Biology Reference
In-Depth Information
indicates that these sequences have been conserved for
>
500 million years,
when invertebrates and vertebrates diverged.
Sequenced genomes often are searched for transposable elements. TEs are
ancient and are present in nearly all organisms, are very diverse, and may consti-
tute up to 80% of the genomic DNA. There are thousands of different TE families.
Identification and annotation of TEs found in genomes is a challenge due to this
diversity.
Wicker et al. (2007)
proposed a unified hierarchical classification system
based on the transposition method, sequence similarities, and structural relation-
ships.
Kapitonov and Jurka (2008)
also produced a database of eukaryotic repeti-
tive and TEs and called it Repbase. Repbase categorizes eukaryotic TEs as either
retrotransposons or DNA transposons and places them into five major classes:
long terminal repeat (LTR-retrotransposons, non-LTR retrotransposons, cut-and-
paste DNA transposons, rolling-circle DNA transposons (
Helitrons
), and self-syn-
thesizing DNA transposons (
Polintons
) (
Kapitonov and Jurka 2008
). Each class is
composed of superfamilies and each superfamily consists of numerous families.
7.9 DNA-Sequence Data Banks
DNA-sequence data banks are expanding rapidly and are important resources
for the research community. There are three major DNA sequence data-
bases: the DNA Data Bank of Japan (DDBJ), the European Molecular Biology
Laboratory Nucleotide Sequence Data Library (EMBL), and the GenBank Genetic
Sequence Data Bank (GenBank). Subsets of these databases have been orga-
nized. For example, there is a database of metazoan mitochondrial DNA
sequences (
Lanave et al. 2000
), a eukaryotic promoter database (
Perier et al.
2000
), database of restriction enzymes and methylases (
Roberts and Macelis
2000
), a database for intron sequence and evolution (
Schisler and Palmer 2000
),
a database for homeo domains (
Banerjee-Basu et al. 2000
), and many others
(
Wheeler et al. 2000
). The InSatDb is microsatellite database of fully sequenced
insect genomes (
Archak et al. 2007
). The journal
Nucleic Acids Research
pub-
lishes an annual list of hundreds of online databases covering significant
aspects of molecular biology, many of which are interconnected or hyperlinked
(
Galperin and Fernandez-Suarez 2011
). VectorBase is a data resource for inverte-
brate vector genomics and includes the genomes of mosquitoes, ticks, body lice,
and other arthropod vectors of disease agents (
Lawson et al. 2009
). SilkDB is a
repository for silk moth genetic and genomic data (
Wang et al. 2005
). There is a
Hymenoptera genome database (
Munoz-Torres et al. 2011
), a butterfly database
(
Papanicolaou et al. 2008
), an aphid database (
Legeal et al. 2010
), and a locust
database (
Zongyuan et al. 2006
). No doubt others will be added as more arthro-
pod genome sequences are obtained.
