Review

doi:10.1515/bchm3.1995.376.4.201

Cited by 27 publications

(2 citation statements)

References 65 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Microsatellites have been hypothesized to be an important source of quantitative genetic variation and evolutionary adaptation [34-36]. The high mutational rate suggest that microsatellites can act like adjustable tuning knobs through which specific genes are able to rapidly adjust the norm of reaction in response to minor or major shifts in evolutionary demands [37].…”

Section: Discussionmentioning

confidence: 99%

Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon

et al. 2011

View full text Add to dashboard Cite

BackgroundThe black tiger shrimp (Penaeus monodon) is one of the most important aquaculture species in the world, representing the crustacean lineage which possesses the greatest species diversity among marine invertebrates. Yet, we barely know anything about their genomic structure. To understand the organization and evolution of the P. monodon genome, a fosmid library consisting of 288,000 colonies and was constructed, equivalent to 5.3-fold coverage of the 2.17 Gb genome. Approximately 11.1 Mb of fosmid end sequences (FESs) from 20,926 non-redundant reads representing 0.45% of the P. monodon genome were obtained for repetitive and protein-coding sequence analyses.ResultsWe found that microsatellite sequences were highly abundant in the P. monodon genome, comprising 8.3% of the total length. The density and the average length of microsatellites were evidently higher in comparison to those of other taxa. AT-rich microsatellite motifs, especially poly (AT) and poly (AAT), were the most abundant. High abundance of microsatellite sequences were also found in the transcribed regions. Furthermore, via self-BlastN analysis we identified 103 novel repetitive element families which were categorized into four groups, i.e., 33 WSSV-like repeats, 14 retrotransposons, 5 gene-like repeats, and 51 unannotated repeats. Overall, various types of repeats comprise 51.18% of the P. monodon genome in length. Approximately 7.4% of the FESs contained protein-coding sequences, and the Inhibitor of Apoptosis Protein (IAP) gene and the Innexin 3 gene homologues appear to be present in high abundance in the P. monodon genome.ConclusionsThe redundancy of various repeat types in the P. monodon genome illustrates its highly repetitive nature. In particular, long and dense microsatellite sequences as well as abundant WSSV-like sequences highlight the uniqueness of genome organization of penaeid shrimp from those of other taxa. These results provide substantial improvement to our current knowledge not only for shrimp but also for marine crustaceans of large genome size.

show abstract

Section: Discussionmentioning

confidence: 99%

Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon

et al. 2011

View full text Add to dashboard Cite

show abstract

“…The study of repeat frequency and its distribution pattern in the genome is expected to help in understanding their significance. There is accumulating evidence to suggest that SSRs function to regulate gene expression [6] , [7] .…”

Section: Introductionmentioning

confidence: 99%

Next generation sequencing (NGS) database for tandem repeats with multiple pattern 2°-shaft multicore string matching

Rao¹,

Raju

2016

Genomics Data

View full text Add to dashboard Cite

Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research in recent years. To provide the comprehensive NGS resource for the research, in this paper , we have considered 10 loci/codi/repeats TAGA, TCAT, GAAT, AGAT, AGAA, GATA, TATC, CTTT, TCTG and TCTA. Then we developed the NGS Tandem Repeat Database (TandemRepeatDB) for all the chromosomes of Homo sapiens, Callithrix jacchus, Chlorocebus sabaeus, Gorilla gorilla, Macaca fascicularis, Macaca mulatta, Nomascus leucogenys, Pan troglodytes, Papio anubis and Pongo abelii genome data sets for all those locis. We find the successive occurence frequency for all the above 10 SSR (simple sequence repeats) in the above genome data sets on a chromosome-by-chromosome basis with multiple pattern 2° shaft multicore string matching.

show abstract

The Codes of Life

Barbieri¹,

Hoffmeyer²

2008

Biosemiotics

View full text Add to dashboard Cite

Aims and Scope of the SeriesCombining research approaches from biology, philosophy and linguistics, the emerging field of biosemiotics proposes that animals, plants and single cells all engage in semiosis -the conversion of physical signals into conventional signs. This has important implications and applications for issues ranging from natural selection to animal behaviour and human psychology, leaving biosemiotics at the cutting edge of the research on the fundamentals of life.The Springer book series Biosemiotics draws together contributions from leading players in international biosemiotics, producing an unparalleled series that will appeal to all those interested in the origins and evolution of life, including molecular and evolutionary biologists, ecologists, anthropologists, psychologists, philosophers and historians of science, linguists, semioticians and researchers in artificial life, information theory and communication technology.

show abstract

Review

Cited by 27 publications

References 65 publications

Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon

Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon

Next generation sequencing (NGS) database for tandem repeats with multiple pattern 2°-shaft multicore string matching

The Codes of Life

Contact Info

Product

Resources

About