Intron gain and loss in segmentally duplicated genes in rice

Background  

Introns are under less selection pressure than exons, and consequently, intronic sequences have a higher rate of gain and loss than exons. In a number of plant species, a large portion of the genome has been segmentally duplicated, giving rise to a large set of duplicated genes. The recent completion of the rice genome in which segmental duplication has been documented has allowed us to investigate intron evolution within rice, a diploid monocotyledonous species.     

The genetic basis of evolutionary change in gene expression levels

The regulation of gene expression is an important determinant of organismal phenotype and evolution. However, the widespread recognition of this fact occurred long after the synthesis of evolution and genetics. Here, we give a brief sketch of thoughts regarding gene regulation in the history of evolution and genetics. We then review the development of genome-wide studies of gene regulatory variation in the context of the location and mode of action of the causative genetic changes. In particular, we review mapping of the genetic basis of expression variation through expression quantitative trait locus studies and measuring the cis/trans component of expression variation in allele-specific expression studies. We conclude by proposing a systematic integration of ideas that combines global mapping studies, cis/trans tests and modern population genetics methodologies, in order to directly estimate the forces acting on regulatory variation within and between species.     

Fine mapping of a dominant minute-grain gene, Mi3, in rice

Grain weight is a major determinant of rice grain yield and is widely believed to be controlled by quantitative trait loci (QTL). We have previously reported a new major gene, Mi3, regulating grain length in rice, and that the Mi3 allele from Y34 functioned in a dominant manner. In this paper we report the fine mapping and candidate analysis of Mi3. By employing a chromosome walking strategy in the F₂ population of 9311/Y34, the Mi3 gene was finally narrowed to an interval of ~?41.6?kb between the markers RM6881 and LM9 in the pericentromeric region of rice chromosome 3. According to the rice genome annotations, five putative gene loci, LOC_Os03g_29614, LOC_Os03g_29630, LOC_Os03g_29650, LOC_Os03g_29660 and LOC_Os03g_29680, were located in this candidate region. Mi3 was also determined to be a new gene for grain size in rice by allelic analysis with the previously reported genes. Our results will facilitate the cloning and functional characterization of the Mi3 gene and targeted marker-assisted breeding.     

Intron position affects expression from thetpi promoter in rice

A series of promoter-GUS fusion constructs containing a portion of the rice triosephosphate isomerase (tpi) promoter, the firsttpi intron, and the gene encoding bacterial -glucuronidase (GUS) were made. These constructs were electroporated into rice protoplasts and transient expression was monitored. Inclusion of the first intron from the ricetpi gene enhanced expression of the GUS gene from thetpi promoter when it was placed 5 of the GUS gene. When thetpi intron was placed in the 3-untranslated region no enhancement of GUS gene expression was observed, indicating the importance of position in intron-mediated enhancement of gene expression.     

Intron loss and gain during evolution of the catalase gene family in angiosperms.

Angiosperms (flowering plants), including both monocots and dicots, contain small catalase gene families. In the dicot, Arabidopsis thaliana, two catalase (CAT) genes, CAT1 and CAT3, are tightly linked on chromosome 1 and a third, CAT2, which is more similar to CAT1 than to CAT3, is unlinked on chromosome 4. Comparison of positions and numbers of introns among 13 angiosperm catalase genomic sequences indicates that intron positions are conserved, and suggests that an ancestral catalase gene common to monocots and dicots contained seven introns. Arabidopsis CAT2 has seven introns; both CAT1 and CAT3 have six introns in positions conserved with CAT2, but each has lost a different intron. We suggest the following sequence of events during the evolution of the Arabidopsis catalase gene family. An initial duplication of an ancestral catalase gene gave rise to CAT3 and CAT1. CAT1 then served as the template for a second duplication, yielding CAT2. Intron losses from CAT1 and CAT3 followed these duplications. One subclade of monocot catalases has lost all but the 5''-most and 3''-most introns, which is consistent with a mechanism of intron loss by replacement of an ancestral intron-containing gene with a reverse-transcribed DNA copy of a fully spliced mRNA. Following this event of concerted intron loss, the Oryza sativa (rice, a monocot) CAT1 lineage acquired an intron in a novel position, consistent with a mechanism of intron gain at proto-splice sites.     

水稻“三明”显性核不育基因的定位

"三明显性核不育水稻"突变体是由福建省三明市农业科学研究所于2001年在杂交组合"SE21S/Basmati370"的F2代群体中发现的。其不育性受1个显性基因控制(将该基因命名为SMS)。经过多代回交,该显性不育基因已导入籼稻品种佳福占的遗传背景中(将该不育材料称为佳不育)。为了定位SMS,文章将佳不育与粳稻品种日本晴杂交,并将F1与佳福占测交,构建了一个作图群体。利用SSR和INDEL标记,通过混合分离分析和连锁分析,将SMS定位于第8号染色体上两个INDEL标记ZM30和ZM9之间,约99 kb的区间内。该结果为克隆SMS奠定了基础。     

Structure and expression of a root-specific rice gene

Two rice cDNA clones (COS6 and COS9) were isolated, corresponding to genes that were highly expressed in roots from seedlings and mature plants. A genomic clone (GOS9) corresponding to cDNA clone COS9 was isolated and the intron/exon structure was determined by comparing the nucleotide sequences of the mRNA and the genomic clone. 5 ends and 3 ends of the mRNA were determined by primer extension and S1-nuclease mapping respectively. The open reading frame present in GOS9 potentially encodes a protein (14kDa) that does not show any significant homology to other proteins in databases.     

Genome-wide identification, classification, evolutionary expansion and expression analyses of homeobox genes in rice

Homeobox genes play a critical role in regulating various aspects of plant growth and development. In the present study, we identified a total of 107 homeobox genes in the rice genome and grouped them into ten distinct subfamilies based upon their domain composition and phylogenetic analysis. A significantly large number of homeobox genes are located in the duplicated segments of the rice genome, which suggests that the expansion of homeobox gene family, in large part, might have occurred due to segmental duplications in rice. Furthermore, microarray analysis was performed to elucidate the expression profiles of these genes in different tissues and during various stages of vegetative and reproductive development. Several genes with predominant expression during various stages of panicle and seed development were identified. At least 37 homeobox genes were found to be differentially expressed significantly (more than two-fold; P < 0.05) under various abiotic stress conditions. The results of the study suggest a critical role of homeobox genes in reproductive development and abiotic stress signaling in rice, and will facilitate the selection of candidate genes of agronomic importance for functional validation.     

Identification of cis-elements conferring high levels of gene expression in non-green plastids

Although our knowledge about the mechanisms of gene expression in chloroplasts has increased substantially over the past decades, next to nothing is known about the signals and factors that govern expression of the plastid genome in non-green tissues. Here we report the development of a quantitative method suitable for determining the activity of cis-acting elements for gene expression in non-green plastids. The in vivo assay is based on stable transformation of the plastid genome and the discovery that root length upon seedling growth in the presence of the plastid translational inhibitor kanamycin is directly proportional to the expression strength of the resistance gene nptII in transgenic tobacco plastids. By testing various combinations of promoters and translation initiation signals, we have used this experimental system to identify cis-elements that are highly active in non-green plastids. Surprisingly, heterologous expression elements from maize plastids were significantly more efficient in conferring high expression levels in root plastids than homologous expression elements from tobacco. Our work has established a quantitative method for characterization of gene expression in non-green plastid types, and has led to identification of cis-elements for efficient plastid transgene expression in non-green tissues, which are valuable tools for future transplastomic studies in basic and applied research.     

Muscle differentiation in a colonial ascidian: organisation, gene expression and evolutionary considerations

Background  

Ascidians are tunicates, the taxon recently proposed as sister group to the vertebrates. They possess a chordate-like swimming larva, which metamorphoses into a sessile adult. Several ascidian species form colonies of clonal individuals by asexual reproduction. During their life cycle, ascidians present three muscle types: striated in larval tail, striated in the heart, and unstriated in the adult body-wall.     

Chromothripsis,a credible chromosomal mechanism in evolutionary process

Chromosoma - The recent discovery of a new class of massive chromosomal rearrangements, occurring during one unique cellular event and baptized “chromothripsis,” deeply modifies our...     

Characterization of a rice pollen-specific gene and its expression

Pollen development requires a large number of genes expressed in both sporophytic and gametophytic tissues. We have isolated a pollen-specific gene, PS1, from rice. PS1 is a unique gene in the rice genome and encodes a 164 amino acid long protein. RNA blot analysis shows that PS1 mRNAs accumulate specifically in rice anthers. When introduced into rice tissues by microprojectile bombardment, the PS1 promoter drives expression of a marker gene, β-glucuronidase, specifically in rice pollen. The PS1 gene and the deduced amino acid sequence of the PS1 protein share significant levels of homology with another monocot pollen-specific gene—the maize Zm-13 gene and its deduced protein, respectively. PS1 also shows some homology with the dicot tomato anther-specific gene LAT-52. Interestingly, the structure of the PS1 gene is more similar to that of the LAT-52 gene than to Zm-13. The coding regions of both PS1 and LAT-52 are interrupted by a single intron, and the positions of the introns are conserved in these genes. Moreover, there is considerable sequence homology in the introns of the PS1 and LAT-52 genes in regions immediately upstream of the 3' splice sites. The upstream regulatory sequences of the PS1 gene show several regions of homology with other pollen- or anther-specific genes from a number of plant species. The conservation of coding sequences of PS1 from rice, Zm-I3 from maize, and LAT-52 from tomato suggests a functional conservation of their gene products. Similarities in the regulatory regions of PS1 and other anther- or pollen-specific genes among monocotyledonous and dicotyledonous species indicate that at least some regulatory features controlling gene expression in male reproductive tissues are conserved. This is supported by the preservation of pollen-specific expression from the rice PS1 promoter when it is introduced into tobacco plants by Agrobacterium Ti plasmid-mediated transformation.