Showing papers by "Christopher E. Lane published in 2008"
TL;DR: This work states that accurate identification of gene transfers and replacements involving eukaryotic donor and recipient genomes represents a potentially formidable challenge for the phylogenomics community as more protist genomes are sequenced and concatenated data sets grow.
Abstract: Resolving the structure of the eukaryotic tree of life remains one of the most important and challenging tasks facing biologists. The notion of six eukaryotic 'supergroups' has recently gained some acceptance, and several papers in 2007 suggest that resolution of higher taxonomic levels is possible. However, in organisms that acquired photosynthesis via secondary (i.e. eukaryote-eukaryote) endosymbiosis, the host nuclear genome is a mosaic of genes derived from two (or more) nuclei, a fact that is often overlooked in studies attempting to reconstruct the deep evolutionary history of eukaryotes. Accurate identification of gene transfers and replacements involving eukaryotic donor and recipient genomes represents a potentially formidable challenge for the phylogenomics community as more protist genomes are sequenced and concatenated data sets grow.
181 citations
TL;DR: The H. andersenii mtDNA shares a number of features in common with the genome of the cryptophyte Rhodomonas salina, including general architecture, gene content, and the presence of a large repeat-rich intergenic region, but it appears unable to produce a functional tRNA.
Abstract: Cryptophytes are an enigmatic group of unicellular eukaryotes with plastids derived by secondary (i.e., eukaryote-eukaryote) endosymbiosis. Cryptophytes are unusual in that they possess four genomes–a host cell-derived nuclear and mitochondrial genome and an endosymbiont-derived plastid and 'nucleomorph' genome. The evolutionary origins of the host and endosymbiont components of cryptophyte algae are at present poorly understood. Thus far, a single complete mitochondrial genome sequence has been determined for the cryptophyte Rhodomonas salina. Here, the second complete mitochondrial genome of the cryptophyte alga Hemiselmis andersenii CCMP644 is presented. The H. andersenii mtDNA is 60,553 bp in size and encodes 30 structural RNAs and 36 protein-coding genes, all located on the same strand. A prominent feature of the genome is the presence of a ~20 Kbp long intergenic region comprised of numerous tandem and dispersed repeat units of between 22–336 bp. Adjacent to these repeats are 27 copies of palindromic sequences predicted to form stable DNA stem-loop structures. One such stem-loop is located near a GC-rich and GC-poor region and may have a regulatory function in replication or transcription. The H. andersenii mtDNA shares a number of features in common with the genome of the cryptophyte Rhodomonas salina, including general architecture, gene content, and the presence of a large repeat region. However, the H. andersenii mtDNA is devoid of inverted repeats and introns, which are present in R. salina. Comparative analyses of the suite of tRNAs encoded in the two genomes reveal that the H. andersenii mtDNA has lost or converted its original trnK(uuu) gene and possesses a trnS-derived 'trnK(uuu)', which appears unable to produce a functional tRNA. Mitochondrial protein coding gene phylogenies strongly support a variety of previously established eukaryotic groups, but fail to resolve the relationships among higher-order eukaryotic lineages. Comparison of the H. andersenii and R. salina mitochondrial genomes reveals a number of cryptophyte-specific genomic features, most notably the presence of a large repeat-rich intergenic region. However, unlike R. salina, the H. andersenii mtDNA does not possess introns and lacks a Lys-tRNA, which is presumably imported from the cytosol.
43 citations
TL;DR: In this article, the authors applied microscopic and molecular tools to 13 publicly available Hemiselmis strains in an effort to clarify species boundaries and recognized four new marine species of Hemiselms from the waters around North America.
Abstract: Cryptomonads are a ubiquitous and diverse assemblage of aquatic flagellates. The relatively obscure genus Hemiselmis includes some of the smallest of these cells. This genus contained only two species until 1967, when Butcher described seven new marine species mainly on the basis of observations with the light microscope. However, from these seven taxa, only H. amylifera and H. oculata were validly published. Additionally, the features Butcher used to distinguish species have since been questioned, and the taxonomy within Hemiselmis has remained clouded due to the difficulty in unambiguously applying his classification and validating many of his species. As a result, marine strains are often placed into one of three species—H. rufescens Parke, H. virescens Droop, or the invalid H. brunnescens Butcher—based on cell color alone. Here we applied microscopic and molecular tools to 13 publicly available Hemiselmis strains in an effort to clarify species boundaries. SEM failed to provide sufficient morphological variation to distinguish species of Hemiselmis, and results from LM did not correlate with clades found using both molecular phylogenetic and nucleomorph genome karyotype analysis, indicating a high degree of morphological plasticity within species. On the basis of molecular characters and collection geography we recognize four new marine species of Hemiselmis—H. cryptochromatica sp. nov., H. andersenii sp. nov., H. pacifica sp. nov., and H. tepida sp. nov.—from the waters around North America.
33 citations
TL;DR: Using morphological and molecular analyses (rbcL gene sequences), three new species, Botryocladia bermudana, B. exquisita and B. flookii, are described from the coastal waters and national aquarium of Bermuda and are joined by two others in the island's flora.
Abstract: Using morphological and molecular analyses (rbcL gene sequences), three new species, Botryocladia bermudana, B. exquisita and B. flookii, are described from the coastal waters and national aquarium of Bermuda. The new taxa are joined by two others in the island’s flora, B. occidentalis and B. wynnei, the last representing a new distributional record. The cryptic species, B. bermudana, is the most common of all Botryocladia species in the islands and was known from Bermuda in the past as B. pyriformis (Borgesen) Kylin. Analysis of rbcL sequences shows that B. bermudana is most closely related to B. caraibica from the Caribbean. These two species share many characteristics in addition to their phylogentic positioning. Botryocladia exquisita is anatomically and molecularly most similar to the much smaller B. monoica from the Caribbean and Gulf of Mexico, and B. flookii bears a striking superficial resemblance to B. macaronesica from the Canary Islands. Several anatomical and reproductive characteristics differentiate the two.
23 citations
TL;DR: It is suggested that nucleomorph karyotype similarity is not a reliable indicator of evolutionary affinity and provides a starting point for further investigation of the fine‐scale dynamics of nucleomorph genome evolution within members of the genus Cryptomonas.
Abstract: Cryptophytes are unicellular, biflagellate algae with plastids (chloroplasts) derived from the uptake of a red algal endosymbiont. These organisms are unusual in that the nucleus of the engulfed red alga persists in a highly reduced form called a nucleomorph. Nucleomorph genomes are remarkable in their small size ( 99% identical to one another. These results suggest that nucleomorph karyotype similarity is not a reliable indicator of evolutionary affinity and provides a starting point for further investigation of the fine-scale dynamics of nucleomorph genome evolution within members of the genus Cryptomonas.
18 citations