increased sequencing efficiency and reduced errors, enabling large-scale genomic projects like the Human Genome Project by streamlining sample handling and preparation.