Evidence for Positive Selection on a Sexual Reproduction Gene in the Diatom Genus Thalassiosira (Bacillariophyta)

Single likelihood ancestor counting (SLAC), fixed effects likelihood (FEL), and several random effects likelihood (REL) methods were utilized to identify positively and negatively selected sites in sexually induced gene 1 (Sig1) of four different Thalassiosira species. The SLAC analysis did not find any sites affected by positive selection but suggested 13 sites influenced by negative selection. The SLAC approach may be too conservative because of low sequence divergence. The FEL and REL analyses revealed over 60 negatively selected sites and two positively selected sites that were unique to each method. The REL method may not be able to reliably identify individual sites under selection when applied to short sequences with low divergence. Instead, we proposed a new alignment-wide test for adaptive evolution based on codon models with variation in synonymous and nonsynonymous substitution rates among sites and found evidence for diversifying evolution without relying on site-by-site testing. The performance of the FEL and REL approaches was evaluated by subjecting the tests to a type I error rate simulation analysis, using the specific characteristics of the Sig1 data set. Simulation results indicated that the FEL test had reasonable Type I errors, while REL might have been too liberal, suggesting that the two positively selected sites identified by FEL (codons 94 and 174) are not likely to be false positives. The evolution of these codon sites, one of which is located in functional domain II, appears to be associated with divergence among the three major Thalassiosira lineages. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Martin Kreitman]     

Molecular characterisation of two novel maize LRR receptor-like kinases, which belong to the SERK gene family

Genes encoding two novel members of the leucine-rich repeat receptor-like kinase (LRR-RLK) superfamily have been isolated from maize (Zea mays L.). These genes have been named ZmSERK1 and ZmSERK2 since features such as a putative leucine zipper (ZIP) and five leucine rich repeats in the extracellular domain, a proline-rich region (SPP) just upstream of the transmembrane domain and a C-terminal extension (C) after the kinase domain identify them as members of the SERK (omatic mbryogenesis eceptor-like inase) family. ZmSERK1 and ZmSERK2 are single-copy genes and show 79% identity among each other in their nucleotide sequences. They share a conserved intron/exon structure with other members of the SERK family. In the maize genome, ZmSERK1 maps to position 76.9 on chromosome arm 10L and ZmSERK2 to position 143.5 on chromosome arm 5L, in regions generally not involved in duplications. ZmSERK1 is preferentially expressed in male and female reproductive tissues with strongest expression in microspores. In contrast, ZmSERK2 expression is relatively uniform in all tissues investigated. Both genes are expressed in embryogenic and non-embryogenic callus cultures. Received: 20 June 2000 / Accepted: 25 September 2000     

Molecular Evolution and Positive Selection of the Symbiotic Gene NORK in Medicago truncatula

Understanding the selective constraints of partner specificity in mutually beneficial symbiosis is a significant, yet largely unexplored, prospect of evolutionary biology. These selective constraints can be explored through the study of nucleotide polymorphism at loci controlling specificity. The membrane-anchored receptor NORK (nodulation receptor kinase) of the legume Medicago truncatula controls early steps of root infection by two symbiotic microorganisms: nitrogen-fixing bacteria (rhizobia) and endomycorrhizal fungi (Glomales). We analyzed the diversity of the gene NORK by sequencing 4 kilobases in 28 inbred lines sampled from natural populations. We detected 33 polymorphic sites with only one nonsynonymous change. Analysis based on Tajima’s D and Fay and Wu’s H summary statistics revealed no departure from the neutral model. We analyzed divergence using sequences from the closely related species M. coerulea. The McDonald-Kreitman test indicated a significant excess of nonsynonymous changes contributing to this divergence. Furthermore, maximum-likelihood analysis of a molecular phylogeny of a few legume species indicated that a number of amino acid sites, likely located in the receptor domain of the protein, evolved under the regime of positive selection. Further research should focus on the rate and direction of molecular coevolution between microorganisms’ signaling molecules and legumes’ receptors. [Reviewing Editor: Dr. Deborah Charlesworth] Sequence data were deposited in the GenBank database under accession nos. AY676428 to AY676457 and AJ884582.     

Polymorphism of the (CTG)n Repeat of the Myotonin Protein Kinase Gene in Populations of the Sakha Republic (Yakutia) and Central Asia

The allele frequency distribution of the (CTG)_n repeat located in the 3′-terminal region of the myotonin protein kinase gene (DMPK) was compared for populations of Yakutia (three ethnogeographic groups of Yakuts, Evenks, Evens, Yukaghirs, and Dolgans) and Central Asia (Kazakhs, Uzbeks, and Uighurs) and other ethnic groups. The populations of the two regions proved to considerably differ from each other: features characteristic of Asian Mongoloids were more distinct in the populations of Yakutia, while the Central Asian populations were closer to European populations. The (CTG)_n allele spectrum of Yakuts was considered in connection with the high incidence of myotonic dystrophy in Yakutia. The results support the hypothesis of the founder effect for the spread of myotonic dystrophy in Yakuts. Data on the (CTG)_n polymorphism were used to estimate the phylogenetic relationships of the populations under study.__________Translated from Molekulyarnaya Biologiya, Vol. 39, No. 3, 2005, pp. 385–393.Original Russian Text Copyright © 2005 by Fedorova, Khusainova, Kutuev, Sukhomyasova, Nikolaeva, Kulichkin, Akhmetova, Salimova, Svyatova, Berezina, Platonov, Khusnutdinova.     

Characterization of the Brassinosteroid Insensitive 1 Genes of Cotton

Suppression of brassinosteroid (BR) biosynthesis in cotton ovules by treatment with brassinazole inhibits fiber formation, indicating that BR plays an important role in cotton fiber development. Plant responses to brassinosteroids (BR) are mediated through a plasma membrane-bound leucine-rich repeat (LRR) receptor-like protein kinase known as BRI1. Mutations in the BRI1 genes of several species result in dwarfed plants with reduced sensitivity to BR. A single expressed sequence tag (EST) from cotton with strong sequence similarity to Arabidopsis BRI1 ( AtBRI1 ) was identified in a search of publicly available databases. With this EST as a starting point, full-length cDNAs and genomic coding sequences from upland cotton ( Gossypium hirsutum ) BRI1 ( GhBRI1 ) were obtained and characterized. Ectopic expression of this coding sequence in BR-insensitive Arabidopsis plants resulted in recovery of normal growth indicating that GhBRI1 is a functional homologue of AtBRI1. G. hirsutum is an allotetraploid (AADD) derived from diploid ancestors. Analysis of several GhBRI1 cDNAs showed two distinct sequences indicating the presence of two GhBRI1 genes, denoted GhBRI1-1 and GhBRI1-2. Sequence comparisons between these GhBRI1 coding sequences and those from related A and D genome diploid Gossypium species ( G. arboreum and G. thurberi ) indicated that GhBRI1-1 is likely to the A sub-genome orthologue while GhBRI1-2 is from the D sub-genome.     

Likelihood Analysis of the Chalcone Synthase Genes Suggests the Role of Positive Selection in Morning Glories (<Emphasis Type="Italic">Ipomoea</Emphasis>)

Chalcone synthase (CHS) is a key enzyme in the biosynthesis of flavonoides, which are important for the pigmentation of flowers and act as attractants to pollinators. Genes encoding CHS constitute a multigene family in which the copy number varies among plant species and functional divergence appears to have occurred repeatedly. In morning glories (Ipomoea), five functional CHS genes (A–E) have been described. Phylogenetic analysis of the Ipomoea CHS gene family revealed that CHS A, B, and C experienced accelerated rates of amino acid substitution relative to CHS D and E. To examine whether the CHS genes of the morning glories underwent adaptive evolution, maximum-likelihood models of codon substitution were used to analyze the functional sequences in the Ipomoea CHS gene family. These models used the nonsynonymous/synonymous rate ratio ( = d_N/d_S) as an indicator of selective pressure and allowed the ratio to vary among lineages or sites. Likelihood ratio test suggested significant variation in selection pressure among amino acid sites, with a small proportion of them detected to be under positive selection along the branches ancestral to CHS A, B, and C. Positive Darwinian selection appears to have promoted the divergence of subfamily ABC and subfamily DE and is at least partially responsible for a rate increase following gene duplication.     

Isolation and preliminary characterization of gas1-1, a mutation causing partial suppression of the phenotype conferred by the gibberellin-insensitive (gai) mutation in Arabidopsis thaliana (L.) Heyhn

The semi-dominant gai mutation of arabidopsis confers a dark-green dwarf phenotype resembling that of gibberellin (GA)-deficient mutants. In contrast to GA-deficient mutants, gai mutants do not respond to GA treatments and accumulate higher levels of bioactive GAs than are found in wild-type controls. The gai mutation thus alters the responses of plant cells to GA, indicating that the GAI (wild-type) gene product is involved in GA reception and/or signal transduction. Here we describe the isolation and preliminary characterization of a mutation, gas1-1, which is not linked to gai and which partially suppresses the effect of the gai mutation. Double mutant, gai gas1-1, homozygotes are less severely dwarfed and lighter green than gai GAS1 controls. However, comparisons of the effects of treatments with exogenous GA demonstrate that gas1-1 does not increase the GA responsiveness of the gai mutant. Thus the gas1-1 mutation appears to reduce the GA-dependency of plant growth, and identifies a gene (GAS1) whose product is a candidate GA signal-transduction component.Abbreviations GA gibberellin - GA₃ gibberellic acid We thank Maarten Koornneef (Wageningen Agricultural University, The Netherlands) for providing mutant seed stocks; Mark Aarts and Bernard Mulligan (University of Nottingham, UK) for performing the -irradiation. This work was made possible by AFRC/BBSRC PMB Grants PG208/520 and PG208/0600, and by a grant from the Gatsby Charitable Foundation. P.C. was supported by a Human Capital and Mobility Fellowship from the EC.     

Mapping of RFLP and qualitative trait loci in Brassica rapa and comparison to the linkage maps of B. napus,B. oleracea,and Arabidopsis thaliana

A linkage map of restriction fragment length polymorphisms (RFLPs) was constructed for oilseed, Brassica rapa, using anonymous genomic DNA and cDNA clones from Brassica and cloned genes from the crucifer Arabidopsis thaliana. We also mapped genes controlling the simply inherited traits, yellow seeds, low seed erucic acid, and pubescence. The map included 139 RFLP loci organized into ten linkage groups (LGs) and one small group covering 1785 cM. Each of the three traits mapped to a single locus on three different LGs. Many of the RFLP loci were detected with the same set of probes used to construct maps in the diploid B. oleracea and the amphidiploid B. napus. Comparisons of the linkage arrangements between the diploid species B. rapa and B. oleracea revealed six LGs with at least two loci in common. Nine of the B. rapa LGs had conserved linkage arrangements with B. napus LGs. The majority of loci in common were in the same order among the three species, although the distances between loci were largest on the B. rapa map. We also compared the genome organization between B. rapa and A. thaliana using RFLP loci detected with 12 cloned genes in the two species and found some evidence for a conservation of the linkage arrangements. This B. rapa map will be used to test for associations between segregation of RFLPs, detected by cloned genes of known function, and traits of interest.     

Analysis of two linked genes coding for the acyl carrier protein (ACP) from Arabidopsis thaliana (columbia)

Two linked genes, A1 and A2, coding for nearly identical isoforms of the acyl carrier protein (ACP) were isolated from an Arabidopsis thaliana (columbia) genomic library and sequenced. The amino acids deduced from the nucleotide sequence of the two genes indicate they encode distinct transit peptides, but the mature proteins are the same except for residue 79. Both genes are predicted to contain three introns in similar positions, although they differ in sequence and length. The introns interrupt regions coding for a) the transit peptide, b) the junction of the transit peptide and mature protein, and c) the highly conserved domain surrounding serine 38 to which the phosphopantetheine is attached. Primer extension analysis indicates that at least A1 is active in young plants.     

Studies on the behavior of organelles and their nucleoids in the root apical meristem of Arabidopsis thaliana (L.) Col.

The behavior of cell nuclei, mitochondrial nucleoids (mt-nucleoids) and plastid nucleoids (ptnucleoids) was studied in the root apical meristem of Arabidopsis thaliana. Samples were embedded in Technovit 7100 resin, cut into thin sections and stained with 4′-6-diamidino-2-phenylindole for light-microscopic autoradiography and microphotometry. Synthesis of cell nuclear DNA and cell division were both active in the root apical meristem between 0 μm and 300 μm from the central cells. It is estimated that the cells generated in the lower part of the root apical meristem enter the elongation zone after at least four divisions. Throughout the entire meristematic zone, individual cells had mitochondria which contained 1–5 mt-nucleoids. The number of mitochondria increased gradually from 65 to 200 in the meristem of the central cylinder. Therefore, throughout the meristem, individual mitochondria divided either once or twice per mitotic cycle. By contrast, based on the incorporation of [³H]thymidine into organelle nucleoids, syntheses of mitochondrial DNA (mtDNA) and plastid DNA (ptDNA) occurred independently of the mitotic cycle and mainly in a restricted region (i.e., the lower part of the root apical meristem). Fluorimetry, using a videointensified microscope photon-counting system, revealed that the amount of mtDNA per mt-nucleoid in the cells in the lower part of the meristem, where mtDNA synthesis was active, corresponded to more than 1 Mbp. By contrast, in the meristematic cells just below the elongation zone of the root tip, the amount of mtDNA per mt-nucleoid fell to approximately 170 kbp. These findings strongly indicate that the amount of mtDNA per mitochondrion, which has been synthesized in the lower part of the meristem, is gradually reduced as a result of continual mitochondrial divisions during low levels of mtDNA synthesis. This phenomenon would explain why differentiated cells in the elongation zone have mitochondria that contain only extremely small amounts of mtDNA. This work was supported by a Grant-in Aid (T.K.) for Special Research on Priority Areas (Project No. 02242102, Cellular and Molecular Basis for Reproduction Processes in Plants) from the Ministry of Education, Science and Culture of Japan and by a Grant-in Aid (T.K.) for Original and Creative Research Project on Biotechnology from the Research Council, Ministry of Agriculture, Forestry and Fisheries of Japan.     

Phosphorylation of Arabidopsis response regulator 7 (ARR7) at the putative phospho-accepting site is required for ARR7 to act as a negative regulator of cytokinin signaling

Cytokinins are plant hormones that regulate diverse aspects of plant growth and development. Arabidopsis cytokinin signal transduction utilizes a multi-step two-component signaling (TCS) system by histidyl–aspartidyl phosphorelays. We here show that phosphorylation of ARR7, an A-type response regulator that acts as a negative regulator of cytokinin signaling, is required for its function in plants. Phosphorylation of ARR7 is inhibited in vitro by mutation in a putative phospho-accepting Asp residue into an Asn residue (ARR7^D85N). While ectopic expression of ARR7 decreases root-growth inhibition, callus formation, and cytokinin-inducible gene expression, overexpression of ARR7 ^D85N at the similar level does not generate these phenotypes. ARR7^D85N is localized to the nucleus and the half-life of this mutant protein is similar to that of ARR7 in Arabidopsis mesophyll protoplasts. These results suggest that the phosphorylation of ARR7 is necessary for ARR7-mediated cytokinin response.     

Selective adaptation to copper of populations ofAgrostis tenuis andFestuca rubra (Poaceae)

Populations ofAgrostis Tenuis andFestuca rubra, tolerant and non-tolerant towards Zn and Pb, were studied in regard to their adaptability by natural selection, towards a third metal (Cu) and the time required for the appearance of such tolerance. It was found that Zn and Pb tolerant and non-tolerant populations are likely to select the character of Cu-tolerance within the course of only one generation. More specifically, Zn and Pb tolerant populations show a better adaptability compared with non-tolerant ones. The amount of tolerance to copper obtained by artificial selection is comparable with that of populations growing naturally on copper mines.     

Selection against homozygotes in the ADH polymorphic system of Drosophila melanogaster associated with the lethal factor l(2) Stm

In the natural populations ⁺Tüb, ⁺Prov, and ⁺Rov, similar Adh ^F allele frequencies occur (q _F=0.11, 0.18, and 0.08, respectively). However, there is a discrepancy in that the Adh ^F allele in ⁺Tüb is closely linked to the lethal factor 1(2)Stm, which reduces relative fitness of the F phenotype to zero. In spite of this, polymorphism is maintained also in ⁺Tüb, because the heterozygotes are superior to the homozygous S type (relative fitness=0.88). Under laboratory culture conditions, in ⁺Tüb the relative fitness of the S genotype further decreases to 0.6. After outcrossing the lethal factor, relative fitnesses for S, FS, and F become 0.6, 1, and 0.48, respectively, implying that fitness for S remains the same. Relative values for S, FS, and F in ⁺Prov, not affected by the lethal factor, are calculated by the maximum average fitness method to be 1, 1.2, and 0.2 under the assumption that heterozygous FS are similarly superior to S as in the natural ⁺Tüb population and all allele frequencies found are stable equilibrium values.     

The Stasis and Possible Patterns of Selection in Evolution of a Group of Related Species from the Bat Genus <Emphasis Type="Italic">Myotis</Emphasis> (Chiroptera,Vespertilionidae)

Phenotypic evolutionary rates were measured for craniometric characters in five extant closely related OTUs from the bat genus Myotis (Chiroptera, Vespertilionidae): M. myotis, M. blythii oxygnathus, M. b. omari, M. b. blythii, and M. nattereri using Lynch’s and Gingerich’s approaches. Cranial shape appeared to be more conservative than cranial size. Estimates for evolutionary rates were found to be lower than expected if the divergence had been produced solely by mutation and random drift. So, it can be concluded that stabilizing selection was the principal factor that maintained craniometric characters during the evolution of the studied species and prevented their greater diversification. The observed differences between the OTUs could be established by random drift or directional selection of rather moderate intensity. The rates of divergence between the ancestors of M. nattereri and the common ancestors of M. blythii and M. myotis apparently were higher than the rates of following divergence between M. myotis, M. b. oxygnathus, M. b. omari and M. b. blythii.     

The binding of lectins to carbohydrate moieties on haemocytes of the insects,Blaberus craniifer (Dictyoptera) and Extatosoma tiaratum (Phasmida)

Summary The specificity and distribution of carbohydrate moieties, which act as receptors for lectins on the haemocytes of two insect species, Blaberus craniifer and Extatosoma tiaratum, were investigated. Four peroxidase-labelled lectins were utilised as probes: wheat-germ agglutinin, Ricinus communis (120) agglutinin, concanavalin A and Lens culinaris agglutinin, and binding visualised by reaction with DAB/H₂O₂. The lectin-binding studies indicated that Blaberus and Extatosoma plasmatocytes, and Extatosoma spreading granular cells possess surface N-acetyl-D-glucosamine, D-galactose and mannose moieties; Extatosoma cystocytes have D-galactose and mannose; whilst Blaberus granular cells/cystocytes and Extatosoma fine granular cells have mannose determinants.