YIA Current Analysis

Analysis

Genome Browser

The YIA Comparative Genomics browser shows alignments of markers, genomic sequences, and expressed sequences to a common reference sequence, rice chromosome 1 (IRGSP TIGR Release 3). Two approaches are used to examine colinearity at a high resolution between genomes of rice, maize, and sorghum:

Hybridization of rice overgo probes to sorghum and maize BAC clones. Data are shown for 288 probes hybridized to a minimum tiling path of sorghum BACs that span corresponding regions of rice chromosome 1. The same probes were also hybridized to the ZMMBBc filter set, constituting ~7x coverage of the maize genome.
Alignment of sorghum and maize genomic sequences to rice. Data are currently shown for completed maize BACs deposited with GenBank as of 31-Jan-2005 and four additional BACs completed by Dr. Dick McCombie's lab at CSHL (and since deposited with GenBank). These BAC sequences are aligned to rice chromosome 1 using WABA (Kent & Zahler, 2000 Genome Res 10:1115-25). To broaden the context of these comparisons, additional alignments are shown of maize and rice genomic survey sequences and expressed sequences from a variety of cereals. These latter data are derived from Gramene and methods are described therein.

Additional documentation is found within the Browser itself.

YIA Synteny Viewer in Gramene

The YIA data on synteny between rice and maize can be viewed in the synteny view through Gramene. For a brief description of these data please click here.

Simple Sequence Repeat (SSR) Identification in Maize and Sorghum

Datasets:

SSRs were identified in the following sequence datasets:

Maize:
maize_bacends
maize_est
maize_markers
maize_meth_reads
maize_tigr_hicot_cluster
maize_unigenes

Sorghum:
sorghum_est_new
sorghum_orion
sorghum_pratt

The following steps were applied to the maize sequences (for sorghum sequences, only the SSR identification step was applied):

Identify SSR:
SSRs were identified as:
1. A Dinucleotide repeated 9 or more times
2. A Trinucleotide repeated 6 or more times
3. A Tetranucleotide repeated 5 or more times
Make Unique Loci:
To identify multiple instances of the same SSR loci, sequences comprising the SSR plus 50 flanking nucleotides on each side were aligned by BLAT and clustered using stringent criteria (>= 96% match). SSRs having the same Cluster_ID are presumed to represent the same locus.
Add FPC and Genetic Map Information:
Where possible, SSRs were anchored to the Jan 2004 FPC map. Many SSRs were derived from BACs that directly contributed to the FPC map. Other SSRs were derived from sequences (such as Cornsensus Unigenes) that have previously been anchored to the FPC map by overgo hybridization (information that is provided with the FPC map release).
Add Correspondences to the IRGSP Rice Assembly (TIGR Release 3)
Using sequence alignments of physically anchored maize sequences to rice, we have constructed pair-wise correspondences between the rice sequence and the maize FPC map (see Synteny Viewer section). These correspondences to rice were added to the subset of SSRs that were anchored to the FPC map in the previous step. Other SSRs that were derived from non-repetitive sequences, such as Cornsensus unigenes, were mapped to rice by alignment of their source sequence.

Data Description:

Table: ALL SSR FPC Rice
Table description: contains maize SSRs only
Fields description :

Table : SSR Hits
Table description: contains maize and sorghum SSRs
Field description: