Evolution of chorion gene families in Lepidoptera: Characterization of 15 cDNAs from the gypsy moth

Fifteen unique chorion protein-encoding cDNAs from gypsy moth have been completely sequenced. These sequences are encoded by a family of genes, based on pairwise similarity values of 78–100% within a 225-nt region. Pairwise comparisons and maximum parsimony analysis strongly support the existence of two clusters of 11 and four sequences each, called noel and noc2. While noc2 consists of two subclusters, there is little character support for subclusters within noel. The highly localized character-state distribution on the parsimony tree in gypsy moth is reminiscent of that in Bombyx mori, specifically for those chorion families that have been shown to undergo gene conversion. Gene conversion thus becomes a reasonable explanation for the homogeneity of noel sequences and for their distinctness from noc2. The relationship between the two major clusters of chorion sequences in gypsy moth (noel, noc2) and Bombyx mori (Bm , Bm ) has been addressed through mixed-species tree construction. All four groups cluster separately, thus providing no direct evidence of orthologous sequences. However, the occurrence of gene conversion could have eliminated such evidence. The relationship between the chorion gene tree and the species cladogenic event is discussed, as are biases in codon usage, base composition, and nucleotide transformations.Correspondence to: J.C. Regier     

Epigenetic silencing may aid evolution by gene duplication

Gene duplication is commonly regarded as the main evolutionary path toward the gain of a new function. However, even with gene duplication, there is a loss-versus-gain dilemma: most newly born duplicates degrade to pseudogenes, since degenerative mutations are much more frequent than advantageous ones. Thus, something additional seems to be needed to shift the loss versus gain equilibrium toward functional divergence. We suggest that epigenetic silencing of duplicates might play this role in evolution. This study began when we noticed in a previous publication (Lynch M, Conery JS [2000] Science 291:1151–1155) that the frequency of functional young gene duplicates is higher in organisms that have cytosine methylation (H. sapiens, M. musculus, and A. thaliana) than in organisms that do not have methylated genomes (S. cerevisiae, D. melanogaster, and C. elegans). We find that genome data analysis confirms the likelihood of much more efficient functional divergence of gene duplicates in mammals and plants than in yeast, nematode, and fly. We have also extended the classic model of gene duplication, in which newly duplicated genes have exactly the same expression pattern, to the case when they are epigenetically silenced in a tissue- and/or developmental stage-complementary manner. This exposes each of the duplicates to negative selection, thus protecting from pseudogenization. Our analysis indicates that this kind of silencing (i) enhances evolution of duplicated genes to new functions, particularly in small populations, (ii) is quite consistent with the subfunctionalization model when degenerative but complementary mutations affect different subfunctions of the gene, and (iii) furthermore, may actually cooperate with the DDC (duplication– degeneration–complementation) process. Dedicated to the memory of Susumu Ohno     

Evolutionary conservation and disease gene association of the human genes composing pseudogenes

Pseudogenes, the 'genomic fossils' present portrayal of evolutionary history of human genome. The human genes configuring pseudogenes are also now coming forth as important resources in the study of human protein evolution. In this communication, we explored evolutionary conservation of the genes forming pseudogenes over the genes lacking any pseudogene and delving deeper, we probed an evolutionary rate difference between the disease genes in the two groups. We illustrated this differential evolutionary pattern by gene expressivity, number of regulatory miRNA targeting per gene, abundance of protein complex forming genes and lesser percentage of protein intrinsic disorderness. Furthermore, pseudogenes are observed to harbor sequence variations, over their entirety, those become degenerative disease-causing mutations though the disease involvement of their progenitors is still unexplored. Here, we unveiled an immense association of disease genes in the genes casting pseudogenes in human. We interpreted the issue by disease associated miRNA targeting, genes containing polymorphisms in miRNA target sites, abundance of genes having disease causing non-synonymous mutations, disease gene specific network properties, presence of genes having repeat regions, affluence of dosage sensitive genes and the presence of intrinsically unstructured protein regions.     

Primate evolution of an olfactory receptor cluster: diversification by gene conversion and recent emergence of pseudogenes.

The olfactory receptor (OR) subgenome harbors the largest known gene family in mammals, disposed in clusters on numerous chromosomes. We have carried out a comparative evolutionary analysis of the best characterized genomic OR gene cluster, on human chromosome 17p13. Fifteen orthologs from chimpanzee (localized to chromosome 19p15), as well as key OR counterparts from other primates, have been identified and sequenced. Comparison among orthologs and paralogs revealed a multiplicity of gene conversion events, which occurred exclusively within OR subfamilies. These appear to lead to segment shuffling in the odorant binding site, an evolutionary process reminiscent of somatic combinatorial diversification in the immune system. We also demonstrate that the functional mammalian OR repertoire has undergone a rapid decline in the past 10 million years: while for the common ancestor of all great apes an intact OR cluster is inferred, in present-day humans and great apes the cluster includes nearly 40% pseudogenes.     

Dramatic changes in patterning gene expression during metamorphosis are associated with the formation of a feather-like antenna by the silk moth, Bombyx mori

Many moths use sex pheromones to find their mates in the dark. Their antennae are well developed with lateral branches to receive the pheromone efficiently. However, how these structures have evolved remains elusive, because the mechanism of development of these antennae has not been studied at a molecular level. To elucidate the developmental mechanism of this type of antenna, we observed morphogenesis, cell proliferation, cell death and antennal patterning gene expression in the branched antenna of the silk moth, Bombyx mori. Region-specific cell proliferation and almost ubiquitous apoptosis occur during early pupal stages and appear to shape the lateral branch cooperatively. Antennal patterning genes are expressed in a pattern largely conserved among insects with branchless antennae until the late 5th larval instar but most of them change their expression dramatically to a pattern prefiguring the lateral branch during metamorphosis. These findings imply that although antennal primordium is patterned by conserved mechanisms before metamorphosis, most of the antennal patterning genes are reused to form the lateral branch during metamorphosis. We propose that the acquisition of a new regulatory circuit of antennal patterning genes may have been an important event during evolution of the sensory antenna with lateral branches in the Lepidoptera.     

The α-gliadin gene family. II. DNA and protein sequence variation, subfamily structure, and origins of pseudogenes

 The derived amino-acid sequences of all reported α-gliadin clones are compared and analyzed, and the patterns of sequence change within the α-gliadin family are examined. The most variable sequences are two polyglutamine domains. These two domains are characteristic features of the α-gliadin storage proteins and account for most of the variation in protein size of this otherwise highly conserved protein family. In addition, their encoding DNA sequences form microsatellites. Single-base substitutions in the α-gliadin genes show a preponderance of transitions, including the C to T substitution which contributes to the generation of stop codons, and consequently to the observation that approximately 50% of the α-gliadin genes are pseudogenes. In one unusual gene, a microsatellite has expanded to 321 bp as compared to the normal 36–72 bp, and may result from similar mechanisms that produce polyglutamine-associated genetic diseases in humans. A comparison of the 27 reported sequences show several α-gliadin gene subfamilies, at least some of which are genome specific. Received: 1 October 1996/Accepted: 20 December 1996     

Unusual evolutionary conservation of 5S rRNA pseudogenes inAspergillus nidulans: Similarity of the DNA sequence associated with the pseudogenes with the mouse immunoglobulin switch region

Summary AllAspergillus nidulans 5S rRNA pseudogenes known so far are the result of integration of an approx. 0.2-kbp-long DNA sequence into the 5S rRNA genes. This sequence, called block C, is present in at least five copies in theA. nidulans genome and seems to be associated either with 5S rRNA genes or pseudogenes. In contrast to the 78% sequence conservation of the C-block in pseudogenes, the truncated 5 halves of the pseudogenes are very highly conserved (96.9–100%). We postulate that the 5S rRNA pseudogenes are still a subject of concerted evolution. The C-block sequence shows similarity to the switch region of the mouse heavy chain immunoglobulin gene. A characteristic motif GGGTGAG is repeated several times in both sequences; the sequence conservation is 63%.     

Drosophila melanogaster eggshell development: Localization of the s19 chorion gene

Summary Further IF screening ofDrosophila melanogaster geographic strains has revealed a variant of the s19 major chorion protein. Developmental analysis of F1 hybrids indicates that the source of the variation is found in the structural gene for this protein. The linkage group of the variant gene was determined to be the third, and the gene was localized by several methods of recombination analysis. The s19 gene was found to be tightly linked to thesepia locus, as had been previously found for the s18 gene (Yannoni and Petri 1980). Lack of recombination between the s19 and s18 genes in double heterozygotes suggested that these two genes are within 0.3 map units of each other. Although more precise localization of the s19 gene failed, the s18 gene could be more specifically located to the right ofsepia, betweensepia andhairy. Contrary to our prediction (ibid.), the s19 and s18 genes have been found to be tightly linked in spite of the fact that they display somewhat different developmental stage specificity.     

The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment

The size distributions of deletions, insertions, and indels (i.e., insertions or deletions) were studied, using 78 human processed pseudogenes and other published data sets. The following results were obtained: (1) Deletions occur more frequently than do insertions in sequence evolution; none of the pseudogenes studied shows significantly more insertions than deletions. (2) Empirically, the size distributions of deletions, insertions, and indels can be described well by a power law, i.e., f _k = Ck ^–b , where f _k is the frequency of deletion, insertion, or indel with gap length k, b is the power parameter, and C is the normalization factor. (3) The estimates of b for deletions and insertions from the same data set are approximately equal to each other, indicating that the size distributions for deletions and insertions are approximately identical. (4) The variation in the estimates of b among various data sets is small, indicating that the effect of local structure exists but only plays a secondary role in the size distribution of deletions and insertions. (5) The linear gap penalty, which is most commonly used in sequence alignment, is not supported by our analysis; rather, the power law for the size distribution of indels suggests that an appropriate gap penalty is w _k = a + b ln k, where a is the gap creation cost and blnk is the gap extension cost. (6) The higher frequency of deletion over insertion suggests that the gap creation cost of insertion (a _i ) should be larger than that of deletion (a _d ); that is, a _i – a _d = In R, where R is the frequency ratio of deletions to insertions. Correspondence to: W.-H. Li     

Discrimination and production of disparlure enantiomers by the gypsy moth and the nun moth

ABSTRACT. Two odour receptor cells were physiologically identified within male antennal hair sensillae of the gypsy moth, Lymantria dispar L, and the nun moth, L. monacha L. In the gypsy moth, one cell responded to (+)-disparlure, while a neighbouring cell responded to (-)-disparlure. In the nun moth both cells responded to (+)-disparlure. The lack of sensitivity to (-)-disparlure in the nun moth was corroborated by electroantennogram (EAG) recordings, which indicated no affinity to this enantiomer. Single cell responses of male gypsy moth to different concentrations of the synthetic enantiomers of disparlure were then compared to responses elicited by hexane extracts of female glands of both species. The gypsy moth's extracts stimulated almost exclusively the receptor cell specialized for (+)-disparlure, while both cells were simultaneously stimulated by the extracts of the nun moths. From the response characteristic of the cells it is estimated that pheromone production of the nun moth is about 10% (+) and 90% (-)-disparlure, and that of the gypsy moth is almost 100% (+)-disparlure. Stimulation of the antenna of each species by female gland extracts of both species did not indicate the presence of receptors for other hexane elutable pheromone components in either species.     

Characterization by isoelectric focusing of chorion protein variants inDrosophila melanogaster and their use in developmental and linkage analysis

Summary Drosophila melanogaster chorion proteins are characterized on one-dimensional isoelectric focusing (IF) gels. The six major chorion components previously identified on SDS gels are shown to resolve into at least 11 components in our IF system. IF screening of 102 geographic strains ofDrosophila melanogaster revealed seven cases of variation in major chorion components. Two strains, Crimea and Falsterbo, which were monomorphic for a variant B1 protein and two strains, Skafto and Lausanne, which were monomorphic for a variant C1 protein, were chosen for further study. After IF developmental analysis of F1 hybrids had indicated that the sources of the variation resided in the structural genes for these proteins, each variant was crossed to a multiply marked and inverted strain (BLT) to determine the linkage group of the variant gene. To localize genes to more specific sites multiply marked 3rd (SKERO) or X-chromosomal (CB1) (X-PLE) mapping strains were used. In both Crimea and Falsterbo the gene for the B1 protein is located near map location 26 on the 3rd chromosome. In both Lausanne and Skafto the C1 gene is located on the X chromosome. Hence, for the first time, we have demonstrated genetically the non-linkage of two chorion genes, B1 and C1.     

Heterochrony and the introduction of novel modes of morphogenesis during the evolution of moth choriogenesis

Summary Choriogenesis in silkmoths (superfamily Bombycoidea) and in a sphingid moth (super-family Sphingoidea) differ in major, but discrete, ways. In silkmoths, the predominant lamellar component assembles early in choriogenesis to form a thin framework. Subsequently, the lamellar framework is modified, first by expansion, and then by densification. Finally, ornate surface structures called aeropyle crowns form in some silkmoths, but they are absent in the species described here. In the sphingid, lamellar framework formation occurs throughout choriogenesis rather than largely during the early stages as in silkmoths. Lamellar densification occurs, but lamellar expansion and aeropyle crown formation do not. An evolutionary model is presented that accounts for the observed morphogenetic differences. Patterns of chorion protein synthesis in the sphingid differ from those in silkmoths in ways that are interpretable in light of the observed morphogenetic differences and the previously postulated functions of the proteins in silkmoths.     

The evolution of protein sequences by repetitious gene duplication: Clostridial flavodoxin

Summary Internal regularities of amino acid sequences of flavodoxins, FMN-containing, low molecular weight flavoproteins, were statistically examined using the minimum mutation method. The sequence ofClostridium pasteurianum flavodoxin shows statistically significant evidence of repetitious internal gene duplications at different levels of structure. Peptide pairs with a low chance probability of occurrence were frequently observed at a shift of 5 residues. The pairs with the lowest chance probabilites are a pair of heptapeptides at positions 39–45 vs. 44–50, a 5 residue shift (p = 9 × 10^–6). Most of the related pairs are consistent and could best be explained by the repeating pentapeptide sequence: (Lys-Gly-Ala-Asp-Val-)_n and appropriate gaps. Internal repetitions with longer shifts were also suggested for other flavodoxins. Repetitious gene duplication is proposed for the early stages of flavodoxin evolution.     

Gene evolution and regulation in the chorion complex of Bombyx mori. Hybridization and sequence analysis of multiple developmentally middle A/B chorion gene pairs

Twenty-two pairs of chorion genes belonging to the A and B multigene families have been characterized and mapped within two segments of a 320 kb (1 kb = 10(3) bases or base-pairs) chromosomal walk in the domesticated silkmoth Bombyx mori. Eighteen of the gene pairs belong to two groups that are typified by the previously characterized A/B.L12 and A/B.L11 chorion gene pairs, and are defined by two respective types of short (approx. 280 base-pairs) bidirectional promoter sequences. In the chromosome, the L12-like and L11-like pairs are interspersed with each other and with the remaining four gene pairs, which have unrelated promoter sequences. We have sequenced the promoter regions and adjacent small exons of all L12-like and L11-like A and B genes in the walk. The L12-like promoters are highly conserved, whereas L11-like promoters are somewhat more variable. Reconsideration of previous data on RNA accumulation and disappearance during choriogenesis, in the light of the sequences, indicates that L12-like genes are developmentally early-middle, while L11-like genes correspond to two developmental subgroups, middle I and middle II. Sequence comparisons of all these promoters, as well as the previously characterized promoters of the developmentally late HcA and HcB genes, identify short elements of possible regulatory significance. The sequences, as well as extensive cross-hybridization analysis with short probes derived from the reference A/B.L12 gene pair, under carefully controlled conditions of stringency, indicate the occurrence of sequence transfers among A or B genes. These sequence transfers, which could result from gene conversions or unequal crossovers, are less abundant than in the HcA and HcB families, but do result in a patchwork of similarities and differences in the A and B genes. The transfers appear to be least frequent between the moderately divergent A genes that belong to different temporal classes, while the L12-like and L11-like B genes appear to be extensively homogenized in sequence.     

苹果蠹蛾线粒体DNA COⅠ基因克隆与序列分析

本研究采集新疆阿拉尔地区苹果蠹蛾Cydia pomonella(L.)幼虫,对其线粒体DNA细胞色素氧化酶Ⅰ亚基(COⅠ)基因进行了扩增、克隆和测序,并对COⅠ序列进行了分析。结果显示:苹果蠹蛾DNA扩增出的COⅠ基因序列片段长度为709bp,序列中A+T含量极高,占68.7%,而G+C的含量只有31.3%。经基因序列比对,与其它几种食心虫的同源性为85.4%～88.1%,遗传距离为0.130～0.162;采用NJ法构建了卷蛾科系统树,所得的聚类结果与传统的分类结果基本一致。本研究结果为苹果蠹蛾快速鉴定的DNA条形码技术研究提供重要基础。     

Evolution of the autosomal chorion cluster inDrosophila. IV. The HawaiianDrosophila: Rapid protein evolution and constancy in the rate of DNA divergence

Summary Autosomal chorion geness18, s15, ands19 are shown to diverge at extremely rapid rates in closely related taxa of HawaiianDrosophila. Their nucleotide divergence rates are at least as fast as those of intergenic regions that are known to evolve more extensively between distantly related species. Their amino acid divergence rates are the fastest known to date. There are two nucleotide replacement substitutions for every synonymous one. The molecular basis for observed length and substitution mutations is analyzed. Length mutations are strongly associated with direct repeats in general, and with tandem repeats in particular, whereas the rate for an average transition is twice that for an average transversion.The DNA sequence of the cluster was used to construct a phylogenetic tree for five taxa of the Hawaiian picture-winged species group ofDrosophila. Assignment of observed base substitutions occurring in various branches of the tree reveals an excess of would-be homoplasies in a centrally localized 1.8-kb segment containing thes15 gene. This observation may be a reflection of ancestral excess polymorphisms in the segment. The chorion cluster appears to evolve at a constant rate regardless of whether the central 1.8-kb segment is included or not in the analysis. Assuming that the time of divergence ofDrosophila grimshawi and theplanitibia subgroup coincides with the emergence of the island of Kauai, the overall rate of base substitution in the cluster is estimated to be 0.8% million years, whereas synonymous sites are substituted at a rate of 1.2%/million years.