Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes

BACKGROUND: Kinesins, a superfamily of molecular motors, use microtubules as tracks and transport diverse cellular cargoes. All kinesins contain a highly conserved ~350 amino acid motor domain. Previous analysis of the completed genome sequence of one flowering plant (Arabidopsis) has resulted in identification of 61 kinesins. The recent completion of genome sequencing of several photosynthetic and non-photosynthetic eukaryotes that belong to divergent lineages offers a unique opportunity to conduct a comprehensive comparative analysis of kinesins in plant and non-plant systems and infer their evolutionary relationships. RESULTS: We used the kinesin motor domain to identify kinesins in the completed genome sequences of 19 species, including 13 newly sequenced genomes. Among the newly analyzed genomes, six represent photosynthetic eukaryotes. A total of 529 kinesins was used to perform comprehensive analysis of kinesins and to construct gene trees using the Bayesian and parsimony approaches. The previously recognized 14 families of kinesins are resolved as distinct lineages in our inferred gene tree. At least three of the 14 kinesin families are not represented in flowering plants. Chlamydomonas, a green alga that is part of the lineage that includes land plants, has at least nine of the 14 known kinesin families. Seven of ten families present in flowering plants are represented in Chlamydomonas, indicating that these families were retained in both the flowering-plant and green algae lineages. CONCLUSION: The increase in the number of kinesins in flowering plants is due to vast expansion of the Kinesin-14 and Kinesin-7 families. The Kinesin-14 family, which typically contains a C-terminal motor, has many plant kinesins that have the motor domain at the N terminus, in the middle, or the C terminus. Several domains in kinesins are present exclusively either in plant or animal lineages. Addition of novel domains to kinesins in lineage-specific groups contributed to the functional diversification of kinesins. Results from our gene-tree analyses indicate that there was tremendous lineage-specific duplication and diversification of kinesins in eukaryotes. Since the functions of only a few plant kinesins are reported in the literature, this comprehensive comparative analysis will be useful in designing functional studies with photosynthetic eukaryotes

SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data

We propose a method for predicting splice graphs that enhances curated gene models using evidence from RNA-Seq and EST alignments. Results obtained using RNA-Seq experiments in Arabidopsis thaliana show that predictions made by our SpliceGrapher method are more consistent with current gene models than predictions made by TAU and Cufflinks. Furthermore, analysis of plant and human data indicates that the machine learning approach used by SpliceGrapher is useful for discriminating between real and spurious splice sites, and can improve the reliability of detection of alternative splicing. SpliceGrapher is available for download at http://SpliceGrapher.sf.net

Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii

<p>Abstract</p> <p>Background</p> <p>Genome-wide computational analysis of alternative splicing (AS) in several flowering plants has revealed that pre-mRNAs from about 30% of genes undergo AS. <it>Chlamydomonas</it>, a simple unicellular green alga, is part of the lineage that includes land plants. However, it diverged from land plants about one billion years ago. Hence, it serves as a good model system to study alternative splicing in early photosynthetic eukaryotes, to obtain insights into the evolution of this process in plants, and to compare splicing in simple unicellular photosynthetic and non-photosynthetic eukaryotes. We performed a global analysis of alternative splicing in <it>Chlamydomonas reinhardtii </it>using its recently completed genome sequence and all available ESTs and cDNAs.</p> <p>Results</p> <p>Our analysis of AS using BLAT and a modified version of the Sircah tool revealed AS of 498 transcriptional units with 611 events, representing about 3% of the total number of genes. As in land plants, intron retention is the most prevalent form of AS. Retained introns and skipped exons tend to be shorter than their counterparts in constitutively spliced genes. The splice site signals in all types of AS events are weaker than those in constitutively spliced genes. Furthermore, in alternatively spliced genes, the prevalent splice form has a stronger splice site signal than the non-prevalent form. Analysis of constitutively spliced introns revealed an over-abundance of motifs with simple repetitive elements in comparison to introns involved in intron retention. In almost all cases, AS results in a truncated ORF, leading to a coding sequence that is around 50% shorter than the prevalent splice form. Using RT-PCR we verified AS of two genes and show that they produce more isoforms than indicated by EST data. All cDNA/EST alignments and splice graphs are provided in a website at <url>http://combi.cs.colostate.edu/as/chlamy</url>.</p> <p>Conclusions</p> <p>The extent of AS in <it>Chlamydomonas </it>that we observed is much smaller than observed in land plants, but is much higher than in simple unicellular heterotrophic eukaryotes. The percentage of different alternative splicing events is similar to flowering plants. Prevalence of constitutive and alternative splicing in <it>Chlamydomonas</it>, together with its simplicity, many available public resources, and well developed genetic and molecular tools for this organism make it an excellent model system to elucidate the mechanisms involved in regulated splicing in photosynthetic eukaryotes.</p

Alternative Splicing and Protein Diversity: Plants Versus Animals

Plants, unlike animals, exhibit a very high degree of plasticity in their growth and development and employ diverse strategies to cope with the variations during diurnal cycles and stressful conditions. Plants and animals, despite their remarkable morphological and physiological differences, share many basic cellular processes and regulatory mechanisms. Alternative splicing (AS) is one such gene regulatory mechanism that modulates gene expression in multiple ways. It is now well established that AS is prevalent in all multicellular eukaryotes including plants and humans. Emerging evidence indicates that in plants, as in animals, transcription and splicing are coupled. Here, we reviewed recent evidence in support of co-transcriptional splicing in plants and highlighted similarities and differences between plants and humans. An unsettled question in the field of AS is the extent to which splice isoforms contribute to protein diversity. To take a critical look at this question, we presented a comprehensive summary of the current status of research in this area in both plants and humans, discussed limitations with the currently used approaches and suggested improvements to current methods and alternative approaches. We end with a discussion on the potential role of epigenetic modifications and chromatin state in splicing memory in plants primed with stresses

Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes-2

<p><b>Copyright information:</b></p><p>Taken from "Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes"</p><p>BMC Genomics 2006;7():18-18.</p><p>Published online 31 Jan 2006</p><p>PMCID:PMC1434745.</p><p>Copyright © 2006 Richardson et al; licensee BioMed Central Ltd.</p>Green brackets indicate plant specific groups, mixed clades are shown in blue brackets and black brackets indicate protozoan species. Green circle and blue square indicate gene duplications in flowering plants and dicots, respectively. See Fig. 2 legend for an explanation of support values. Support values in italicized blue font indicate those clades supported in the parsimony analyses except for the exclusion of 128382 (see text). For full names of species see Fig. 1 legend. Fl. Plants, flowering plants

Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes-1

<p><b>Copyright information:</b></p><p>Taken from "Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes"</p><p>BMC Genomics 2006;7():18-18.</p><p>Published online 31 Jan 2006</p><p>PMCID:PMC1434745.</p><p>Copyright © 2006 Richardson et al; licensee BioMed Central Ltd.</p>ent to the nodes. Support values above each branch correspond to Bayesian posterior probabilities whereas values below each branch correspond to parsimony jackknife support. In both cases the leftmost values are for the amino-acid-plus-gap-characters analyses and the rightmost values are for amino-acid-characters analyses. Bayesian posterior probabilities for the amino-acid-plus-gap-characters are also shown in bold. If a branch was unresolved in one of the other three analyses, it is indicated by "-" at the respective node. If a branch was contradicted in one of these other three analyses, it is indicated by underlined red font at the respective node with the single highest posterior probability or jackknife support value for the contradicting clade(s) shown. Ungrouped kinesins are presented on the left side of the main polytomy, with the exception of the plant-specific ungrouped family that is shown on the upper right of the tree. The and unresolved blocks each contain 4 and 9 sequences, respectively (See Additional files and these sequence IDs). Brackets denote the major eukaryotic groupings in accordance with Baldauf's nomenclature [50]. Blue brackets indicate taxa that are from multiple groups, black brackets indicate protozoan species and red brackets are reserved for opisthokonts. Although Pt00151235 is grouped within this family by Bayesian analysis, we favor the parsimony resolution of it as a member of the Kinesin-10 family. For full names of species see Fig. 1 legend

Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes-13

<p><b>Copyright information:</b></p><p>Taken from "Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes"</p><p>BMC Genomics 2006;7():18-18.</p><p>Published online 31 Jan 2006</p><p>PMCID:PMC1434745.</p><p>Copyright © 2006 Richardson et al; licensee BioMed Central Ltd.</p>y classifications are shown to the right of the proteins

Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes-14

<p><b>Copyright information:</b></p><p>Taken from "Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes"</p><p>BMC Genomics 2006;7():18-18.</p><p>Published online 31 Jan 2006</p><p>PMCID:PMC1434745.</p><p>Copyright © 2006 Richardson et al; licensee BioMed Central Ltd.</p>lication map based upon [94]. All accession numbers should be prefixed with "OSBCCO" if searching [100]