Identification of novel random amplified polymorphic DNAs (RAPDs) on the W chromosome of the domesticated silkworm, Bombyx mori, and the wild silkworm, B. mandarina, and their retrotransposable element-related nucleotide sequences

A history of the genetic and molecular identification of genes and their functions controlling insect sex determination

The genetics of the sex determination regulatory cascade in Drosophila melanogaster has a fascinating history, interlinked with the foundation of the Genetics discipline itself. The discovery that alternative splicing rather than differential transcription is the molecular mechanism underlying the upstream control of sex differences in the Drosophila model system was surprising. This notion is now fully integrated into the scientific canon, appearing in many genetics textbooks and online education resources. In the last three decades, it was a key reference point for starting evolutionary studies in other insect species by using homology-based approaches. This review will introduce a very brief history of Drosophila genetics. It will describe the genetic and molecular approaches applied for the identifying and cloning key genes involved in sex determination in Drosophila and in many other insect species. These comparative analyses led to supporting the idea that sex-determining pathways have evolved mainly by recruiting different upstream signals/genes while maintaining widely conserved intermediate and downstream regulatory genes. The review also provides examples of the link between technological advances and research achievements, to stimulate reflections on how science is produced. It aims to hopefully strengthen the related historical and conceptual knowledge of general readers of other disciplines and of younger geneticists, often focused on the latest technical-molecular approaches.

An Efficient Duplex PCR Method for Sex Identification of the European Grapevine Moth Lobesia botrana (Lepidoptera: Tortricidae) at Any Developmental Stage

Many genetic studies in insects require sex identification of individuals in all developmental stages. The most common sex chromosome system in lepidopterans is WZ/ZZ; the W chromosome is present only in females. Based on two W chromosome-specific short sequences (CpW2 and CpW5) described in Cydia pomonella (L.) (Lepidoptera: Tortricidae), we identified homologous female-specific sequences in Lobesia botrana Den. & Schiff, a polyphagous and very harmful species present in Chile since 2008. From this starting point, we extended the sequence information using the inverse PCR method, identifying the first W-specific sequences described up to now for the moth. Finally, we developed a duplex PCR method for rapid and sensitive determination of sex in L. botrana from larva to adult. The method showed a detection limit of 1 pg of genomic DNA; a blind panel of samples exhibited exact correspondence with the morphological identification. These results will be very useful for studies requiring sex-specific analyses at any developmental stage, contributing also to the understanding of gene expression in the insect, as well as to the eventual development of control protocols against the moth, such as the development of genetic sexing strains for the implementation of the sterile insect technique.

Characterization of the First W-Specific Protein-Coding Gene for Sex Identification in Helicoverpa armigera

Helicoverpa armigera is a globally-important crop pest with a WZ (female)/ZZ (male) sex chromosome system. The absence of discernible sexual dimorphism in its egg and larval stages makes it impossible to address any sex-related theoretical and applied questions before pupation unless a W-specific sequence marker is available for sex diagnosis. To this end, we used one pair of morphologically pre-sexed pupae to PCR-screen 17 non-transposon transcripts selected from 4855 W-linked candidate reads identified by mapping a publicly available egg transcriptome of both sexes to the male genome of this species and detected the read SRR1015458.67499 only in the female pupa. Subsequent PCR screenings of this read and the previously reported female-specific RAPD (random amplified polymorphic DNA) marker AF18 with ten more pairs of pre-sexed pupae and different annealing positions and/or temperatures as well as its co-occurrence with the female-specific transcript splicing isoforms of doublesex gene of H. armigera (Hadsx) and amplification and sequencing of their 5′ unknown flanking sequences in three additional pairs of pre-sexed pupae verified that SRR1015458.67499 is a single copy protein-coding gene unique to W chromosome (named GUW1) while AF18 is a multicopy MITE transposon located on various chromosomes. Test application of GUW1 as a marker to sex 30 neonates of H. armigera yielded a female/male ratio of 1.14: 1.00. Both GUW1 and Hadsx splicing isoforms assays revealed that the H. armigera embryo cell line QB-Ha-E-1 is a male cell line. Taken together, GUW1 is not only a reliable DNA marker for sexing all stages of H. armigera and its cell lines, but also represents the first W-specific protein-coding gene in lepidopterans.

Molecular sexing of Lepidoptera

We developed a universal method of Lepidoptera molecular sexing. The method is based on comparing the number of copies of the same gene in different sexes. Males of the majority of lepidopteran species have two Z chromosomes, whereas females have only one Z chromosome. Correspondingly, the number of copies of each gene located on this chromosome differs by two times between males and females. For quantitative estimation, we used qPCR. Via multiple alignment of the kettin (a Z chromosome gene) nucleotide sequences, we detected the most conserved fragment and designed primers with broad interspecies specificity for Lepidoptera. Using these primers, we successfully determined the sex of three lepidopteran species belonging to different superfamilies. The developed method is a simple, cost-effective and high-throughput technique for routine sexing. The sex of lepidopteran individuals can be examined at any developmental stage.

Identification and functional analysis of a Masculinizer orthologue in Trilocha varians (Lepidoptera: Bombycidae)

We recently showed that the Masculinizer gene (Masc) plays a primary role in sex determination in the lepidopteran model insect Bombyx mori. However, it remains unknown whether this Masc protein-dependent sex determination system is conserved amongst lepidopteran insects or within the family Bombycidae. Here we cloned and characterized a Masc homologue (TvMasc) in Trilocha varians (Lepidoptera: Bombycidae), a species closely related to B. mori. To elucidate the role of TvMasc in the sex determination cascade of T. varians, TvMasc expression was knocked down in early embryos by the injection of small interfering RNAs (siRNAs) that targeted TvMasc mRNAs. Both female- and male-type splice variants of Tvdsx, a doublesex (dsx) homologue in T. varians were observed in control siRNA-injected embryos. By contrast, only female-type splice variants were observed in TvMasc siRNA-injected embryos. These results indicate that the TvMasc protein directly or indirectly regulates the splicing patterns of Tvdsx. Furthermore, we found that male-type splice variants of B. mori dsx (Bmdsx) were produced in TvMasc-overexpressing BmN4 cells. The mRNA level of B. mori Imp, a gene whose product induces male-specific Bmdsx splicing also increased. These results suggest that Masc genes play similar roles in the sex-determination cascade in Bombycidae.

Postintegration stability of the silkworm piggyBac transposon

The piggyBac transposon is the most widely used vector for generating transgenic silkworms. The silkworm genome contains multiple piggyBac-like sequences that might influence the genetic stability of transgenic lines. To investigate the postintegration stability of piggyBac in silkworms, we used random insertion of the piggyBac [3 × p3 EGFP afm] vector to generate a W chromosome-linked transgenic silkworm, named W-T. Results of Southern blot and inverse PCR revealed the insertion of a single copy in the W chromosome of W-T at a standard TTAA insertion site. Investigation of 11 successive generations showed that all W-T females were EGFP positive and all males were EGFP negative; PCR revealed that the insertion site was unchanged in W-T offspring. These results suggested that endogenous piggyBac-like elements did not affect the stability of piggyBac inserted into the silkworm genome.

A single female-specific piRNA is the primary determiner of sex in the silkworm

The silkworm Bombyx mori uses a WZ sex determination system that is analogous to the one found in birds and some reptiles. In this system, males have two Z sex chromosomes, whereas females have Z and W sex chromosomes. The silkworm W chromosome has a dominant role in female determination, suggesting the existence of a dominant feminizing gene in this chromosome. However, the W chromosome is almost fully occupied by transposable element sequences, and no functional protein-coding gene has been identified so far. Female-enriched PIWI-interacting RNAs (piRNAs) are the only known transcripts that are produced from the sex-determining region of the W chromosome, but the function(s) of these piRNAs are unknown. Here we show that a W-chromosome-derived, female-specific piRNA is the feminizing factor of B. mori. This piRNA is produced from a piRNA precursor which we named Fem. Fem sequences were arranged in tandem in the sex-determining region of the W chromosome. Inhibition of Fem-derived piRNA-mediated signalling in female embryos led to the production of the male-specific splice variants of B. mori doublesex (Bmdsx), a gene which acts at the downstream end of the sex differentiation cascade. A target gene of Fem-derived piRNA was identified on the Z chromosome of B. mori. This gene, which we named Masc, encoded a CCCH-type zinc finger protein. We show that the silencing of Masc messenger RNA by Fem piRNA is required for the production of female-specific isoforms of Bmdsx in female embryos, and that Masc protein controls both dosage compensation and masculinization in male embryos. Our study characterizes a single small RNA that is responsible for primary sex determination in the WZ sex determination system.

The silkworm W chromosome is a source of female-enriched piRNAs

In the silkworm, Bombyx mori, the W chromosome plays a dominant role in female determination. However, neither protein-coding genes nor transcripts have so far been isolated from the W chromosome. Instead, a large amount of functional transposable elements and their remnants are accumulated on the W chromosome. PIWI-interacting RNAs (piRNAs) are 23-30-nt-long small RNAs that potentially act as sequence-specific guides for PIWI proteins to silence transposon activity in animal gonads. In this study, by comparing ovary- and testis-derived piRNAs, we identified numerous female-enriched piRNAs. Our data indicated that female-enriched piRNAs are derived from the W chromosome. Moreover, comparative analyses on piRNA profiles from a series of W chromosome mutant strains revealed a striking enrichment of a specific set of transposon-derived piRNAs in the putative sex-determining region. Collectively, we revealed the nature of the silkworm W chromosome as a source of piRNAs.

Genetic diversity analysis with RAPD linked to sex identification in the sugar cane borer Diatraea saccharalis

Diatraea saccharalis is an insect that causes considerable losses in the sugar cane crop. Our aim was to contribute to the knowledge of the biology of D. saccharalis, with the report of DNA fragments involved in the differentiation between the male and female of this species using the RAPD sex molecular marker GyakuU-13, which is specific for the W chromosome of Bombyx mori. Another point evaluated in this study was the genetic diversity of a D. saccharalis population maintained by inbreeding in a laboratory culture. The profile of sex-specific fragments was analyzed, and the genetic variability of this population was estimated. An analysis of the molecular markers showed only one fragment, of approximately 700 bp, that could be considered as a female sex marker in D. saccharalis.

The birds and the bees and the flowers and the trees: lessons from genetic mapping of sex determination in plants and animals

The ability to identify genetic markers in nonmodel systems has allowed geneticists to construct linkage maps for a diversity of species, and the sex-determining locus is often among the first to be mapped. Sex determination is an important area of study in developmental and evolutionary biology, as well as ecology. Its importance for organisms might suggest that sex determination is highly conserved. However, genetic studies have shown that sex determination mechanisms, and the genes involved, are surprisingly labile. We review studies using genetic mapping and phylogenetic inferences, which can help reveal evolutionary pattern within this lability and potentially identify the changes that have occurred among different sex determination systems. We define some of the terminology, particularly where confusion arises in writing about such a diverse range of organisms, and highlight some major differences between plants and animals, and some important similarities. We stress the importance of studying taxa suitable for testing hypotheses, and the need for phylogenetic studies directed to taxa where the patterns of changes can be most reliably inferred, if the ultimate goal of testing hypotheses regarding the selective forces that have led to changes in such an essential trait is to become feasible.

Identification of 2chromosome region translocated onto the W chromosome by RFLP with EST-cDNA clones in the Gensei-kouken strains of the mulberry silkworm, Bombyx mori L

In silkworms, sex-limited strains are either obtained spontaneously or induced by X-rays or gamma rays. When a fragment of an autosome carrying a dominant allele of those genes responsible for certain characters is translocated onto a W chromosome, the female of the successive generations will express these phenotypic characters and sex discrimination can be facilitated. Gensei-kouken strains are sex-limited strains of silkworms developed by irradiating the pupae with gamma rays, by which a portion of the second chromosome is translocated onto the W chromosome. In these improved strains, the females are yellow-blooded and spin yellow cocoons. By using the EST-cDNA clones mapped on the Z chromosome, we identified the sex according to the polymorphic banding pattern or intensity of the signals. Furthermore, by using the clones on the second chromosome, the region of the second chromosome translocated onto the W chromosome was also defined. In both the A95 and A 96 strains selected for the present study, only the mid-portion of the second chromosome was translocated. The differences in length of the fragments translocated in these strains are discussed.

A Bombyx mandarina mutant exhibiting translucent larval skin is controlled by the molybdenum cofactor sulfurase gene

During the maintenance of the wild silkworm, Bombyx mandarina, a mutant phenotype exhibiting translucent skin was identified. Based on the crossing experiments with the domesticated silkworm, Bombyx mori, we found that the mutant was controlled by molybdenum cofactor sulfurase (MoCoS) gene. We designated the mutant ''Ozaki's translucent'' (og(Z)). We found a 2.1-kb deletion containing the transcription initiation site, exons 1 and 2, and the 5' end of exon 3 of the MoCoS gene. The transcript of the MoCoS gene was not detected in the og(Z) homozygote. We concluded that og(Z) is a complete loss-of-function allele generated by a disruption of the MoCoS gene.

Evolution of genome size and complexity in Pinus

BACKGROUND

Genome evolution in the gymnosperm lineage of seed plants has given rise to many of the most complex and largest plant genomes, however the elements involved are poorly understood.

METHODOLOGY/PRINCIPAL FINDINGS

Gymny is a previously undescribed retrotransposon family in Pinus that is related to Athila elements in Arabidopsis. Gymny elements are dispersed throughout the modern Pinus genome and occupy a physical space at least the size of the Arabidopsis thaliana genome. In contrast to previously described retroelements in Pinus, the Gymny family was amplified or introduced after the divergence of pine and spruce (Picea). If retrotransposon expansions are responsible for genome size differences within the Pinaceae, as they are in angiosperms, then they have yet to be identified. In contrast, molecular divergence of Gymny retrotransposons together with other families of retrotransposons can account for the large genome complexity of pines along with protein-coding genic DNA, as revealed by massively parallel DNA sequence analysis of Cot fractionated genomic DNA.

CONCLUSIONS/SIGNIFICANCE

Most of the enormous genome complexity of pines can be explained by divergence of retrotransposons, however the elements responsible for genome size variation are yet to be identified. Genomic resources for Pinus including those reported here should assist in further defining whether and how the roles of retrotransposons differ in the evolution of angiosperm and gymnosperm genomes.

Novel RNA sequences associated with late male killing in Homona magnanima

Maternally inherited female-biased sex ratios have been documented in many invertebrate species. One cause of such biased sex ratios is male killing, i.e. only males die. In most species, male killing occurs during embryonic stages (early male killing) and is associated with cytoplasmic bacteria, including Wolbachia, Spiroplasma, Rickettsia, Flavobacteria and gamma proteobacteria. However, the oriental tea tortrix, Homona magnanima, is one of the few species in which male death occurs in the larval or pupal stage, and is thus an example of late male killing. We partially purified the agent causing late male killing in H. magnanima and showed that it consists of two RNA sequences. This represents an entirely novel agent causing late male killing.

Identification of the female-determining region of the W chromosome in Bombyx mori

The W chromosome of the silkworm Bombyx mori is devoid of functional genes, except for the putative female-determining gene (Fem). To localize Fem, we investigated the presence of W-specific DNA markers on strains in which an autosomal fragment containing dominant marker genes was attached to the W chromosome. We produced new W-chromosomal fragments from the existing Zebra-W strain (T(W;3)Ze chromosome) by X-irradiation, and then carried out deletion mapping of these and sex-limited yellow cocoon strains (T(W;2)Y-Chu, -Abe and -Ban types) from different Japanese stock centers. Of 12 RAPD markers identified in the normal W chromosomes of most silkworm strains in Japan, the newly irradiated W(B-YL-YS)Ze chromosome contained three, the T(W;2)Y-Chu chromosome contained six, and the T(W;2)Y-Abe and -Ban chromosomes contained only one (W-Rikishi). To investigate the ability of the reduced W-chromosome translocation fragments to form heterochromatin bodies, which are found in nuclei of normal adult female sucking stomachs, we examined cells of the normal type p50 strain and the T(W;2)Y-Chu and -Abe strains. A single sex heterochromatin body was found in nuclei of p50 females, whereas we detected only small sex heterochromatin bodies in the T(W;2)Y-Chu strain and no sex heterochromatin body in the T(W;2)Y-Abe strain. Since adult females of all strains were normal and fertile, we conclude that only extremely limited region, containing the W-Rikishi RAPD sequence of the W chromosome, is required to determine femaleness. Based on a comparison of the normal W-chromosome and 7 translocation and W-deletion strains we present a map of Fem relative to the 12 W-specific RAPD markers.

Identification of Y chromosomal PCR marker and production of a selected strain for molecular sexing in the brown planthopper, Nilaparvata lugens

A laboratory colony was established in order to enable molecular sexing in premature stages in the brown planthopper, Nilaparvata lugens. We found four male-specific amplified fragment length polymorphisms (AFLPs) in the planthopper, and sequenced one of the AFLPs along with its 5' flanking region (1,423 bp in total). PCR primers were designed based on the nucleotide sequence information so that the PCR product was present in male planthoppers and absent in female planthoppers. However, we could not completely distinguish males from females, because the PCR amplification product was absent in some of the males screened. We, therefore, established a laboratory colony, in which all males carried this sequence. We can directly sex pre-adult stages in this colony using our PCR primers, making this strain of considerable value for studies that require sex separation in egg and nymphal stages.

Sex determination in the silkworm, Bombyx mori: a female determinant on the W chromosome and the sex-determining gene cascade

In insects, the sex is determined completely by genetic mechanisms, which at least in somatic tissues, are cell autonomous. The sex of the silkworm, Bombyx mori, is strongly controlled by the presence of the W chromosome. Genetic studies using translocations and deletions of W suggested that a presumptive feminizing gene (Fem) is located in a limited region of the W chromosome. Recent genomic studies revealed a small number of potential candidates for the Fem gene in this region. In addition, a Bombyx homologue of the Drosophila sex determining gene doublesex has been identified on an autosome and analyzed. Whereas the Drosophila doublesex gene is regulated by activation of splicing in females, the Bombyx doublesex gene (Bmdsx) encodes female- and male-specific mRNAs regulated via male-specific repression of splicing. The vitellogenin gene (Vg) is a target of the BmDSX protein, which directly binds to the Vg promoter. Furthermore, as ectopic expression of the male-type Bmdsx induces male-like transformation of the sexual organs, BmDSX may control sex-specific morphological characteristics in Bombyx. This suggests that although upstream events in Drosophila and Bombyx sex determination differ, similarities between the two species do exist in downstream genetic control of sex determination.

The female-killing chromosome of the silkworm, Bombyx mori, was generated by translocation between the Z and W chromosomes

Bombyx mori is a female-heterogametic organism (female, ZW; male, ZZ) that appears to have a putative feminizing gene (Fem) on the W chromosome. The paternally transmitted mutant W chromosome, Df(p ( Sa ) + ( p )W + ( od ))Fem, derived from the translocation-carrying W chromosome (p ( Sa ) + ( p )W + ( od )), is inert as femaleness determinant. Moreover, this Df(p ( Sa ) + ( p )W + ( od ))Fem chromosome has been thought to have a female-killing factor because no female larvae having the Df(p ( Sa ) + ( p )W + ( od ))Fem chromosome are produced. Initially, to investigate whether the Df(p ( Sa ) + ( p )W + ( od ))Fem chromosome contains any region of the W chromosome or not, we analyzed the presence or absence of 12 W-specific RAPD markers. The Df(p ( Sa ) + ( p )W + ( od ))Fem chromosome contained 3 of 12 W-specific RAPD markers. These results strongly indicate that the Df(p ( Sa ) + ( p )W + ( od ))Fem chromosome contains the region of the W chromosome. Moreover, by using phenotypic and molecular markers, we confirmed that the Df(p ( Sa ) + ( p )W + ( od ))Fem chromosome is connected with a partially deleted Z chromosome and that this fused chromosome behaves as a Z chromosome during male meiosis. Furthermore, we demonstrated that the ZZW-type triploid female having the Df(p ( Sa ) + ( p )W + ( od ))Fem chromosome is viable. Therefore, we concluded that the Df(p ( Sa ) + ( p )W + ( od ))Fem chromosome does not have a female-killing factor but that partial deletion of the Z chromosome causes the death of the ZW-type diploid female having the Df(p ( Sa ) + ( p )W + ( od ))Fem chromosome. Additionally, our results of detailed genetic analyses strongly indicate that the female-killing chromosome composed of the Df(p ( Sa ) + ( p )W + ( od ))Fem chromosome and deleted Z chromosome was generated by translocation between the Z chromosome and the translocation-carrying W chromosome, p ( Sa ) + ( p )W + ( od ).

Molecular characterization and genomic distribution of Isis: a new retrotransposon of Drosophila buzzatii

A new transposable element, Isis, is identified as a LTR retrotransposon in Drosophila buzzatii. DNA sequence analysis shows that Isis contains three long ORFs similar to gag, pol and env genes of retroviruses. The ORF1 exhibits sequence homology to matrix, capsid and nucleocapsid gag proteins and ORF2 encodes a putative protease (PR), a reverse transcriptase (RT), an Rnase H (RH) and an integrase (IN) region. The analysis of a putative env product, encoded by the env ORF3, shows a degenerated protein containing several stop codons. The molecular study of the putative proteins coded by this new element shows striking similarities to both Ulysses and Osvaldo elements, two LTR retrotransposons, present in D. virilis and D. buzzatii, respectively. Comparisons of the predicted Isis RT to several known retrotransposons show strong phylogenetic relationships to gypsy-like elements, particulary to Ulysses retrotransposon. Studies of Isis chromosomal distribution show a strong hybridization signal in centromeric and pericentromeric regions, and a scattered distribution along all chromosomal arms. The existence of insertional polymorphisms between different strains and high molecular weight bands by Southern blot suggests the existence of full-sized copies that have been active recently. The presence of euchromatic insertion sites coincident between Isis and Osvaldo could indicate preferential insertion sites of Osvaldo element into Isis sequence or vice versa. Moreover, the presence of Isis in different species of the buzzatii complex indicates the ancient origin of this element.

Isolation and characterization of sex chromosome rearrangements generating male muscle dystrophy and female abnormal oogenesis in the silkworm, Bombyx mori

In deletion-mapping of W-specific RAPD (W-RAPD) markers and putative female determinant gene (Fem), we used X-ray irradiation to break the translocation-carrying W chromosome (W( Ze )). We succeeded in obtaining a fragment of the W( Ze ) chromosome designated as Ze (W), having 3 of 12 W-RAPD markers (W-Bonsai, W-Yukemuri-S, W-Yukemuri-L). Inheritance of the Ze (W) fragment by males indicates that it does not include the Fem gene. On the basis of these results, we determined the relative positions of W-Yukemuri-S and W-Yukemuri-L, and we narrowed down the region where Fem gene is located. In addition to the Ze (W) fragment, the Z chromosome was also broken into a large fragment (Z(1)) having the +( sch ) (1-21.5) and a small fragment (Z(2)) having the +( od ) (1-49.6). Moreover, a new chromosomal fragment (Ze (W)Z(2)) was generated by a fusion event between the Ze (W) and the Z(2) fragments. We analyzed the genetic behavior of the Z(1) fragment and the Ze (W)Z(2) fragment during male (Z/Z(1) Ze (W)Z(2)) and female (Z(1) Ze (W)Z(2)/W) meiosis using phenotypic markers. It was observed that the Z(1) fragment and the Z or the W chromosomes separate without fail. On the other hand, non-disjunction between the Ze (W)Z(2) fragment and the Z chromosome and also between the Ze (W)Z(2) fragment and the W chromosome occurred. Furthermore, the females (2A: Z/Ze (W)Z(2)/W) and males (2A: Z/Z(1)) resulting from non-disjunction between the Ze (W)Z(2) fragment and the W chromosome had phenotypic defects: namely, females exhibited abnormal oogenesis and males were flapless due to abnormal indirect flight muscle structure. These results suggest that Z(2) region of the Z chromosome contains dose-sensitive gene(s), which are involved in oogenesis and indirect flight muscle development.

Cloning and alternative splicing analysis of Bombyx mori transformer-2 gene using silkworm EST database

We have identified Bombyx mori transformer-2 gene (Bmtra-2) cDNA by blasting the EST database of B. mori. It was expressed in the whole life of the male and female silkworm and was observed as a band of 1.3 kb by Northern blot analysis. By comparing corresponding ESTs to the Bmtra-2 DNA sequence, it was revealed that there were eight exons and seven introns, and all splice sites of exons/introns conformed to the GT/AG rule. Bmtra-2 pre-mRNA can produce multiple mRNAs encoding six distinct isoforms of BmTRA-2 protein using an alternative splicing pathway during processing. Six types of Bmtra-2 cDNA clones were identified by reverse transcription-polymerase chain reaction. All isoforms of BmTRA-2 protein contain two arginine/serine-rich domains and one RNA recognition motif, showing striking organizational similarity to Drosophila TRA-2 proteins.

Genetic mapping of Z chromosome and identification of W chromosome-specific markers in the silkworm, Bombyx mori

In the silkworm, Bombyx mori, the female is the heterogametic (ZW) sex and the male is homogametic (ZZ). The female heterogamety is a typical situation in the insect order Lepidoptera. Although the W chromosome in silkworm is strongly female determining, no W-linked gene for a morphological character has been found on it. The Z chromosome carries important traits of economic value as well as genes for various phenotypic traits, but only 2% of molecular information based on its relative size is known. Studies conducted so far indicate that the Z-linked genes are not dosage compensated. In the present study, we constructed a genetic map of randomly amplified polymorphic DNA fragments (RAPD), simple sequence repeats (SSR), and fluorescent intersimple sequence repeat PCR (FISSR) markers for the Z chromosome using a backcross mapping population. A total of 16 Z-linked markers were identified, characterized, and mapped using od, a recessive trait for translucent skin as an anchor marker yielding a total recombination map of 334.5 cM. The linkage distances obtained suggested that the markers were distributed throughout the Z chromosome. Four RAPD and four SSR markers that were linked to W chromosome were also identified. The proposed mapping approach should be useful to identify and map sex-linked traits in the silkworm. The economic and evolutionary significance of Z- and W-linked genes in silkworm, in particular, and lepidopterans, in general, is discussed.

Partial deletions of the W chromosome due to reciprocal translocation in the silkworm Bombyx mori

In the silkworm, Bombyx mori (female, ZW; male, ZZ), femaleness is determined by the presence of a single W chromosome, irrespective of the number of autosomes or Z chromosomes. The W chromosome is devoid of functional genes, except the putative female-determining gene (Fem). However, there are strains in which chromosomal fragments containing autosomal markers have been translocated on to W. In this study, we analysed the W chromosomal regions of the Zebra-W strain (T(W;3)Ze chromosome) and the Black-egg-W strain (T(W;10)+(w-2) chromosome) at the molecular level. Initially, we undertook a project to identify W-specific RAPD markers, in addition to the three already established W-specific RAPD markers (W-Kabuki, W-Samurai and W-Kamikaze). Following the screening of 3648 arbitrary 10-mer primers, we obtained nine W-specific RAPD marker sequences (W-Bonsai, W-Mikan, W-Musashi, W-Rikishi, W-Sakura, W-Sasuke, W-Yukemuri-L, W-Yukemuri-S and BMC1-Kabuki), almost all of which contained the border regions of retrotransposons, namely portions of nested retrotransposons. We confirmed the presence of eleven out of twelve W-specific RAPD markers in the normal W chromosomes of twenty-five silkworm strains maintained in Japan. These results indicate that the W chromosomes of the strains in Japan are almost identical in type. The Zebra-W strain (T(W;3)Ze chromosome) lacked the W-Samurai and W-Mikan RAPD markers and the Black-egg-W strain (T(W;10)+(w-2) chromosome) lacked the W-Mikan RAPD marker. These results strongly indicate that the regions containing the W-Samurai and W-Mikan RAPD markers or the W-Mikan RAPD marker were deleted in the T(W;3)Ze and T(W;10)+(w-2) chromosomes, respectively, due to reciprocal translocation between the W chromosome and the autosome. This deletion apparently does not affect the expression of Fem; therefore, this deleted region of the W chromosome does not contain the putative Fem gene.

Retrotransposable elements on the W chromosome of the silkworm, Bombyx mori

The sex chromosomes of the silkworm, Bombyxmori, are designated ZW(XY) for females and ZZ(XX) for males. The W chromosome of B. mori does not recombine with the Z chromosome and autosomes and no genes for morphological characters have been mapped to the W chromosome as yet. Furthermore, femaleness is determined by the presence of a single W chromosome, regardless of the number of autosomes or Z chromosomes. To understand these interesting features of the W chromosome, it is necessary to analyze the W chromosome at the molecular biology level. Initially to isolate DNA sequences specific for the W chromosome as randomly amplified polymorphic DNA (RAPD) markers, we compared the genomic DNAs between males and females by PCR with arbitrary 10-mer primers. To the present, we have identified 12 W-specific RAPD markers, and with the exception of one RAPD marker, all of the deduced amino acid sequences of these W-specific RAPD markers show similarity to previously reported amino acid sequences of retrotransposable elements from various organisms. After constructing a genomic DNA lambda phage library of B. mori we obtained two lambda phage clones, one containing the W-Kabuki RAPD sequence and one containing the W-Samurai RAPD sequence and found that these DNA sequences comprised nested structures of many retrotransposable elements. To further analyze the W chromosome, we obtained 14 W-specific bacterial artificial chromosome (BAC) clones from three BAC libraries and subjected these clones to shotgun sequencing. The resulting assembly of sequences did not produce a single contiguous sequence due to the presence of many retrotransposable elements. Therefore, we coupled PCR with shotgun sequencing. Through these analyses, we found that many long terminal repeat (LTR) and non-LTR retrotransposons, retroposons, DNA transposons and their derivatives, have accumulated on the W chromosome as strata. These results strongly indicate that retrotransposable elements are the main structural component of the W chromosome.

The genetics and genomics of the silkworm, Bombyx mori

We review progress in applying molecular genetic and genomic technologies to studies in the domesticated silkworm, Bombyx mori, highlighting its use as a model for Lepidoptera, and in sericulture and biotechnology. Dense molecular linkage maps are being integrated with classical linkage maps for positional cloning and marker-assisted selection. Classical mutations have been identified by a candidate gene approach. Cytogenetic and sequence analyses show that the W chromosome is composed largely of nested full-length long terminal repeat retrotransposons. Z-chromosome-linked sequences show a lack of dosage compensation. The downstream sex differentiation mechanism has been studied via the silkworm homolog of doublesex. Expressed sequence tagged databases have been used to discover Lepidoptera-specific genes, provide evidence for horizontal gene transfer, and construct microarrays. Physical maps using large-fragment bacterial artificial chromosome libraries have been constructed, and whole-genome shotgun sequencing is underway. Germline transformation and transient expression systems are well established and available for functional studies, high-level protein expression, and gene silencing via RNA interference.

Detachment analysis of the translocated W chromosome shows that the female-specific randomly amplified polymorphic DNA (RAPD) marker, female-218, is derived from the second chromosome fragment region of the translocated W chromosome of the sex-limited p(B) silkworm (Bombyx mori ) strain

The sex chromosomes of the silkworm, Bombyx mori, are designated ZW for the female and ZZ for the male. We previously characterized a female-specific randomly amplified polymorphic DNA (RAPD) marker, designated Female-218, from the translocation-bearing W chromosomes. These W chromosomes contain a region of the second chromosome, which carries visible larval markers of the p loci. We used strain TWPB in which female larvae have black skin due to the p(B) gene (T(W;2)p(B), +p/+p) while male larvae have whitish skin (+p/+p). To determine whether the Female-218 RAPD marker is derived from the "W region" or a "second chromosome fragment", we induced a detachment of the translocated W chromosome, T(W;2)p(B), by treating the eggs with hot water at an early developmental stage. After hot water treatment, we obtained 27 white female larvae out of 4850 female larvae. The Female-218 RAPD marker was not amplified in 26 out of 27 white female larvae, and was amplified from one white female larva. Moreover, we obtained 11 black male larvae out of 5377 male larvae. Eight out of 11 black male larvae became adult moths, and the Female-218 RAPD marker was amplified from all eight male moths. Examination of the genetic relationship between the Female-218 RAPD marker and the second chromosome fragment of the translocated W chromosome strongly indicates that the Female-218 RAPD marker is amplified from the region of second chromosome fragment of the T(W;2)p(B) chromosome.

Divergent long-terminal-repeat retrotransposon families in the genome of Paragonimus westermani

To gain information on retrotransposons in the genome of Paragonimus westermani, PCR was carried out with degenerate primers, specific to protease and reverse transcriptase (rt) genes of long-terminal-repeat (LTR) retrotransposons. The PCR products were cloned and sequenced, after which 12 different retrotransposon-related sequences were isolated from the trematode genome. These showed various degrees of identity to the polyprotein of divergent retrotransposon families. A phylogenetic analysis demonstrated that these sequences could be classified into three different families of LTR retrotransposons, namely, Xena, Bel, and Gypsy families. Of these, two mRNA transcripts were detected by reverse transcriptase-PCR, showing that these two elements preserved their mobile activities. The genomic distributions of these two sequences were found to be highly repetitive. These results suggest that there are diverse retrotransposons including the ancient Xena family in the genome of P. westermani, which may have been involved in the evolution of the host genome.

An Ac -like Transposable Element Family With Transcriptionally Active Y-Linked Copies in the White Campion, Silene latifolia

An RFLP genomic subtraction was used to isolate male-specific sequences in the species Silene latifolia. One isolated fragment, SLP2, shares similarity to a portion of the Activator (Ac) transposase from Zea mays and to related proteins from other plant species. Southern blot analysis of male and female S. latifolia genomic DNA shows that SLP2 belongs to a low-copy-number repeat family with two Y-linked copies. Screening of a S. latifolia male genomic library using SLP2 as a probe led to the isolation of five clones, which were partially sequenced. One clone contains two large open reading frames that can be joined into a sequence encoding a putative protein of 682 amino acids by removing a short intron. Database searches and phylogenetic analysis show that this protein belongs to the hAT superfamily of transposases, closest to Tag2 (Arabidopsis thaliana), and contains all of the defined domains critical for the activity of these transposases. PCR with genomic and cDNA templates from S. latifolia male, female, and hermaphrodite individuals revealed that one of the Y-linked copies is transcriptionally active and alternatively spliced. This is the first report of a transcriptionally active transposable element (TE) family in S. latifolia and the first DNA transposon residing on a plant Y chromosome. The potential activity and regulation of this TE family and its use for Y chromosome gene discovery is discussed.

W-derived BAC probes as a new tool for identification of the W chromosome and its aberrations in Bombyx mori

We isolated four W chromosome-derived bacterial artificial chromosome (W-BAC) clones from Bombyx mori BAC libraries by the polymerase chain reaction and used them as probes for fluorescence in situ hybridization (FISH) on chromosome preparations from B. mori females. All four W-BAC probes surprisingly highlighted the whole wild-type W sex chromosome and also identified the entire original W-chromosomal region in W chromosome-autosome translocation mutants. This is the first successful identification of a single chromosome by means of BAC-FISH in species with holokinetic chromosomes. Genomic in situ hybridization (GISH) by using female-derived genomic probes highlighted the W chromosome in a similar chromosome-painting manner. Besides the W, hybridization signals of W-BAC probes also occurred in telomeric and/or subtelomeric regions of the autosomes. These signals coincided well with those of female genomic probes except one additional GISH signal that was observed in a large heterochromatin block of one autosome pair. Our results support the opinion that the B. mori W chromosome accumulated transposable elements and other repetitive sequences that also occur, but scattered, elsewhere in the respective genome.

Genomic sequence of a 320-kb segment of the Z chromosome of Bombyx mori containing a kettin ortholog

The sex chromosome constitution of the silkworm, Bombyx mori, is ZW in the female and ZZ in the male. Very little molecular information is available about the Z chromosome in Lepidoptera, although the topic is interesting because of the absence of gene dosage compensation in this chromosome. We constructed a 320-kb BAC contig around the Bmkettin gene on the Z chromosome in Bombyx and determined its nucleotide sequence by the shotgun method. We found 13 novel protein-coding sequences in addition to Bmkettin. All the transposable elements detected in the region were truncated, and no LTR retrotransposons were found, in stark contrast to the situation on the W chromosome. In this 320-kb region, four genes for muscle proteins (Bmkettin, Bmtitin1, Bmtitin2, and Bmprojectin) are clustered, together with another gene (Bmmiple) on the Z chromosome in B. mori; their orthologs are also closely linked on chromosome 3 in Drosophila, suggesting a partial synteny. Real-time RT-PCR experiments demonstrated that transcripts of 13 genes of the 14 Z-linked genes found accumulated in larger amounts in males than in female moths, indicating the absence of gene dosage compensation. The implications of these findings for the evolution and function of the Z chromosome in Lepidoptera are discussed.

Moth sex chromatin probed by comparative genomic hybridization (CGH)

Abstract: Comparative genomic hybridization (CGH) with a probe mixture of differently labeled genomic DNA from females and males highlighted the W chromosomes in mitotic plates and the W chromatin in polyploid interphase nuclei of the silkworm Bombyx mori, the flour moth Ephestia kuehniella, and the wax moth Galleria mellonella. The overproportionate fluorescence signal indicated an accumulation of repetitive sequences in the respective W chromosomes. Measurements of the fluorescence signals revealed two components, one that is present also in male DNA (non-W chromosomes) and another one that is present only in or preponderantly in female DNA (W chromosomes). While the W chromosomes of E. kuehniella and G. mellonella had both components, that of B. mori appeared to lack the latter component. Our results show that CGH can be applied to obtain a first estimate of the sequence composition of sex chromosomes in species from which otherwise little is known on the molecular level.

Nested retrotransposons on the W chromosome of the wild silkworm Bombyx mandarina

The W chromosome of the silkworms Bombyx mori or B. mandarina is recombinationally isolated from the Z chromosome and the autosomes. We previously characterized a female-specific randomly amplified polymorphic DNA (RAPD), designated W-Yamato, derived from the W chromosome of the wild silkworm Bombyx mandarina. To further analyse the W chromosome of B. mandarina, we obtained a lambda phage clone that contains the W-Yamato RAPD sequence and sequenced the 16.7 kb DNA insert. We found that this DNA comprises a nested structure of at least seven elements: six retrotransposons and one transposable element-like sequence. The transposable element-like sequence is inserted into a micropia-like retrotransposon (Karate). The Karate and the non-long terminal repeat (non-LTR) retrotransposon BMC1 are inserted into a 412-like retrotransposon (Judo). Furthermore, this Judo, and two non-LTR retrotransposons (Kurosawa and Kendo) are inserted into a Pao-like retrotransposon (Yamato). These results indicate that the retrotransposons inserted into the W chromosome are not efficiently removed but accumulate gradually as strata without recombination.

Identification and analysis of sex chromosomes by comparative genomic hybridization (CGH)

Comparative Genome Hybridization (CGH) can be used as a universal method for the identification of molecularly differentiated sex chromosomes. This is profitable in species with homomorphic sex chromosomes or when chromosomes are unfavourable for cytogenetics, e.g. when size differences are insufficient, chromosomes numerous and/or banding methods fail. In this method, genomic DNA from females competes as a probe with that from males for binding to the chromosome targets. Easy extraction and labelling methods afford a method that can be applied even when few specimens are available, e.g. when specimens for investigation have to be collected in the field - CGH also offers the possibility to obtain a rough estimate of the DNA composition of the sex chromosome.

CsRn1, a novel active retrotransposon in a parasitic trematode, Clonorchis sinensis, discloses a new phylogenetic clade of Ty3/gypsy-like LTR retrotransposons

We screened the genome of a trematode, Clonorchis sinensis, in order to identify novel retrotransposons and thereby provide additional information on retrotransposons for comprehensive phylogenetic study. Considering the vast potential of retrotransposons to generate genetically variable regions among individual genomes, randomly amplified polymorphic DNAs (RAPDs) detected by arbitrarily primed polymerase chain reactions were selected as candidates for retrotransposon-related sequences. From RAPD analysis, we isolated and characterized a novel retrotransposon in C. sinensis as the first member of uncorrupted long-terminal-repeat (LTR) retrotransposons in phylum Platyhelminthes. The retrotransposon, which was named Clonorchis sinensis Retrotransposon 1 (CsRn1), showed a genomewide distribution and had a copy number of more than 100 per haploid genome. CsRn1 encoded an uninterrupted open reading frame (ORF) of 1,304 amino acids, and the deduced ORF exhibited similarities to the pol proteins of Ty3/gypsy-like LTR retrotransposons. The mobile activity of master copies was predicted by sequence analysis and confirmed by the presence of mRNA transcripts. Phylogenetic analysis of Ty3/gypsy-like LTR retrotransposons detected a new clade comprising CsRn1, Kabuki of Bombyx mori, and an uncharacterized element of Drosophila melanogaster. With its high repetitiveness and preserved mobile activity, it is proposed that CsRn1 may play a significant role in the genomic evolution of C. sinensis.

Sex-linked period genes in the silkmoth, Antheraea pernyi: implications for circadian clock regulation and the evolution of sex chromosomes

Regulation of the period (per) gene is a critical feature of circadian clock function in insects. Here, we show that per is sex-linked in the silkmoth, Antheraea per-nyi. The previously described silkmoth per gene is found on the Z chromosome. Silkmoth per is not dosage compensated at either the RNA or the protein level. Although earlier studies showed the presence of an oscillating endogenous antisense per transcript, we show that this transcript comes from a locus on the female-specific W chromosome. We further demonstrate the presence of a homolog of per on W that encodes a truncated protein. Rhythmicity of male (ZZ) moths demonstrates that neither of the W-linked per-like genes is essential for clock function. The presence of a per allele with duplications on W provides insight into the evolution of the sex chromosomes.

A complete full-length non-LTR retrotransposon, BMC1, on the W chromosome of the silkworm, Bombyx mori

In the silkworm, Bombyx mori, a non-long terminal repeat (non-LTR) retrotransposon, BMC1, is considered to be a LINE (long interspersed nuclear element)-like element. So far, a BMC1 containing two intact open reading frames (ORFs) has not been found. However, we discovered a complete full-length BMC1 on the W chromosome. This BMC1 is 5091 bp and contains a 5' untranslated region (5'-UTR), two intact ORFs, and 3'-UTR which terminates in a poly(A) tail. ORF1 encodes a putative nucleic acid-binding protein, while ORF2 encodes a protein containing an endonuclease domain and a reverse transcriptase domain.

Molecular structure of the copia-like retrotransposable element Yokozuna on the W chromosome of the silkworm, Bombyx mori

We discovered a novel retrotransposable element, designated Yokozuna, on the W chromosome of Bombyx mori. The size of this element is 4738 bp, including a 208-bp long terminal repeat (LTR) on one side and a 183-bp LTR on the other. This retrotransposable element is flanked by a 5-bp target site duplication, TAATT. Yokozuna contains a single long open reading frame (ORF) and the whole deduced amino acid sequence of ORF reveals strong homology with copia of Drosophila. Moreover, an alignment analysis of the reverse transcriptase (RT) sequences suggested that the Yokozuna element is the first Bombyx retrotransposable element belonging to the Ty1-copia group. The number of Yokozuna per haploid genome is approximately four copies. Although Yokozuna was discovered on the W chromosome, it is not specific for the W chromosome.