PLANT PHYSIOLOGY GENOME ANALYSIS

Computational Finishing of Large Sequence Contigs Reveals Interspersed Nested Repeats and Gene Islands in the rf1-Associated Region of Maize

Kronmiller, B. A., Wise, R. P. — Thu, 01 Oct 2009 06:20:40 PDT

The architecture of grass genomes varies on multiple levels. Large long terminal repeat retrotransposon clusters occupy significant portions of the intergenic regions, and islands of protein-encoding genes are interspersed among the repeat clusters. Hence, advanced assembly techniques are required to obtain completely finished genomes as well as to investigate gene and transposable element distributions. To characterize the organization and distribution of repeat clusters and gene islands across large grass genomes, we present 961- and 594-kb contiguous sequence contigs associated with the rf1 (for restorer of fertility1) locus in the near-centromeric region of maize (Zea mays) chromosome 3. We present two methods for computational finishing of highly repetitive bacterial artificial chromosome clones that have proved successful to close all sequence gaps caused by transposable element insertions. Sixteen repeat clusters were observed, ranging in length from 23 to 155 kb. These repeat clusters are almost exclusively long terminal repeat retrotransposons, of which the paleontology of insertion varies throughout the cluster. Gene islands contain from one to four predicted genes, resulting in a gene density of one gene per 16 kb in gene islands and one gene per 111 kb over the entire sequenced region. The two sequence contigs, when compared with the rice (Oryza sativa) and sorghum (Sorghum bicolor) genomes, retain gene colinearity of 50% and 71%, respectively, and 70% and 100%, respectively, for high-confidence gene models. Collinear genes on single gene islands show that while most expansion of the maize genome has occurred in the repeat clusters, gene islands are not immune and have experienced growth in both intragene and intergene locations.

Gene Content and Virtual Gene Order of Barley Chromosome 1H

Thu, 01 Oct 2009 06:20:40 PDT

Chromosome 1H (approximately 622 Mb) of barley (Hordeum vulgare) was isolated by flow sorting and shotgun sequenced by GSFLX pyrosequencing to 1.3-fold coverage. Fluorescence in situ hybridization and stringent sequence comparison against genetically mapped barley genes revealed 95% purity of the sorted chromosome 1H fraction. Sequence comparison against the reference genomes of rice (Oryza sativa) and sorghum (Sorghum bicolor) and against wheat (Triticum aestivum) and barley expressed sequence tag datasets led to the estimation of 4,600 to 5,800 genes on chromosome 1H, and 38,000 to 48,000 genes in the whole barley genome. Conserved gene content between chromosome 1H and known syntenic regions of rice chromosomes 5 and 10, and of sorghum chromosomes 1 and 9 was detected on a per gene resolution. Informed by the syntenic relationships between the two reference genomes, genic barley sequence reads were integrated and ordered to deduce a virtual gene map of barley chromosome 1H. We demonstrate that synteny-based analysis of low-pass shotgun sequenced flow-sorted Triticeae chromosomes can deliver linearly ordered high-resolution gene inventories of individual chromosomes, which complement extensive Triticeae expressed sequence tag datasets. Thus, integration of genomic, transcriptomic, and synteny-derived information represents a major step toward developing reference sequences of chromosomes and complete genomes of the most important plant tribe for mankind.

Evolutionary and Expression Signatures of Pseudogenes in Arabidopsis and Rice

Wed, 02 Sep 2009 10:00:32 PDT

Pseudogenes () are nonfunctional genomic sequences resembling functional genes. Knowledge of s can improve genome annotation and our understanding of genome evolution. However, there has been relatively little systemic study of s in plants. In this study, we characterized the evolution and expression patterns of s in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). In contrast to animal s, many plant s experienced much stronger purifying selection. In addition, plant s experiencing stronger selective constraints tend to be derived from relatively ancient duplicates, suggesting that they were functional for a relatively long time but became s recently. Interestingly, the regions 5' to the first stops in the s have experienced stronger selective constraints compared with 3' regions, suggesting that the 5' regions were functional for a longer period of time after the premature stops appeared. We found that few s have expression evidence, and their expression levels tend to be lower compared with annotated genes. Furthermore, s with expressed sequence tags tend to be derived from relatively recent duplication events, indicating that expression may be due to insufficient time for complete degeneration of regulatory signals. Finally, larger protein domain families have significantly more s in general. However, while families involved in environmental stress responses have a significant excess of s, transcription factors and receptor-like kinases have lower than expected numbers of s, consistent with their elevated retention rate in plant genomes. Our findings illustrate peculiar properties of plant s, providing additional insight into the evolution of duplicate genes and benefiting future genome annotation.