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PubMed2026

Two domesticated species of rice shaped the population structure of Xanthomonas oryzae pv. oryzae in Africa.

African rice (Oryza glaberrima) was independently domesticated in West Africa around 3000 years ago, and has long been intertwined in the history of the region. Asian rice (Oryza sativa), which was introduced in Africa when European settlers arrived, gradually replaced African rice and has since dominated rice cultivation in the continent. Domesticated rice species are affected by bacterial leaf blight (BLB), which is caused by the pathogen Xanthomonas oryzae pv. oryzae (Xoo). Here we show that the bacterial leaf blight pathogen in Africa (AfXoo) belongs to a distinct phylogroup from the one circulating in Asia (AsXoo), and has a different evolutionary history. Analysis of 87 AfXoo genomes identified five main populations, including highly clonal ones, and a more diverse and recombinant population. Tip-dating analysis revealed that the AfXoo population went through a period of expansion, then decline and more recent recovery. We hypothesize this followed the rise and fall of African rice, and that the introduction of O. sativa served as a bottleneck leading to the emergence of current AfXoo populations. We show that AfXoo has a highly conserved repertoire of type III effectors (T3E), but that nonetheless there is variation especially between populations. In the case of transcription activator-like effectors (TALEs), variation can arise quickly through rearrangements, and we hypothesize that the TALE repertoire of AfXoo has been selected to allow the bacteria to colonize both species of cultivated rice found in the continent. Our research provides an attempt to decipher the genetic history of bacterial blight in West Africa, and its past and present impact on rice cultivation in the region.

Journal Article↗
PubMed1993

Molecular cloning of cDNAs encoding two types of gonadotrophin alpha subunit from the masu salmon, Oncorhynchus masou: construction of specific oligonucleotides for the alpha 1 and alpha 2 subunits.

Two types of cDNA (GTH alpha 1 and -alpha 2) encoding the alpha subunits of masu salmon (Oncorhynchus masou) gonadotrophin were cloned by the reverse transcription-polymerase chain reaction for pituitary mRNAs. The nucleotide sequences showed that the GTH alpha 1 cDNA was 380 bp long, encoding 119 amino acids, and that GTH alpha 2 cDNA was 365 bp long, encoding 114 amino acids. The masu salmon alpha subunit types had a few differences between the sequences, with homologies of 80% (nucleotide sequence) and 72% (amino acid sequence). The structural difference between the alpha 1 and alpha 2 subunits was predicted using hydropathic analysis. The evolutionary interval between masu and chum salmon was estimated to be 4.0 and 2.3 million years by comparing their GTH alpha 1 and -alpha 2 subunits respectively. These time values are roughly consistent with the evolutionary time interval (3.0 million years) estimated from fossil records and an isozyme study. Specific synthetic oligonucleotide probes were constructed and used for genomic Southern blot analyses. The restriction fragment sizes of the GTH alpha 1 and -alpha 2 genes were similar, and when their patterns were compared with those from four other teleosts, each species showed a different pattern from the others, but no difference between their respective alpha 1 and alpha 2 genes. Therefore, the structural features of the GTH alpha 1 and -alpha 2 genes may have diverged in a similar manner in these five teleosts.

Amino Acid Sequence↗
PubMed2000

The development of Archaeopteris: new evolutionary characters from the structural analysis of an Early Famennian trunk from southeast Morocco.

A 5 m long trunk of a young Archaeopteris/Callixylon erianum tree from the Late Devonian of Morocco shows new branching patterns for early lignophytes. This progymnosperm tree produces a helical pattern of traces that we infer belonged to reduced, short-lived, primary (apical) branches (type A) as well as two types of adventitious traces (types B and H). We infer that type-B traces supplied branches that initiate close to the site of attachment on the trunk of some, but not all type-A branches in an irregular but nonrandom pattern. Unlike ephemeral type-A branches, those of type B persist and become long-lived, potentially permanent units of the architecture of Archaeopteris trees. Type-H adventitious traces are also short-lived and occur singly or in serial groups, but differ from traces of either type A or B branches by lacking differentiation into a readily identifiable organ category. We interpret type-H traces as supplying latent primordia that could develop into either adventitious roots or shoots depending on extrinsic factors. Our new data suggest that Archaeopteris had a wide range of branch primordium amplitude. Type-B branches compare with axillary lateral branch buds of some Early Carboniferous spermatophytes (Calamopitys) and are a major developmental departure from the strictly apical, pseudomonopodial shoot branching of older aneurophyte progymnosperms. Type-H traces suggest that Archaeopteris trees had some potential for formation of adventitious roots or shoots in response to environmental factors, such as partial burial by overbank sedimentation. Collectively, these novel methods of tree branching may partly explain the extraordinary success and worldwide dominance of Archaeopteris forests on fluvially dominated, Late Devonian floodplains.

Journal Article↗
PubMed1999

Studies on karyotype evolution in higher primates in relation to human chromosome 14 and 9 by comparative mapping of immunoglobulin C epsilon genes with fluorescence in situ hybridization.

Karyotypic homologies in relation to human chromosome 14 and 9 were studied through comparative mapping of the immunoglobulin C epsilon genes in higher primates by fluorescence in situ hybridization (FISH) technique. The C epsilon genes will be suitable probes for the analysis of evolutionary rearrangements due to that the multiple recombinational events such as gene duplications and deletions have occurred repeatedly in the immunoglobulin CH gene family (IGH@) during the course of primate evolution. IGH@ locating on the terminal region of human chromosome 14 (HSA14), at band HSA14q32.33, has generated multiple pseudogenes and among subclasses of IGH@ the C epsilon genes have shown most dynamic changes with generating both truncated type (C epsilon 2) and processed type (C epsilon 3) pseudogenes. In this study, chromosomal homologies and rearrangements on HSA14 (C epsilon 1) and HSA9 (C epsilon 3) in relation to the evolutionary genesis of their primate homologous chromosomes in speciation were investigated by comparative mapping with FISH and chromosome painting (ZOO-FISH) techniques. Comparative mapping of the C epsilon 1 gene at HSA14q32.33 was carried out in seven species of nonhuman primates: common chimpanzee (PTR), pygmy chimpanzee (PPA), gorilla (GGO), orangutan (PPY), white-handed gibbon (HLA), agile gibbon (HAG), and Japanese macaque (MFU). The C epsilon 1 gene was assigned to the telomeric region of HSA14 homologues in each species, namely, PTR15q32, PPA15q32, GGO18q16, PPY15q32, HLA17qter, HAG17qter, and MFU7q29, respectively. These results suggested that HSA14 has high degree of syntenic organization with its primate homologues confirmed by ZOO-FISH. Concerning HSA9, comparative mapping of the C epsilon 3 gene at HSA9p24.2-->p24.1 was performed. The mapped positions indicated the HSA9 homologous regions detected by ZOO-FISH in each species, namely, PTR11q34, PPA11q34, GGO13q22, PPY13q16, HLA8qter, HAG8qter, and MFU14q22, respectively, suggesting that several dynamic chromosomal rearrangements including at least twice pericentric inversions have occurred during the course of hominoid evolution. The comparison of syntenic groups and painting results has provided a hypothesis of the evolutionary genesis of HSA9 and its homologues with defined breakpoints on the present chromosomes. Likewise, studies on karyotype evolution will be promoted by combining comparative mapping with ZOO-FISH that can more clearly define the chromosomal rearrangements among species.

Animals↗
PubMed1991

Structural analysis of the gene encoding rat cholesterol alpha-hydroxylase, the key enzyme for bile acid biosynthesis.

The gene encoding cholesterol 7 alpha-hydroxylase (P450VIIA) was isolated from rat genomic DNA. The gene spanned about 11 kilobases and contained six exons. Blotting analysis of genomic DNA and complete matching of restriction maps of several isolated genomic clones indicated that there appeared to be only one gene in the rat genome. The putative transcription initiation site was present 61 base pairs upstream from the ATG codon. The typical TATA sequence and CCAAT promoter element were found at 24 and 47 base pairs upstream from the transcription initiation site, respectively. Alignment of several P450 proteins showed that the cholesterol 7 alpha-hydroxylase gene shared location of introns with none of the other P450 genes except for intron 5, which was in the same position as intron 10 of the gene encoding P450IVA1. The alignment also indicated that the distal helix of cholesterol 7 alpha-hydroxylase contained an asparagine in place of the well conserved threonine that is postulated to be involved in the O2 binding site. Unusual residues, Asn-126 and Thr-442, were also found at the sites where all other P450s have positively charged amino acids, which are considered to be involved in interaction with heme propionate. These replacements may be related to the unique function and unusual lability of the hydroxylase. Analysis of evolutionary distance between the cholesterol 7 alpha-hydroxylase gene and other known P450 genes indicated that yeast P450LIA is most closely related to P450VIIA. This finding suggests that the cholesterol 7 alpha-hydroxylase gene is an evolutionarily old P450 gene.

Amino Acid Sequence↗
PubMed1990

[Quantitative analysis of the teleost brain: evolutionary and adaptive features of encephalization. II. Primary brain subdivisions].

1. Frequently there is an opposition between olfactory and visual senses. Fresh water fishes are generally macrosomatic and microptic, marine fishes (especially coral reef fishes) are microsmatic and macroptic while piscivorous pelagic fishes are macrosmatic and macroptic. 2. The importance of the cerebellum is a function of both the fish's activity level and its body size. 3. There is a marked opposition between the diencephalon and the medulla oblongata and a greater one between the non-olfactory-telencephalon (NOT) and the medulla oblongata (MA). Although it is not possible to give an accurate evolutionary significance, the ratio of NOT/MA is low in primitive teleostean fishes and high in more derived species (Acanthuridae and Tetraodontiformes).

Animals↗
PubMed1993

Apolipoprotein A-I domains involved in lecithin-cholesterol acyltransferase activation. Structure:function relationships.

A series of mutant apolipoprotein (apoA-I) constructs were designed and then expressed in cell culture to identify structural domains within the mature native apoA-I protein that participate in the activation of the plasma enzyme, lecithin-cholesterol acyltransferase (LCAT). Evolutionary conservation analysis has shown previously that apoA-I contains eight repeats containing 22 amino acids and two repeats containing 11 amino acids that are highly conserved among species as well as within the apolipoprotein supergene family. These tandem repeats begin at residue 44 and are usually marked by a proline residue, with six of the 22-mer repeats showing high amphipathic alpha-helical character. To determine if specific 11- or 22-amino acid domains are essential for maximal LCAT activation within the entire native protein, each of the 10 repeats was sequentially deleted using a polymerase chain reaction based method of mutagenesis. The wild-type and mutant apoA-I gene constructs were expressed in Chinese hamster ovary (CHO) cells and stable lines established. Wild-type and mutant apoA-I protein were purified from 48-96-h conditioned serum-free medium and characterized by SDS-polyacrylamide gel electrophoresis and Western blot analysis. Wild-type apoA-I showed a single migrating band of 28,000 daltons that corresponded to the mobility of human plasma apoA-I, whereas apoA-I deletion mutants (lacking 22- or 11-mer repeats) showed the corresponding shift to lower molecular size. To measure the relative LCAT activation of all deletion mutant apoA-I proteins relative to wild-type apoA-I, an assay system utilizing small unilamellar vesicles as the lipid substrate was used. The results of these studies suggest that several central amphipathic alpha-helical regions within the mature protein are critical in LCAT activation.

Animals↗
PubMed1995

Comparative morphology of kinetoplastids.

The common structural plan of bodonids, cryptobiids and trypanosomatids permits placing them in one phylum Kinetoplastidae. Analysis of evolutionary changes in the initial "bodonid" structural plan in separate groups within the Kinetoplastidae, illustrated by an evolutionary series of homologous characters, enables us to conclude that the cryptobiids occupy an intermediate position in kinetoplastid evolution between the free-living bodonids and Trypanosoma spp from lower vertebrates and can be considered to be potential ancestors of the latter.

Animals↗
PubMed1996

The normal and abnormal genu of the corpus callosum: an evolutionary, embryologic, anatomic, and MR analysis.

PURPOSE: To define the normal and abnormal genu of the corpus callosum by examining its evolution and embryology and by analyzing its normal and abnormal appearance on MR images. METHODS: A reference line was drawn from the mamillary body through the anterior commissure and corpus callosum-the MAC line. This line was used to evaluate the genu in adult mammal brains, in human fetal brains, on MR images of 1800 patients with normal corpora callosi, and on MR images of 113 patients with callosal anomalies. RESULTS: In primates, increased frontal lobe size is associated with an anteriorly shifted genu. In human fetal development, the anterior body of the corpus callosum develops before the definitive genu. The normal human genu always projects in front of the MAC line. In none of the 113 patients with callosal anomalies was there only a normal genu. CONCLUSIONS: The human corpus callosum develops bidirectionally, not from front to back. The MAC line is a useful frame of reference to study the evolution and embryology of the genu and to distinguish the normal from the abnormal genu of the human corpus callosum.

Adult↗
PubMed2005

The glucosinolate-myrosinase system in an ecological and evolutionary context.

Functional analysis of natural variation in the model species Arabidopsis thaliana has enabled the cloning of many glucosinolate biosynthesis and hydrolysis genes. Variation in these genes is central to understanding the ecological role of the glucosinolate-myrosinase defense system, and allows us to dissect the evolutionary and ecological forces that shape polymorphism at underlying loci. These same genes are also variable in other crucifer species, suggesting the presence of recurring selection, possibly mediated by insects. By utilizing the genomic tools available in A. thaliana to investigate these loci fully, it might be possible to generate detailed evolutionary or ecological models to apply to other species.

Animals↗
PubMedDate not supplied

Zipf's law and human transcriptomes: an explanation with an evolutionary model.

Detailed analysis of human gene expression data reveals several patterns of relationship between transcript frequency and abundance rank. In muscle and liver, organs composed primarily of a homogeneous population of differentiated cells, they obey Zipf's law. In cell lines, epithelial tissue and compiled transcriptome data, only high-rankers deviate from it. We propose an evolutionary process model during which expression level changes stochastically proportionally to its intensity, providing a novel interpretation of transcriptome data and of evolutionary constraints on gene expression.

Evolution, Molecular↗
PubMedDate not supplied

Developmental system drift and flexibility in evolutionary trajectories.

The comparative analysis of homologous characters is a staple of evolutionary developmental biology and often involves extrapolating from experimental data in model organisms to infer developmental events in non-model organisms. In order to determine the general importance of data obtained in model organisms, it is critical to know how often and to what degree similar phenotypes expressed in different taxa are formed by divergent developmental processes. Both comparative studies of distantly related species and genetic analysis of closely related species indicate that many characters known to be homologous between taxa have diverged in their morphogenetic or gene regulatory underpinnings. This process, which we call "developmental system drift" (DSD), is apparently ubiquitous and has significant implications for the flexibility of developmental evolution of both conserved and evolving characters. Current data on the population genetics and molecular mechanisms of DSD illustrate how the details of developmental processes are constantly changing within evolutionary lineages, indicating that developmental systems may possess a great deal of plasticity in their responses to natural selection.

Animals↗
PubMed2001

Maque, a family of extremely short interspersed repetitive elements: characterization, possible mechanism of transposition, and evolutionary implications.

Database analysis revealed a novel family of very short interspersed repetitive elements named Maque in the African malaria mosquito, Anopheles gambiae. Past mobility of Maque was demonstrated by evidence of its insertion that resulted in a target duplication. Approximately 220 copies of Maque were present in the A. gambiae genome. Although only approximately 60 bp long, Maque has the appearance of a distinct transposition unit. Eleven of the 12 Maque elements found in the database were flanked by 9-14 bp direct repeats, indicating that their transposition was relatively recent. Sequence comparison and phylogenetic analyses suggest that there are at least two subgroups within the Maque family, suggesting that they may have been originated from more than one source. Five of the 12 Maque elements had at least one other repetitive element nearby. Three of the Maque elements were found near genes. However, Maque was not found in the coding regions of genes or in any of the expressed sequence tags (ESTs), which is consistent with its significantly biased distribution toward A + T rich regions. Several characteristics of Maque indicate that it is likely a non-autonomous retro-element. The evolutionary origin of Maque and the differences between Maque and other known retro-elements including short interspersed repetitive elements (SINEs) are discussed. A hypothesis is proposed in which short sequences containing just the reverse transcriptase recognition signal (RTRS) could potentially contribute to exon shuffling and the genesis of some primordial SINEs.

Animals↗
PubMed2003

ELISA: structure-function inferences based on statistically significant and evolutionarily inspired observations.

UNLABELLED: The problem of functional annotation based on homology modeling is primary to current bioinformatics research. Researchers have noted regularities in sequence, structure and even chromosome organization that allow valid functional cross-annotation. However, these methods provide a lot of false negatives due to limited specificity inherent in the system. We want to create an evolutionarily inspired organization of data that would approach the issue of structure-function correlation from a new, probabilistic perspective. Such organization has possible applications in phylogeny, modeling of functional evolution and structural determination. ELISA (Evolutionary Lineage Inferred from Structural Analysis, http://romi.bu.edu/elisa) is an online database that combines functional annotation with structure and sequence homology modeling to place proteins into sequence-structure-function "neighborhoods". The atomic unit of the database is a set of sequences and structural templates that those sequences encode. A graph that is built from the structural comparison of these templates is called PDUG (protein domain universe graph). We introduce a method of functional inference through a probabilistic calculation done on an arbitrary set of PDUG nodes. Further, all PDUG structures are mapped onto all fully sequenced proteomes allowing an easy interface for evolutionary analysis and research into comparative proteomics. ELISA is the first database with applicability to evolutionary structural genomics explicitly in mind. AVAILABILITY: The database is available at http://romi.bu.edu/elisa.

Amino Acid Sequence↗
PubMed1993

Silent substitutions in mammalian genomes and their evolutionary implications.

An analysis of silent substitutions in pairwise comparisons of homologous genes from different mammals has shown that, in spite of individual fluctuations, their frequencies (which are very strongly correlated with the frequency of substitutions per synonymous site calculated according to Li et al. 1985) do not vary, on the average, with the GC levels of silent positions. This holds in the general case, in which silent positions of pairs of homologous genes share the same composition, namely in the human/other primates, human/artiodactyls, and in the mouse/rat pairs, as well as in the special cases in which the composition of silent positions are different, namely in the human/rabbit and the human/rat (or human/mouse) pairs. A slightly lower frequency found for low GC values in the human/bovine and human/pig pairs seems to be due to the specific gene samples used. These results contradict the previously claimed existence of differences in mutation rates and of mutational biases in third codon positions of coding sequences located in different isochores of mammalian genomes. They also imply that the variations in nucleotide precursor pools through the cell cycle and the differences in replication timing, or in repair efficiency, which were reported for different isochores, do not lead, as claimed, to differences in mutation rates, not in mutational biases in mammals. The differences claimed appear to be due to using small gene samples when individual fluctuations from gene to gene are relatively large.

Animals↗
PubMed1985

Antigenic conservation and divergence between the viral-specific proteins of poliovirus type 1 and various picornaviruses.

Immuneprecipitation analyses of various picornavirus-infected cell lysates were performed using antisera to poliovirus type 1-specific structural and nonstructural proteins. The results showed differing patterns of antigenic conservation and divergence. However, the VP3 and 2C polypeptides were strongly antigenically conserved among the large majority of these viruses. This conservation was especially notable given the degree of divergence exhibited by the other viral proteins and may be due to environmental pressure exerted by interaction with the host cell. The results, furthermore, allowed for an analysis of the evolutionary relationship of the tested viruses. This analysis showed a particularly strong antigenic relationship between the proteins of the poliovirus group and coxsackievirus A21 as well as a weaker, but significant, relationship with coxsackieviruses B1 and B3.

Antigens, Viral↗
PubMed2005

The evolution and function of adult attachment: a comparative and phylogenetic analysis.

Although the evolutionary functions of attachment in infant-caregiver relationships are undisputed, it is unclear what functions--if any--attachment serves in adult romantic relationships. The objective of this research was to examine the evolution and function of adult attachment (i.e., pair bonding) by applying comparative and phylogenetic methods to archival data collected on 2 diverse samples of mammalian species. The authors found that species exhibiting adult attachment were more likely than others to be characterized by paternal care, developmental immaturity or neoteny, small social groups, and small body sizes. The authors also used phylogenetic techniques to reconstruct the evolution of adult attachment and test alternative evolutionary models of the comparative correlates of pair bonding. Phylogenetic analyses suggested that the relationship between paternal care and adult attachment may be a functional one (i.e., due to convergent evolution) but that the relationship between neoteny and adult attachment may be due to homology (i.e., shared ancestry). Discussion focuses on the potential of comparative and phylogenetic methods for advancing the science of social and personality psychology.

Adult↗
PubMed1998

Data transferability from model organisms to human beings: insights from the functional genomics of the flightless region of Drosophila.

At what biological levels are data from single-celled organisms akin to a Rosetta stone for multicellular ones? To examine this question, we characterized a saturation-mutagenized 67-kb region of the Drosophila genome by gene deletions, transgenic rescues, phenotypic dissections, genomic and cDNA sequencing, bio-informatic analysis, reverse transcription-PCR studies, and evolutionary comparisons. Data analysis using cDNA/genomic DNA alignments and bio-informatic algorithms revealed 12 different predicted proteins, most of which are absent from bacterial databases, half of which are absent from Saccharomyces cerevisiae, and nearly all of which have relatives in Caenorhabditis elegans and Homo sapiens. Gene order is not evolutionarily conserved; the closest relatives of these genes are scattered throughout the yeast, nematode, and human genomes. Most gene expression is pleiotropic, and deletion studies reveal that a morphological phenotype is seldom observed when these genes are removed from the genome. These data pinpoint some general bottlenecks in functional genomics, and they reveal the acute emerging difficulties with data transferability above the levels of genes and proteins, especially with complex human phenotypes. At these higher levels the Rosetta stone analogy has almost no applicability. However, newer transgenic technologies in Drosophila and Mus, combined with coherency pattern analyses of gene networks, and synthetic neural modeling, offer insights into organismal function. We conclude that industrially scaled robogenomics in model organisms will have great impact if it can be realistically linked to epigenetic analyses of human variation and to phenotypic analyses of human diseases in different genetic backgrounds.

Animals↗