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A major event in land plant evolution is the origin of vascular tissues, which ensure the long-distance transport of water, nutrients and organic compounds. However, the molecular basis for the origin and evolution of plant vascular tissues remains largely unknown., Here, we investigate the evolution of the land plant TAL-type transaldolase ( TAL) gene and its potential function in rice ( Oryza sativa) based on phylogenetic analyses and transgenic experiments, respectively., TAL genes are only present in land plants and bacteria. Phylogenetic analyses suggest that land plant TAL genes are derived from Actinobacteria through an ancient horizontal gene transfer (HGT) event. Further evidence reveals that land plant TAL genes have undergone positive selection and gained several introns following its acquisition by the most recent common ancestor of land plants. Transgenic plant experiments show that rice TAL is specifically expressed in vascular tissues and that knockdown of TAL expression leads to changes in both the number and pattern of vascular bundles., Our findings show that the ancient HGT of TAL from bacteria probably plays an important role in plant vascular development and adaptation to land environments. [ABSTRACT FROM AUTHOR]

A challenge in phylogenetic inference of gene trees is how to properly sample a large pool of homologous sequences to derive a good representative subset of sequences. Such a need arises in various applications, e.g. when (1) accuracy-oriented phylogenetic reconstruction methods may not be able to deal with a large pool of sequences due to their high demand in computing resources; (2) applications analyzing a collection of gene trees may prefer to use trees with fewer operational taxonomic units (OTUs), for instance for the detection of horizontal gene transfer events by identifying phylogenetic conflicts; and (3) the pool of available sequences is biased towards extensively studied species. In the past, the creation of subsamples often relied on manual selection. Here we present an Automated sequence-Sampling method for improving the Taxonomic diversity of gene phylogenetic trees, AST, to obtain representative sequences that maximize the taxonomic diversity of the sampled sequences. To demonstrate the effectiveness of AST, we have tested it to solve four problems, namely, inference of the evolutionary histories of the small ribosomal subunit protein S5 of E. coli, 16 S ribosomal RNAs and glycosyl-transferase gene family 8, and a study of ancient horizontal gene transfers from bacteria to plants. Our results show that the resolution of our computational results is almost as good as that of manual inference by domain experts, hence making the tool generally useful to phylogenetic studies by non-phylogeny specialists. The program is available at http://csbl.bmb.uga.edu/~zhouchan/AST.php. [ABSTRACT FROM AUTHOR]

The significance of horizontal gene transfer (HGT) in eukaryotic evolution remains controversial. Although many eukaryotic genes are of bacterial origin, they are often interpreted as being derived from mitochondria or plastids. Because of their fixed gene pool and gene loss, however, mitochondria and plastids alone cannot adequately explain the presence of all, or even the majority, of bacterial genes in eukaryotes. Available data indicate that no insurmountable barrier to HGT exists, even in complex multicellular eukaryotes. In addition, the discovery of both recent and ancient HGT events in all major eukaryotic groups suggests that HGT has been a regular occurrence throughout the history of eukaryotic evolution. A model of HGT is proposed that suggests both unicellular and early developmental stages as likely entry points for foreign genes into multicellular eukaryotes. [ABSTRACT FROM AUTHOR]

Horizontal gene transfer (HGT) may not only create genome mosaicism, but also introduce evolutionary novelties to recipient organisms. HGT in plastid genomes, though relatively rare, still exists. HGT-derived genes are particularly common in unicellular photosynthetic eukaryotes and they also occur in multicellular plants. In particular, ancient HGT events occurring during the early evolution of primary photosynthetic eukaryotes were probably frequent. There is clear evidence that anciently acquired genes played an important role in the establishment of primary plastids and in the transition of plants from aquatic to terrestrial environments. Although algal genes have often been used to infer historical plastids in plastid-lacking eukaryotes, reliable approaches are needed to distinguish endosymbionts-derived genes from those independently acquired from preferential feeding or other activities. [ABSTRACT FROM AUTHOR]

Background: Horizontal gene transfer (HGT) is traditionally considered to be rare in multicellular eukaryotes such as animals. Recently, many genes of miscellaneous algal origins were discovered in choanoflagellates. Considering that choanoflagellates are the existing closest relatives of animals, we speculated that ancient HGT might have occurred in the unicellular ancestor of animals and affected the long-term evolution of animals. Results: Through genome screening, phylogenetic and domain analyses, we identified 14 gene families, including 92 genes, in the tunicate Ciona intestinalis that are likely derived from miscellaneous photosynthetic eukaryotes. Almost all of these gene families are distributed in diverse animals, suggesting that they were mostly acquired by the common ancestor of animals. Their miscellaneous origins also suggest that these genes are not derived from a particular algal endosymbiont. In addition, most genes identified in our analyses are functionally related to molecule transport, cellular regulation and methylation signaling, suggesting that the acquisition of these genes might have facilitated the intercellular communication in the ancestral animal. Conclusions: Our findings provide additional evidence that algal genes in aplastidic eukaryotes are not exclusively derived from historical plastids and thus important for interpreting the evolution of eukaryotic photosynthesis. Most importantly, our data represent the first evidence that more anciently acquired genes might exist in animals and that ancient HGT events have played an important role in animal evolution. [ABSTRACT FROM AUTHOR]

Although horizontal gene transfer (HGT) is usually considered a disruptive force in recovering organismal phylogeny, it creates important phylogenetic information. In the ‘net of life’, the recipient of an ancient gene transfer can be the ancestor of a lineage that inherits the transferred gene; thus, the transferred gene marks the recipient and its descendants as a monophyletic group. Ancient gene transfer events can also reveal the order of emergence of donor and recipient lineages. In addition, these ancient events can significantly shape the genetic systems of the recipients and can play a part in their long-term evolution. In this article, we discuss the recent progress in phylogenetic application of ancient HGTs and describe two examples of transfer events to the ancestor of red algae and green plants that support a common origin of these two groups. We also address the potential pitfalls of this application. [Copyright &y& Elsevier]

Reports of plant-like and bacterial-like genes for a number of parasitic organisms, most notably those within the Apicomplexa and Kinetoplastida, have appeared in the literature over the last few years. Among the apicomplexan organisms, following discovery of the apicomplexan plastid (apicoplast), the discovery of plant-like genes was less surprising although the extent of transfer and the relationship of transferred genes to the apicoplast remained unclear. We used new genome sequence data to begin a systematic examination of the extent and origin of transferred genes in the Apicomplexa combined with a phylogenomic approach to detect potential gene transfers in four apicomplexan genomes. We have detected genes of algal nuclear, chloroplast (cyanobacterial) and proteobacterial origin. Plant-like genes were detected in species not currently harbouring a plastid (e.g. Cryptosporidium parvum) and putatively transferred genes were detected that appear to be unrelated to the function of the apicoplast. While the mechanism of acquisition for many of the identified genes is not certain, it appears that some were most likely acquired via intracellular gene transfer from an algal endosymbiont while others may have been acquired via horizontal gene transfer. [Copyright &y& Elsevier]

Nucleotide metabolic pathways provide numerous successful targets for antiparasitic chemotherapy, but the human pathogen Cryptosporidium parvum thus far has proved extraordinarily refractory to classical treatments. The genome sequence of C. parvum is approaching completion, and the authors have used this resource to critically assess nucleotide biosynthesis as a target in C. parvum. Genomic analysis indicates that this parasite is entirely dependent on salvage from the host for its purines and pyrimidines.