Colleen A. Murphy

A preliminary investigation of the order Bangiales (Bangiophycidae, Rhodophyta) based on sequences of nuclear small‐subunit ribosomal RNA genes

We investigated phylogenetic relationships among red algae of the order Bangiales by analysis of sequences of the nuclear gene encoding cytosolic small‐subunit ribosomal RNA in Bangia atropurpurea (Roth) C. Ag. and eight samples representing seven species of Porphyra. The ssu‐rDNA range from 1818 to 1845 nucleotides in length, with guanosine plus cytosine ratios between 47.0% and 48.6%. A group IC1 intron occurs in the B atropurpurea ssu‐rDNAs at the same position as in P. spiralis var. amplifolia Oliveira Filho et Coll and several other eukaryote ssu‐rDNAs. The nine sequences form a stable monophyletic group upon phylogenetic analysis. The ssu‐rDNA from B. atropurpurea nests stably within the Porphyra group and is closely related to P. amplissima (Kjellm.) Setchell et Hus in Hus, making the genus Porphyra paraphyletic. No correlation is seen between phylogenetic position and number of cell layers in the Porphyra thallus. We discuss possible taxonomic and evolutionary implications of these observations.

Gene structure of the Kiss1 receptor-2 (Kiss1r-2) in the Atlantic halibut: Insights into the evolution and regulation of Kiss1r genes

Kisspeptin and its receptor, Kiss1r, play an essential role in the control of the onset of puberty in vertebrates. We characterized the cDNA and genomic DNA encoding Kiss1r in Atlantic halibut (Hippoglossus hippoglossus). The 1146bp open reading frame predicts a 381 amino acid protein with high homology to the Kiss1r-2 of other teleost fish. Phylogenetic analysis of Kiss1r sequences suggests that the mammalian Kiss1r-1 form arose by way of a gene duplication prior to the emergence of amphibians. Synteny analysis demonstrated the highly conserved nature of the Kiss1r-2 region in teleosts, suggesting that flanking regulatory sequences are also likely to be conserved. Bioinformatic analysis identified six conserved regions in piscine Kiss1r-2 upstream sequences, providing potential targets for future in-depth investigation of Kiss1r-2 regulation. Kiss1r-2 expression in the brain increased coinciding with the onset of puberty. Expression levels in the gonads were two orders of magnitude lower than those of the brain, a characteristic apparently conserved in other fishes, and expression in gonads was only detected in immature fish.

A molecular investigation of polymorphism in the North Atlantic red alga Chondrus crispus (Gigartinales)

Seven samples of Chondrus crispus Stackhouse, representing widely contrasting forms from both sides of the North Atlantic, were compared by restriction digestion of their plastid DNA. The similar banding patterns confirmed that the seven forms were conspecific and distinct from Chondrus ocellatus Holmes f. ocellatus from Japan, used as an outgroup. Nucleotide sequences of the internal transcribed spacers (ITS1 and ITS21 and the intervening 5.8S rRNA gene of the nuclear rRNA operon were investigated as a potential indicator of genetic divergence among morphological variants of C. crispus. The combined ITS regions were relatively short in Chondrus (between 719 and 731 base pairs [bp] in C. crispus and 724 bp in C. ocellatus f. ocellatus), and the sequence of the 5.8s rDNA fragment (152 bp) was identical in both species. In the aligned ITS regions, there were 0–18 base pair differences (0–2.18% divergence) in pairwise comparisons of the seven forms of C. crispus but no consistent pattern of variation according to gross morphology or geographic origin. However, the ITS sequence differed at 41–54 sites (6.22‐7.56%) between C. crispus and C. ocellatus f. ocellatus, again illustrating the genetic distinctiveness of the latter species.

The Lobster Parasite Anophryoides haemophila (Scuticociliatida: Orchitophryidae): Nuclear 18S rDNA Sequence, Phylogeny and Detection Using Oligonucleotide Primers

ABSTRACT. We have determined the nucleotide sequence of the nuclear gene encoding small‐subunit ribosomal ribonucleic acid of the ciliate Anophryoides haemophila, a parasite of the American lobster Homarus americanus. The gene is 1763 bp in length, and has a guanosine‐plus‐cytosine content of 43.9%. Inferred phylogenetic frameworks strongly support the monophyly of the scuticociliates, and suggest that order Scuticociliatida should be elevated to at least subclass rank. Oligonucleotide probes based on A. haemophila ssu‐rDNA can discriminate between DNAs of A. haemophila and other investigated hymenostome ciliates, and effectively prime polymerase chain reaction‐based detection of A. haemophila deoxyribonucleic acid against at least a 1600‐fold excess of total deoxyribonucleic acid from H. americanus.

Nucleotide sequences of 18S ribosomal RNA genes from the red algae Gracilaria tikvahiae McLachlan, Gracilaria verrucosa (Hudson) Papenfuss and Gracilariopsis sp.

Owing especially to intensive aquaculture in recent years, marine red algae of the family Gracilariaceae have become the major source of agar in the international market. However, because of a high degree of morphological similarity among gracilariacean algae, and morphological plasticity within populations, identification and classification of these algae are often problematic. These difficulties greatly complicate assessment of natural agarophyte stocks, and may raise problems for regulatory approval of agars. Gracilaria tikvahiae McLachlan is the most thoroughly characterized of the hundred-odd described species of Gracilaria, and belongs to the subgenus Textoriella. Gracilaria verrucosa (Hudson) Papenfuss is a widely distributed, economically important species, and is the type of the other (nominate) subgenus. The verrucosa species concept has, however, recently been shown to comprise a number of similar taxa (1). Using organellar DNA restriction profiles, we have identified an assemblage of chiefly European strains conforming to the current concept of G. verrucosa (2); the G. verrucosa nuclear smallsubunit (18S) rDNA sequence below represents one of these strains, from Oslo, Norway. Species recognition has been further complicated by the discovery in the G. verrucosa type locality of an as yet unidentified species of the related genus Gracilariopsis (3) which has frequently been mistaken for G. verrucosa, therefore may be included in the original species concept (2). To assist in characterizing this Gracilariopsis sp., we have determined the sequence of its 18S rDNA for comparison with that recently

Are Ichthyosporea animals or fungi? Bayesian phylogenetic analysis of elongation factor 1α of Ichthyophonus irregularis

Ichthyosporea is a recently recognized group of morphologically simple eukaryotes, many of which cause disease in aquatic organisms. Ribosomal RNA sequence analyses place Ichthyosporea near the divergence of the animal and fungal lineages, but do not allow resolution of its exact phylogenetic position. Some of the best evidence for a specific grouping of animals and fungi (Opisthokonta) has come from elongation factor 1alpha, not only phylogenetic analysis of sequences but also the presence or absence of short insertions and deletions. We sequenced the EF-1alpha gene from the ichthyosporean parasite Ichthyophonus irregularis and determined its phylogenetic position using neighbor-joining, parsimony and Bayesian methods. We also sequenced EF-1alpha genes from four chytrids to provide broader representation within fungi. Sequence analyses and the presence of a characteristic 12 amino acid insertion strongly indicate that I. irregularis is a member of Opisthokonta, but do not resolve whether I. irregularis is a specific relative of animals or of fungi. However, the EF-1alpha of I. irregularis exhibits a two amino acid deletion heretofore reported only among fungi.

The 18S rRNA gene sequences of four commercially important seaweeds

Abstract18S rRNA gene sequences are presented forAhnfeltia plicata, Chondrus crispus, Furcellaria lumbricalis andPalmaria palmata, commercially important marine algae of the North Atlantic. The sequences range from 1765 to 1777 nucleotides in length, with guanine + cytosine content of 50.1% to 52.4%. Sequence divergence between species in different orders was 11.3–12.3%, whereas the variation betweenC. crispus andF. lumbricalis, both from the Gigartinales, was only 3.6%. Based on limited experience with other groups of Rhodophyta, these sequences obtained from single populations are likely to be representative of the species as a whole, with little variation expected among conspecifics regardless of morphological aberration or apparent genetic isolation.

STRUCTURAL, TRANSCRIPTIONAL, AND PHYLOGENETIC ANALYSES OF THE atpB GENE CLUSTER FROM THE PLASTID OF CRYPTOMONASΨ (CRYPTOPHYCEAE)1

Genes encoding the β and ɛ subunits of the H+‐adenosine triphosphatase complex have been identified in the large single‐copy region of the plastid genome from the marine chlorophyll c‐containing alga Cryptomonas Ψ. Sequence analysis shows that the two genes do not overlap as in most land plants but, rather, are separated by a short 11‐bp intergenic region. The genes lack introns and encode polypeptides of 475 and 131 amino acids, respectively. The two genes are co‐transcribed, producing a transcript of approximately 2000 nucleotides. Primer extension analysis of the 5′ end of the transcript indicates two termini, one more prominent than the other. Sequence motifs typical of chloroplast promoters are located at — 10 and — 35 bp from both of these termini. Upstream of the atpBE operon is a gene with similarity to ORF167 of land plant plastids, and downstream is ORF281, which is homologous to a similarly located open reading frame from a brown alga. Phylogenetic analysis of atpB sequences from a variety of eubacteria and plastids shows all plastids arising from a single origin within the cyanobacteria and a clear dichotomy between the green and non‐green lineages, in agreement with trees based on plastid small‐subunit ribosomal RNA sequences.