Phylogeny of Leavenworthia S-alleles suggests unidirectional mating system evolution and enhanced positive selection following an ancient population bottleneck

The adoption of self-fertilization from an ancestral outcrossing state is one of the most common evolutionary transitions in the flowering plants. In the mustard family, outcrossing is typically enforced by sporophytic self-incompatibility (SI), but there are also many self-compatible species. The genus Leavenworthia contains taxa that either possess or lack SI. Here, we present data showing that SI is associated with strict outcrossing and that there is widespread trans-specific sequence polymorphism at the locus involved in the recognition of self-pollen (the S-locus). This ancestral polymorphism is consistent with the presence of an outcrossing mating system in the common ancestor of Leavenworthia species, and suggests that there have been several independent losses of SI in the group. When compared with other mustard species, the bulk of Leavenworthia S-allele sequences are highly diverged from those found in other Brassicaceae and show relatively low levels of nucleotide diversity, a pattern that suggests the common ancestor of the genus likely underwent a strong population bottleneck. The hypothesis of postbottleneck S-locus rediversification is supported by tests showing stronger positive selection acting on S-alleles from Leavenworthia than those found in other Brassicaceae.     

Brassicaceae phylogeny inferred from phytochrome A and ndhF sequence data: tribes and trichomes revisited

The family Brassicaceae comprises 3710 species in 338 genera, 25 recently delimited tribes, and three major lineages based on phylogenetic results from the chloroplast gene ndhF. To assess the credibility of the lineages and newly delimited tribes, we sequenced an approximately 1.8-kb region of the nuclear phytochrome A (PHYA) gene for taxa previously sampled for the chloroplast gene ndhF. Using parsimony, likelihood, and Bayesian methods, we reconstructed the phylogeny of the gene and used the approximately unbiased (AU) test to compare phylogenetic results from PHYA with findings from ndhF. We also combined ndhF and PHYA data and used a Bayesian mixed model approach to infer phylogeny. PHYA and combined analyses recovered the same three large lineages as those recovered in ndhF trees, increasing confidence in these lineages. The combined tree confirms the monophyly of most of the recently delimited tribes (only Alysseae, Anchonieae, and Descurainieae are not monophyletic), while 13 of the 23 sampled tribes are monophyletic in PHYA trees. In addition to phylogenetic results, we documented the trichome branching morphology of species across the phylogeny and explored the evolution of different trichome morphologies using the AU test. Our results indicate that dendritic, medifixed, and stellate trichomes likely evolved independently several times in the Brassicaceae.     

ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny of the Asteraceae

An RNA secondary structure model is presented for the nuclear ribosomal internal transcribed spacers (ITS) based on comparative analysis of 340 sequences from the angiosperm family Asteraceae. The model based on covariation analysis agrees with structural features proposed in previous studies using mainly thermodynamic criteria and provides evidence for additional structural motifs within ITS1 and ITS2. The minimum structure model suggests that at least 20% of ITS1 and 38% of ITS2 nucleotide positions are involved in base pairing to form helices. The sequence alignment enabled by conserved structural features provides a framework for broadscale molecular evolutionary studies and the first family-level phylogeny of the Asteraceae based on nuclear DNA data. The phylogeny based on ITS sequence data is very well resolved and shows considerable congruence with relationships among major lineages of the family suggested by chloroplast DNA studies, including a monophyletic subfamily Asteroideae and a paraphyletic subfamily Cichorioideae. Combined analyses of ndhF and ITS sequences provide additional resolution and support for relationships in the family.     

Phylogenetic relationships of B-related phytochromes in the Brassicaceae: Redundancy and the persistence of phytochrome D

Plants use phytochrome (phy) photoreceptors to detect and respond to changes in the quantities and proportions of red (R) and far-red (FR) light in their environments. The principal mediators of responses to R and FR in Arabidopsis thaliana are phyA and phyB, which are found in all angiosperms surveyed. The present study is concerned with a phytochrome gene pair in Arabidopsis, PHYB and PHYD, which are of relatively recent origin, share high sequence identity, and are partially redundant. Our data suggest that the duplication occurred after the mustard family (Brassicaceae) diverged from its closest relatives but before the radiation of extant Brassicaceae, and that both copies have persisted for up to 40myr. We detected no evidence of positive selection in the divergence of PHYD from PHYB; the evolution of both sequences is constrained by purifying selection. Levels of diversity at both loci are among the lowest observed at nuclear genes in A. thaliana. In common with other loci in A. thaliana, PHYB and PHYD showed elevated levels of intraspecific replacement variation, and each showed an excess of rare nucleotide polymorphisms, consistent with a recent, rapid population expansion. Our results are consistent with the functional importance of amino acid divergence in the central regions of phyB and phyD and suggest specific sites for mutagenesis that may yield insights into the functional differences of phyB and phyD.     

Diversity, Distribution, and Ancient Taxonomic Relationships Within the TIR and Non-TIR NBS-LRR Resistance Gene Subfamilies

Phylogenetic relationships among the NBS-LRR (nucleotide binding site–leucine-rich repeat) resistance gene homologues (RGHs) from 30 genera and nine families were evaluated relative to phylogenies for these taxa. More than 800 NBS-LRR RGHs were analyzed, primarily from Fabaceae, Brassicaceae, Poaceae, and Solanaceae species, but also from representatives of other angiosperm and gymnosperm families. Parsimony, maximum likelihood, and distance methods were used to classify these RGHs relative to previously observed gene subfamilies as well as within more closely related sequence clades. Grouping sequences using a distance cutoff of 250 PAM units (point accepted mutations per 100 residues) identified at least five ancient sequence clades with representatives from several plant families: the previously observed TIR gene subfamily and a minimum of four deep splits within the non-TIR gene subfamily. The deep splits in the non-TIR subfamily are also reflected in comparisons of amino acid substitution rates in various species and in ratios of nonsynonymous-to-synonymous nucleotide substitution rates (K _A/K _S values) in Arabidopsis thaliana. Lower K _A/K _S values in the TIR than the non-TIR sequences suggest greater functional constraints in the TIR subfamily. At least three of the five identified ancient clades appear to predate the angiosperm–gymnosperm radiation. Monocot sequences are absent from the TIR subfamily, as observed in previous studies. In both subfamilies, clades with sequences separated by approximately 150 PAM units are family but not genus specific, providing a rough measure of minimum dates for the first diversification event within these clades. Within any one clade, particular taxa may be dramatically over- or underrepresented, suggesting preferential expansions or losses of certain RGH types within particular taxa and suggesting that no one species will provide models for all major sequence types in other taxa. Received: 13 June 2001 / Accepted: 22 October 2001     

Sequence of the T4 recombination gene, uvsX, and its comparison with that of the recA gene of Escherichia coli.

We have determined the nucleotide sequence of the uvsX gene of bacteriophage T4 which is involved in DNA recombination and damage repair, and whose product catalyzes in vitro reactions related to recombination process in analogous manners to E. coli recA gene product. The coding region consisted of 1170 nucleotides directing the synthesis of a polypeptide of 390 amino acids in length with a calculated molecular weight of 43,760. Amino acid composition, the sequence of seven NH2-terminal amino acids and molecular weight of the protein deduced from the nucleotide sequence were consistent with the data from the analysis of the purified uvsX protein. The nucleotide sequence and the deduced amino acid sequence were compared with those of the recA gene. Although a significant homology was not found in the nucleotide sequences, the amino acid sequences included 23% of identical and 15% of conservatively substituted residues.     

ON COMBINING PROTEIN SEQUENCES AND NUCLEIC ACID SEQUENCES IN PHYLOGENETIC ANALYSIS: THE HOMEOBOX PROTEIN CASE

Abstract— Amino acid encoding genes contain character state information that may be useful for phylogenetic analysis on at least two levels. The nucleotide sequence and the translated amino acid sequences have both been employed separately as character states for cladistic studies of various taxa, including studies of the genealogy of genes in multigene families. In essence, amino acid sequences and nucleic acid sequences are two different ways of character coding the information in a gene. Silent positions in the nucleotide sequence (first or third positions in codons that can accrue change without changing the identity of the amino acid that the triplet codes for) may accrue change relatively rapidly and become saturated, losing the pattern of historical divergence. On the other hand, non-silent nucleotide alterations and their accompanying amino acid changes may evolve too slowly to reveal relationships among closely related taxa. In general, the dynamics of sequence change in silent and non-silent positions in protein coding genes result in homoplasy and lack of resolution, respectively. We suggest that the combination of nucleic acid and the translated amino acid coded character states into the same data matrix for phylogenetic analysis addresses some of the problems caused by the rapid change of silent nucleotide positions and overall slow rate of change of non-silent nucleotide positions and slowly changing amino acid positions. One major theoretical problem with this approach is the apparent non-independence of the two sources of characters. However, there are at least three possible outcomes when comparing protein coding nucleic acid sequences with their translated amino acids in a phylogenetic context on a codon by codon basis. First, the two character sets for a codon may be entirely congruent with respect to the information they convey about the relationships of a certain set of taxa. Second, one character set may display no information concerning a phylogenetic hypothesis while the other character set may impart information to a hypothesis. These two possibilities are cases of non-independence, however, we argue that congruence in such cases can be thought of as increasing the weight of the particular phylogenetic hypothesis that is supported by those characters. In the third case, the two sources of character information for a particular codon may be entirely incongruent with respect to phylogenetic hypotheses concerning the taxa examined. In this last case the two character sets are independent in that information from neither can predict the character states of the other. Examples of these possibilities are discussed and the general applicability of combining these two sources of information for protein coding genes is presented using sequences from the homeobox region of 46 homeobox genes fromDrosophila melanogasterto develop a hypothesis of genealogical relationship of these genes in this large multigene family.     

The primary structure of phosphoenolpyruvate carboxylase of Escherichia coli. Nucleotide sequence of the ppc gene and deduced amino acid sequence

The nucleotide sequence of the ppc gene, the structural gene for phosphoenolpyruvate carboxylase [EC 4.1.1.31], of Escherichia coli K-12 was determined. The gene codes for a polypeptide comprising 883 amino acid residues with a calculated molecular weight of 99,061. The amino acid sequence deduced from the nucleotide sequence was entirely consistent with the protein chemical data obtained with the purified enzyme, including the NH2- and COOH-terminal sequences and amino acid composition. The coding region is preceded by two putative ribosome binding sites, and is followed closely by a good representative of rho-independent terminator. The codon usage in the ppc gene suggests a moderate expression of the gene. The secondary structure of the enzyme was predicted from the deduced amino acid sequence.     

Phylogenetic relationships between the chlorophyll a/b binding protein (CAB) multigene family: An intra- and interspecies study

Summary The genome ofGlycine max (L.) Merr. cv. Dare contains a chlorophyll a/b binding (Cab) protein gene family consisting of 10 genes. The primary structures of two linkedCab genes (Cab 4 andCab 5) were determined. A comparison of the nucleic acid and predicted amino acid sequences ofCab 4 andCab 5 revealed a high degree of similarity (96% and 98%, respectively). Phylogenetic inferences drawn from sequence comparisons between previously characterized soybeanCab 1, 2, and 3 andCab 4 and 5 suggested that soybeanCab 3 was an evolutionarily distant member within this family. We further investigated the molecular evolution of theCab gene family by comparing nucleotide sequences from 25 differentCab genes representing diverse phylogenetic taxa including moncot and dicot species. Phylogenetic inferences from these data support existing morphological phylogenies in that all species within one family clustered together. These data suggested that the Solanaceae were more evolutionarily distant from the monocots than the Fabaceae and Brassicaceae. In addition, these data supported the theory thatCab Type I and II genes originated prior to divergence of the monocots and dicots.     

Cloning and analysis of the nuclear genes for two mitochondrial ribosomal proteins in yeast

Summary Two mitochondrial ribosomal proteins of yeast (Saccharomyces cerevisiae) were purified and their N-terminal amino acid sequences determined. The sequence data were used for the synthesis of oligonucleotide probes to clone the corresponding genes. Thus, the genes for two proteins, termed YMR-31 and YMR-44, were cloned and their nucleotide sequences determined. From the nucleotide sequence data, the coding region of the gene for protein YMR-31 was found to be composed of 369 nucleotide pairs. Comparison of the amino acid sequence of protein YMR-31 and the one deduced from the nucleotide sequence of its gene suggests that it contains an octapeptide leader sequence. The calculated molecular weight of protein YMR-31 without the leader sequence is 12792 dalton. The gene for protein YMR-44 was found to contain a 147 bp intron which contains two sequences conserved among yeast introns. The length of the two exons flanking the intron totals 294 nucleotide pairs which can encode a protein with a calculated molecular weight of 11476 dalton. The gene for protein YMR-31 is located on chromosome VI, while the gene for protein YMR-44 is located on either chromosome XIII or XVI.     

Cladistic analysis of anuran POMC sequences

Procedures for performing cladistic analyses can provide powerful tools for understanding the evolution of neuropeptide and polypeptide hormone coding genes. These analyses can be done on either amino acid data sets or nucleotide data sets and can utilize several different algorithms that are dependent on distinct sets of operating assumptions and constraints. In some cases, the results of these analyses can be used to gauge phylogenetic relationships between taxa. Selecting the proper cladistic analysis strategy is dependent on the taxonomic level of analysis and the rate of evolution within the orthologous genes being evaluated. For example, previous studies have shown that the amino acid sequence of proopiomelanocortin (POMC), the common precursor for the melanocortins and beta-endorphin, can be used to resolve phylogenetic relationships at the class and order level. This study tested the hypothesis that POMC sequences could be used to resolve phylogenetic relationships at the family taxonomic level. Cladistic analyses were performed on amphibian POMC sequences characterized from the marine toad, Bufo marinus (family Bufonidae; this study), the spadefoot toad, Spea multiplicatus (family Pelobatidae), the African clawed frog, Xenopus laevis (family Pipidae) and the laughing frog, Rana ridibunda (family Ranidae). In these analyses the sequence of Australian lungfish POMC was used as the outgroup. The analyses were done at the amino acid level using the maximum parsimony algorithm and at the nucleotide level using the maximum likelihood algorithm. For the anuran POMC genes, analysis at the nucleotide level using the maximum likelihood algorithm generated a cladogram with higher bootstrap values than the maximum parsimony analysis of the POMC amino acid data set. For anuran POMC sequences, analysis of nucleotide sequences using the maximum likelihood algorithm would appear to be the preferred strategy for resolving phylogenetic relationships at the family taxonomic level.     

Nucleotide sequence of the R.meliloti nitrogenase reductase (nifH) gene.

The nucleotide sequence of the structural gene (nifH) of nitrogenase reductase (Fe protein) from R.meliloti 41 with its flanking ends is reported. The amino acid sequence of nitrogenase reductase was deduced from the DNA sequence. The predicted R.meliloti nitrogenase reductase protein consists of 297 amino acid residues, has a molecular weight of 32,740 daltons and contains 5 cysteine residues. The codon usage in the nifH gene is presented. In the 5' flanking region, sequences resembling to consensus sequences of bacterial control regions were found. Comparison of the R.meliloti nifH nucleotide and amino acid sequences with those from different nitrogen-fixing organisms showed that the amino acid sequences are more conserved than the nucleotide sequences. This structural conservation of nitrogenase reductase may be related to its function and may explain the conservation of the nifH gene during evolution.     

Structure and evolution of human α-fetoprotein deduced from partial sequence of cloned cDNA

The nucleotide sequence of a recombinant DNA clone, containing a partial mRNA sequence for human α-fetoprotein (AFP) in the plasmid vector pBR322, has been determined. Two regions of the cloned nucleotide sequence were found to agree with published amino acid sequences of two cyanogen bromide peptides derived from human AFP. Examination of the amino acid sequence, deduced from the cloned portion of the mRNA coding region, reveals extensive homology with the third domain of the human serum albumin molecule. A total of 44% ( ) amino acids and 54% ( ) nucleotides are identical in the two structures. The landmark cysteine residues are found in the same positions in both polypeptide chains, presumably forming the same disulfide bridges in AFP as those found in the albumin. The sequence homology reinforces the evidence that human AFP and albumin constitute a gene family, in analogy to the same family found in rodents. A comparison of the human and rodent sequence data suggests that the rate of molecular evolution has been faster for AFP than for albumin.     

The Phylogenetic Informativeness of Nucleotide and Amino Acid Sequences for Reconstructing the Vertebrate Tree

To aid in future efforts to accurately reconstruct the vertebrate tree, a quantitative measure of phylogenetic informativeness was applied to nucleotide and amino acid sequences for a set of 11 genes. We identified orthologues and assembled published fossil-calibrated divergence times between taxa that had been sequenced for each gene. Rates of molecular evolution for each site were estimated to characterize the molecular evolutionary pattern of genes and to calculate the phylogenetic informativeness. The fast-evolving gene albumin yielded the highest informativeness over the period from 60 million years ago to 500 million years ago. In contrast, calmodulin yielded the lowest informativeness, presumably because functional constraint minimized substitutions in the amino acid sequence. The gene c-myc showed an intermediate level of informativeness. The nucleotide sequence of cytochrome b showed extremely high utility for recent epochs, but low utility for times before 100 million years ago. We ranked nine other genes for their utility during the epochs of the divergence of the muroid rodents, early placental mammals, early vertebrates, and early metazoa, yielding results consistent with, but more precise than, previous studies. Interestingly, DNA sequence always exceeded amino acid sequence in informativeness over all time scales, yet support values were at best moderately higher. For epochs not subject to strong phylogenetic conflict due to convergence, we advocate gleaning the additional power of the threefold increase in number of characters that is present for DNA sequences over resorting to the less noisy but less informative amino acid sequences.     

Cloning and nucleotide sequence of the aspartase gene of Escherichia coli W.

The aspA gene of Escherichia coli W which encodes aspartase was cloned into the plasmid vector pBR322. The nucleotide sequences of aspA and its flanking regions were determined. The aspA gene encodes a protein with a molecular weight of 52,224 consisted of 477 amino acid residues. The amino acid sequence of the protein predicted from the nucleotide sequence was consistent with those of the NH2- and COOH-terminal regions and also with the amino acid composition of the purified aspartase determined previously. Potential promoter and terminator sequences for aspA were also found in the determined sequence.     

Cloning and sequence analysis reveal structural variation among related zein genes in maize

We have isolated a gene encoding one of the 19,000 dalton zein proteins from a maize genomic library constructed in Charon 4A. This gene occurs on a 7.7 kb Eco RI fragment, and based on Southern hybridization analysis, represents one of several homologous sequences present in the maize genome. The nucleotide sequence of the gene predicts a protein composed of 235 amino acids, including a signal peptide of 21 amino acids. There are no intervening sequences in the gene. By comparing the nucleotide sequence of this gene with that of a homologous cDNA clone, we have identified a basis for microheterogeneity within the gene family. The 5′ nucleotide sequences of the genomic and cDNA clones are identical, but they differ in the center of the protein, where repeated amino acid sequences occur. A nucleotide sequence encoding a conserved peptide of 20 amino acids is repeated nine times in the center of both of these clones.