Module 9: Bioinformatics and Genome Evolution

what are homologs?

Genes that descended from a common ancestral gene and constitute a gene family

what are paralogs?

genes that originated by a duplication event, and perform biologically distinct but biochemically related functions

what are orthologs?

genes in different species that are derived from a single ancestral gene in the two species’ last common ancestor, and often have equivalent functions

what is a structural annotation?

an annotation that identifies the location of genes and functional sequences

what is a functional annotation?

an annotation that describes the biochemical, cellular, and biological function of each gene product

what are the experimental approaches for genome annotation and why is it helpful?

comparing cDNA to a genomic sequence to identify transcribed sequences of a genome. It is helpful because it gives information on introns, exons, and splice sites.

what are some difficulties with genome annotation?

• hard when there is a lack of homology between known and unknown genes

• small genes/exons are hard to predict

• coding sequences are often broken into small exons that are dispersed over large distances

which types of sequences are more conserved between species: amino acid or nucleotide sequences?

amino acid sequences

how do conserved protein domains help with annotation?

they can provide insight into biochemical activities of proteins and their function

what are the two methods for identifying conserved noncoding sequences?

Phylogenetic footprinting and phylogenetic shadowing

what can phylogenetic footprinting identify?

conserved non-coding elements in dissimilar species

what can phylogenetic shadowing identify?

it can rule out non-conserved regions in groups of similar species in order to identify the conserved regions

what is shotgun sequencing?

fragments of target DNA are sequenced and overlaps are combined to determine the entire sequence

whole genome shotgun (WGS) sequencing benefits

requires no prior map, has good depth and coverage (30x-100x coverage)

examples of short read sequencing

Sanger, Illumina

example of long-read sequencing

Nanopore

characteristics of whole-genome sequencing

• sequencing the whole genome

• sequencing depth of over 30x

• can identify all kinds of variants (SNPs, INDELS, etc. )

• more than 1 000 000 variants

• most complete coverage

characteristics of whole-exome sequencing

• sequencing the whole exome

• sequencing depth of more than 50X-100X

• can identify all kinds of variants (SNPs, INDELS, etc. )

• ~ 30 000 variants

• info focused on the most understood part of the genome (exons)

depth vs coverage

depth: how many times a specific nucleotide is read

coverage: proportion of the genome sequenced

what is a benefit of long-read sequencing?

it is better with repeating elements in DNA

how does repetitive DNA affect shotgun sequencing?

dispersed repetitive elements can interfere with genome assembly, since they can map to multiple locations in the genome (making it hard to place exons)

how are reference genomes made?

highest-quality fully assembled DNA sequences are used, and individual genomes are compared to it

what are copy-number variants?

repeated sections of genome where each repeat is greater than 1 kb long (many are small but some can be hundred of kb), resulting in alterations of gene dosage

what is metagenomics?

WGS sequencing of DNA isolated from natural communities composed of a range of organisms, and can provide information on species diversity living in particular environments