PCR‐based markers detect genetic variation at growth and immune function‐related loci in chinook salmon (Oncorhynchus tshawytscha)

We developed seven polymerase chain reaction (PCR) based markers that detect genetic variation at loci related to growth (four) and immune function (three) in chinook salmon. One assay shows a length polymorphism following PCR; the others show restriction fragment length polymorphisms (PCR‐RFLP). Two alleles were detected in each assay, and the common alleles were found at frequencies of 0.67–0.95 in seven wild populations in British Columbia, Canada. These loci also amplified in other salmonid species. These markers, by detecting variation linked to genes with high fitness relevance, are expected to be useful in a range of theoretical and applied studies.     

Ericoid mycorrhizal fungi: some new perspectives on old acquaintances

Many ericaceous species colonize as pioneer plants substrates ranging from arid sandy soils to moist mor humus, in association with their mycorrhizal fungi. Thanks to the symbiosis with ericoid mycorrhizal fungi, ericaceous plants are also able to grow in highly polluted environments, where metal ions can reach toxic levels in the soil substrate. For a long time this mycorrhizal type has been regarded as an example of a highly specific interaction between plants and fungi. More recent studies have been challenging this view because some ericoid mycorrhizal endophytes seem also able to colonise plants from very distant taxa. A molecular approach has allowed the investigation of genetic diversity and molecular ecology of ericoid mycorrhizal fungi, and has revealed that ericaceous plants can be very promiscuous, with multiple occupancy of their thin roots. The molecular analysis of sterile morphotypes involved in this symbiosis has also led to deeper understanding of the species diversity of ericoid fungi. Genetic polymorphism of ericoid fungi is wider than previously thought, and often increased by the presence of Group I introns in the nuclear small subunit rDNA.     

The curious case of protein splicing: mechanistic insights suggested by protein semisynthesis.

The gradual accumulation of examples of protein splicing, in which a nested intervening sequence is spliced out of the interior of a polyprotein precursor, suggests that this curious phenomenon might prove to have universal phylogenetic distribution and biological significance. The known examples are reviewed, with the aim of establishing underlying patterns, and a generalized mechanism of autocatalytic protein splicing is proposed. The testable consequences of such a proposal and the possible evolutionary origins of the phenomenon are discussed.     

STRUCTURAL FEATURES OF NUCLEAR GENES IN THE CENTRIC DIATOM THALASSIOSIRA WEISSFLOGII (BACILLARIOPHYCEAE)

Thalassiosira weissflogii (Grun.) Fryxell et Hasle is one of the more commonly studied centric diatoms, and yet molecular studies of this organism are still in their infancy. The ability to identify open reading frames and thus distinguish between introns and exons, coding and noncoding sequence is essential to move from nuclear DNA sequences to predicted amino acid sequences. To facilitate the identification of open reading frames in T. weissflogii , two newly identified nuclear genes encoding β-tubulin and t  -complex polypeptide (TCP)-γ, along with six previously published nuclear DNA sequences, were examined for general structural features. The coding region of the nuclear open reading frames had a G + C content of about 49% and could readily be distinguished from noncoding sequence due to a significant difference in G + C content. The introns were uniformly small, about 100 base pairs in size. Furthermore, the 5' and 3' splice sites of introns displayed the canonical GT/AG sequence, further facilitating recognition of noncoding regions. Six of the nuclear open reading frames displayed relatively little bias in the use of synonymous codons, as exemplified by the cDNAs encoding β-tubulin and TCP-γ. Two open reading frames displayed strong bias in the use of particular codons (although the codons used were different), as exemplified by the cDNA encoding fucoxanthin chlorophyll a/c binding protein. Knowledge of codon bias should facilitate, for example, design of degenerate PCR primers and potential heterologous reporter gene constructs.     

PHYLOGENETIC RELATIONSHIPS AMONG STREPTOPHYTES AS INFERRED FROM CHLOROPLAST SMALL AND LARGE SUBUNIT rRNA GENE SEQUENCES1

To gain insights into the phylogeny of charophytes and into their relationships with other green algae and bryophytes, we analyzed the chloroplast small and large subunit rRNA sequences of charophytes belonging to five orders (Charales, Coleochaetales, Desmidiales, Klebsormidiales, and Zygnematales), of chlorophytes from the four remaining classes of green algae, and of bryophytes representing the three classes reported in this group of land plants. We also probed the gene organization and intron content of the chloroplast rDNA operon in charophytes and bryophytes. The organization of this operon proved to be highly conserved, except in members of the Desmidiales and Zygnematales. Homologous group II introns were identified in the trnA(UGC) gene of all charophyte groups examined and in the trnI(GAU) gene of charophytes from all orders except the Desmidiales and Zygnematales. Phylogenetic analyses of concatenated rDNA sequences consistently placed the prasinophyte Mesostigma viride Lauterborn at the base of the Streptophyta and Chlorophyta, although alternative topologies positioning Mesostigma within the Streptophyta could not be rejected. A sister group relationship was unambiguously established between Chaetosphaeridium globosum (Nordstedt) Klebahn and members of the Coleochaetales. The Charales, Coleochaetales, Desmidiales, and Zygnematales were found to be monophyletic, and a sister group relationship was observed for the Desmidiales and Zygnematales. Although our analyses failed to resolve the branching order of the Coleochaetales, Charales, Desmidiales/Zygnematales, and bryophytes, they revealed that the problematic charophyte taxon Entransia fimbriata Hughes strongly clusters with Klebsormidium flaccidum (Kützing) Silva, Mattox et Blackwell to form a basal lineage relative to the other charophyte orders examined.     

Characterization of the subtilase gene family in tomato (Lycopersicon esculentum Mill.)

The gene family of subtilisin-like serine proteases (subtilases, SBTs) in tomato (Lycopersicon esculentum Mill.) comprises at least 15 members, 12 of which have been characterized in this study. Sequence comparison revealed that tomato subtilases fall into 5 distinct subfamilies. Single genes were shown to exist for LeSBT1, LeSBT2 and tmp, while 5 and 6 genes were found in the LeSBT3/4 and P69 subfamilies, respectively. With the exception of tmp, tomato subtilase genes were found to lack introns. Expression of subtilase genes was confirmed at the mRNA level by northern blot analysis and/or by primer extension experiments. For each of the 5 subtilase subfamilies, a distinctive pattern of expression was observed in tomato organs. At least one of the subtilases was found to be expressed in each organ analysed. Structural features evident from deduced amino acid sequences are discussed with reference to the related mammalian proprotein convertases.     

The Chloroplast Genome of Euglena mutabilis—Cluster Arrangement,Intron Analysis,and Intrageneric Trends

A comparative analysis of the chloroplast genome of Euglena mutabilis underlined a high diversity in the evolution of plastids in euglenids. Gene clusters in more derived Euglenales increased in complexity with only a few, but remarkable changes in the genus Euglena. Euglena mutabilis differed from other Euglena species in a mirror‐inverted arrangement of 12 from 15 identified clusters, making it very likely that the emergence at the base of the genus Euglena, which has been considered a long branch artifact, is truly a probable position. This was corroborated by many similarities in gene arrangement and orientation with Strombomonas and Monomorphina, rendering the genome organization of E. mutabilis in certain clusters as plesiomorphic feature. By RNA analysis exact exon–intron boundaries and the type of the 77 introns identified were mostly determined unambiguously. A detailed intron study of psbC pointed at two important issues: First, the number of introns varied even between species, and no trend from few to many introns could be observed. Second, mat1 was localized in Eutreptiales exclusively in intron 1, and mat2 was not identified. With the emergence of Euglenaceae in most species, a new intron containing mat2 inserted in front of the previous intron 1 and thereby became intron 2 with mat1.     

Interglacial refugia on tropical mountains: Novel insights from the summit rat (Rattus baluensis), a Borneo mountain endemic

Aim

The genetics of organisms currently isolated in refugia has received little attention compared to post‐glacial expansions. We study the population history and connectivity of a rat endemic to montane habitat in Borneo to better understand the history and potential of populations in interglacial mountain refugia.

Location

Sabah, Borneo, Malaysia.

Methods

We performed a field survey of the summit rat (Rattus baluensis) on two mountains, Mt. Kinabalu and Mt. Tambuyukon, its entire known distribution. We sequenced mitogenomes and 27 introns (19 of which were polymorphic) in 49 individuals from both populations. We analysed their current genetic structure and diversity, and inferred their demographic history with approximate Bayesian computation.

Results

Summit rats were tightly associated with mountain mossy forest and scrubland above 2,000 m, facilitating the prediction of their past and future distributions. The genetic analysis supports a Holocene fragmentation of a larger population into smaller ones that are now isolated in interglacial refugia on mountaintops. These findings are consistent with climatic reconstructions and the retreat of upland forest to higher elevations after the Last Glacial Maximum (LGM), ~21 kya.

Main conclusions

The two isolated populations of summit rats formed through the upland shift of their habitat after the LGM. The current trend of global warming will likely lead to diminishing suitable upland habitat and result in the extinction of the population on Mt. Tambuyukon. The population on Mt. Kinabalu, the higher peak, could persist at higher elevations, highlighting the singular value of high tropical mountains as reservoirs of biodiversity during past and ongoing climate change.

     

A tripartite group II intron in mitochondria of an angiosperm plant

In mitochondria of flowering plants the nad5 open reading frame is assembled from five exons via two conventional cis-splicing and two trans-splicing events. Trans-splicing between exons c and d in wheat, petunia and Arabidopsis involves a bipartite group II intron structure, while in Oenothera a large portion of intron domains I–IV is missing from the major genomic locus. This intron region has been lost downstream of exon c and is now found in a distant genomic region. Intragenomic recombination across an 11 nucleotide sequence has separated these intron parts, which now have to be reassembled from three independent RNA precursors. This organisation coexists with highly substoichiometric copy numbers of the bipartite intron arrangement, consistent with an evolutionary origin of the tripartite intron by genomic disruption. Received: 28 August 1996 / Accepted: 11 December 1996