Welcome to Scribd, the world's digital library. Read, publish, and share books and documents. See more
Download
Standard view
Full view
of .
Save to My Library
Look up keyword
Like this
5Activity
0 of .
Results for:
No results containing your search query
P. 1
Leveraging massively parallel pyrosequencing for functional and evolutionary genomics in ferns.

Leveraging massively parallel pyrosequencing for functional and evolutionary genomics in ferns.

Ratings: (0)|Views: 287 |Likes:
Published by Joshua Der
As the sister lineage to seed plants, ferns (i.e. monilophytes) represent an important clade for comparative evolutionary studies of land plants. Additionally, with the evolution and maintenance of free-living photosynthetic gametophyte and sporophyte life stages, ferns are an ideal group for studies of both life-cycle evolution and genome function in independent and functionally differentiated haploid and diploid phases. While the development of genomic resources has been far slower in ferns than in other plants, recent advances in high throughput sequencing technologies have enabled the first large-scale examination of a fern genome and transcriptome. We present an exploration of genome structure and function in the bracken fern, Pteridium aquilinum, utilizing Roche 454 shotgun sequence data derived from both total genomic DNA and a full-length enriched, normalized cDNA library from sexually mature gametophytes. Our genomic sequence data are comprised of more than 711k reads averaging 304 bp long and totaling more than 216 Mb. De novo assembly of these reads has yielded a complete chloroplast genome sequence and our first detailed glimpse into the nuclear genome of a fern, including an examination of gene density, intron structure and the abundance of repetitive sequences (including transposable elements and microsatellites). Our transcriptome data are comprised of more than 681k reads with a mean length of 373 bp. Cleaned reads were assembled in a two-tiered approach. Contigs and singletons resulting from de novo assembly were passed through a secondary assembly, resulting in 38,889 unigenes with a mean length of 685 bp and a total length of 26.7 MB. Unigenes were annotated with the GO-slim vocabulary based on blast similarity searches of the NCBI nr protein database. We also performed an analysis of tribe and orthogroup assignments for each unigene based on the best hit from a custom blast search of the proteins from ten phylogenetically diverse complete plant genomes. Among genes expressed in fern gametophytes are "floral" development genes and flagellar proteins. A Ks plot analysis of duplicate unigene pairs indicates that the genome of Pteridium has experienced a single ancient paleopolyploid event as well as a number of potential recent polyploid events. We also summarize the value of these data for comparative evolutionary and functional genomic studies in land plants.
As the sister lineage to seed plants, ferns (i.e. monilophytes) represent an important clade for comparative evolutionary studies of land plants. Additionally, with the evolution and maintenance of free-living photosynthetic gametophyte and sporophyte life stages, ferns are an ideal group for studies of both life-cycle evolution and genome function in independent and functionally differentiated haploid and diploid phases. While the development of genomic resources has been far slower in ferns than in other plants, recent advances in high throughput sequencing technologies have enabled the first large-scale examination of a fern genome and transcriptome. We present an exploration of genome structure and function in the bracken fern, Pteridium aquilinum, utilizing Roche 454 shotgun sequence data derived from both total genomic DNA and a full-length enriched, normalized cDNA library from sexually mature gametophytes. Our genomic sequence data are comprised of more than 711k reads averaging 304 bp long and totaling more than 216 Mb. De novo assembly of these reads has yielded a complete chloroplast genome sequence and our first detailed glimpse into the nuclear genome of a fern, including an examination of gene density, intron structure and the abundance of repetitive sequences (including transposable elements and microsatellites). Our transcriptome data are comprised of more than 681k reads with a mean length of 373 bp. Cleaned reads were assembled in a two-tiered approach. Contigs and singletons resulting from de novo assembly were passed through a secondary assembly, resulting in 38,889 unigenes with a mean length of 685 bp and a total length of 26.7 MB. Unigenes were annotated with the GO-slim vocabulary based on blast similarity searches of the NCBI nr protein database. We also performed an analysis of tribe and orthogroup assignments for each unigene based on the best hit from a custom blast search of the proteins from ten phylogenetically diverse complete plant genomes. Among genes expressed in fern gametophytes are "floral" development genes and flagellar proteins. A Ks plot analysis of duplicate unigene pairs indicates that the genome of Pteridium has experienced a single ancient paleopolyploid event as well as a number of potential recent polyploid events. We also summarize the value of these data for comparative evolutionary and functional genomic studies in land plants.

More info:

Categories:Types, Research, Science
Published by: Joshua Der on Jan 20, 2010
Copyright:Attribution Non-commercial

Availability:

Read on Scribd mobile: iPhone, iPad and Android.
download as PDF or read online from Scribd
See more
See less

08/03/2012

pdf

 
Leveraging massively parallelpyrosequencing for functional andevolutionary genomics in ferns.
 Joshua Der and Paul Wolf Dept. Biology and Center for Integrated Biosystems,Utah State University
 
Traditional genome sequencing methods are costprohibitive, especially for large genomes
Expressed Sequence Tags (ESTs) are a genome-wideproxy for functional components of the genome
New-generation sequencing technologies:low cost per base, massively high throughput
Roche 454 pyrosequencing: long read lengths, enabling
de novo
genome assembly in non-model organisms
Genomics innon-model organisms
 
Roche 454Pyrosequencing
DNA fragmentation (nebulization)
Fragment size selection and adapter ligation
Single stranded DNA library isolation
Bind library molecule to sequencing bead(1 molecule/bead)
Clonal amplification in emulsion PCR
Bead deposition in PicoTiterPlate
Pyrosequencing and image processing

Activity (5)

You've already reviewed this. Edit your review.
1 thousand reads
1 hundred reads
Anisam Abhi liked this
sabmarko liked this
franlorin liked this

You're Reading a Free Preview

Download
/*********** DO NOT ALTER ANYTHING BELOW THIS LINE ! ************/ var s_code=s.t();if(s_code)document.write(s_code)//-->