https://www.cs.princeton.edu/~bee/courses/read/burge-jmb-1997.pdf

Prediction of Complete Gene Structures in Human Genomic DNA

Repbase Update is a comprehensive database of repetitive elements from diverse eukaryotic organisms. Currently, it contains over 3600 annotated sequences representing different families and subfamilies of repeats, many of which are unreported anywhere else. Each sequence is accompanied by a short description and references to the original contributors. Repbase Update includes Repbase Reports, an electronic journal publishing newly discovered transposable elements, and the Transposon Pub, a web-based browser of selected chromosomal maps of transposable elements. Sequences from Repbase Update are used to screen and annotate repetitive elements using programs such as Censor and RepeatMasker. Repbase Update is available on the worldwide web at http://www.girinst.org/Repbase_Update.html.

Repbase Update, a database of eukaryotic repetitive elements

Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

/pdf/the-tomato-genome-sequence-provides-insights-into-fleshy-7a55qpnrdm.pdf

The tomato genome sequence provides insights into fleshy fruit evolution

Our knowledge of the structure and composition of genomes is rapidly progressing in pace with their sequencing. The emerging data show that a significant portion of eukaryotic genomes is composed of transposable elements (TEs). Given the abundance and diversity of TEs and the speed at which large quantities of sequence data are emerging, identification and annotation of TEs presents a significant challenge. Here we propose the first unified hierarchical classification system, designed on the basis of the transposition mechanism, sequence similarities and structural relationships, that can be easily applied by non-experts. The system and nomenclature is kept up to date at the WikiPoson web site.

A unified classification system for eukaryotic transposable elements

Repbase Update (RU) is a database of representative repeat sequences in eukaryotic genomes. Since its first development as a database of human repetitive sequences in 1992, RU has been serving as a well-curated reference database fundamental for almost all eukaryotic genome sequence analyses. Here, we introduce recent updates of RU, focusing on technical issues concerning the submission and updating of Repbase entries and will give short examples of using RU data. RU sincerely invites a broader submission of repeat sequences from the research community.

/pdf/repbase-update-a-database-of-repetitive-elements-in-3wk87rel1d.pdf

Repbase Update, a database of repetitive elements in eukaryotic genomes

Censor—a program for identification and elimination of repetitive elements from DNA sequences

Integration of retroposed RNA in mammals occurs at staggered breaks resulting from an enzyme-generated pair of nicks at opposite DNA strands, preferably within 15–16 bp. Although consensus sequences associated with the two nicks appear somewhat different from one another, both nicking sites are rich in TA, CA and TG dinucleotide steps which are known as specific DNA sites where kinks may occur under bending constraints. This suggests that during interaction with the endonucleolytic enzyme, or enzymes, DNA undergoes bending at the integration sites and kinks are formed, as initial steps in generating the nicks. Nicking at kinkable sites, particularly at TA steps, may also play a role in integration of other insertion elements.

Paul Klonowski

Papers

Repbase Update, a database of eukaryotic repetitive elements

Censor—a program for identification and elimination of repetitive elements from DNA sequences

Mammalian Retroposons Integrate at Kinkable DNA Sites