Chapter 21 - Genomes and Their Evolution

Scientists may examine complete sets of genes and their interactions now that the genomes of many animals have been fully sequenced, a technique known as genomics. Massive amounts of data have been created and continue to be generated by the sequencing efforts that feed this method.

The necessity to cope with this ever-increasing flow of information has given rise to the discipline of bioinformatics, which is concerned with the use of computational tools to store and interpret biological data.

The enormous diversity of life on Earth today might have resulted from the evolution of developmental processes.

• The term “whole-genome shotgun approach” refers to starting with the cloning and sequencing of DNA fragments from randomly cut DNA. Powerful computer programs then assemble the resulting very large number of overlapping short sequences into a single continuous sequence.

• In the approach, developed by J. Craig Venter and colleagues at Celera Genomics, random DNA fragments are cloned, as shown in the attached image sequenced and then ordered relative to each other.

These technical advancements have also allowed a method known as metagenomics (from the Greek meta, beyond), in which DNA from a whole population of species (a metagenome) is extracted and sequenced from an environmental sample.

Again, computer software separates incomplete sequences and assembles them into individual genomes.

The ability to sequence the DNA of mixed microbial populations is a benefit of this approach since it eliminates the need to cultivate each species individually in the lab, which has hampered the study of microorganisms. So far, this method has been used to study communities in settings as varied as the human gut and ancient soils.

The scientific breakthrough made possible by sequencing genomes and analyzing huge sets of genes have inspired scientists to do comparable systematic investigations of protein sets and their characteristics (such as abundance, chemical changes, and interactions), a method known as proteomics.

(A proteome is the whole collection of proteins expressed by a single cell or group of cells.) Proteins, not the genes that code for them, carry out the majority of the cell's functions. To understand how cells and organisms work, we must investigate when and where proteins are generated in an organism, as well as how they interact in networks.

One significant application of the systems biology method is the identification of gene and protein interaction networks.

For example, to map the protein interaction network in the yeast Saccharomyces cerevisiae, researchers utilized advanced methods to knock off pairs of genes one at a time, resulting in doubly mutant organisms. They next compared the fitness of each double mutant (depending on the size of the cell colony is created) to the fitness predicted by the fitness of the two single mutants.

The researchers reasoned that if the observed fitness matched the prediction, then the products of the two genes did not interact with each other, but if the observed fitness was more or less than the forecast, then the products of the two genes did interact.

Genomes differ in terms of size, the number of genes, and gene density. Thousands of genomes have been sequenced, with tens of thousands more in the works or deemed permanent drafts (since they would need more effort than it would be worth to complete them).

Approximately 3,400 metagenomes are among the sequencing in process. There are around 5,000 bacterium genomes and 242 archaeal genomes in the totally sequenced category. There are 283 finished eukaryotic species and 2,635 permanent drafts. Vertebrates, invertebrates, protists, fungi, and plants are among them. Following that, we'll go through everything we've learned about genome size, number of genes, and gene density, with a focus on general trends.

Only 1.5 percent of the human genome codes for proteins or produces rRNAs or tRNAs; the remainder is noncoding DNA, which includes pseudogenes and repetitive DNA with unclear functions. Transposable elements and associated sequences are the most common form of repetitive DNA in multicellular eukaryotes.

There are two forms of transposable elements in eukaryotes: transposons, which travel via a DNA intermediary, and retrotransposons, which are more common and move via an RNA intermediate.

Other types of repetitive DNA include short, noncoding sequences that are tandemly repeated thousands of times (simple sequence DNA, which includes STRs); these sequences are particularly abundant in centromeres and telomeres.

Genome comparisons between highly diverse and closely related species give significant information on ancient and recent evolutionary history, respectively. Analysis of single nucleotide polymorphisms (SNPs) and copy-number variations (CNVs) across individuals within a species can also offer insight on the species' evolution.

Homeotic genes and certain other genes linked with animal development have a homeobox region whose sequence is substantially conserved across numerous species.