Extensive Repeat Regions Research Articles

Moving genes through parasitism

Parasite Genomes Plants that parasitize other plants include species such as mistletoe and members of the endophytic family Rafflesiaceae, which have the largest flowers of any plant but no other recognizable external structures. The impact of extreme host dependency usually results in genome streamlining. Cai et al. assembled the genome of the parasitic Rafflesia Sapria himalayana , hosts of which include members of the grape family. This parasite shows rapid genome evolution that has resulted in extensive gene loss in the chloroplast and photosynthetic machinery but retention of key genes for other organs. Unexpectedly, it has gained extensive repeat regions, resulting in a substantially larger genome than its closest free-living relatives, which may reflect horizontal gene transfer occurring during ancestral host associations. Curr. Biol. 10.1016/j.cub.2020.12.045 (2021).

The LOSS OF APOMEIOSIS (LOA) locus in Hieracium praealtum can function independently of the associated large‐scale repetitive chromosomal structure

Apomixis or asexual seed formation in Hieracium praealtum (Asteraceae) is controlled by two independent dominant loci. One of these, the LOSS OF APOMEIOSIS (LOA) locus, controls apomixis initiation, mitotic embryo sac formation (apospory) and suppression of the sexual pathway. The LOA locus is found near the end of a hemizygous chromosome surrounded by extensive repeats extending along the chromosome arm. Similar apomixis-carrying chromosome structures have been found in some apomictic grasses, suggesting that the extensive repetitive sequences may be functionally relevant to apomixis. Fluorescence in situ hybridization (FISH) was used to examine chromosomes of apomeiosis deletion mutants and rare recombinants in the critical LOA region arising from a cross between sexual Hieracium pilosella and apomictic H.praealtum. The combined analyses of aposporous and nonaposporous recombinant progeny and chromosomal karyotypes were used to determine that the functional LOA locus can be genetically separated from the very extensive repeat regions found on the LOA-carrying chromosome. The large-scale repetitive sequences associated with the LOA locus in H.praealtum are not essential for apospory or suppression of sexual megasporogenesis (female meiosis).

The Vsa Shield of Mycoplasma pulmonis Is Antiphagocytic

The infection of mice with Mycoplasma pulmonis is a model for studying chronic mycoplasmal respiratory disease. Many in vivo and in vitro studies have used the organism to gain a better understanding of host-pathogen interactions in chronic respiratory infection. The organism's Vsa proteins contain an extensive tandem repeat region. The length of the tandem repeat unit varies from as few as 11 amino acids to as many as 19. The number of tandem repeats can be as high as 60. The number of repeats varies at a high frequency due to slipped-strand mispairing events that occur during DNA replication. When the number of repeats is high, e.g., 40, the mycoplasma is resistant to lysis by complement but does not form a robust biofilm. When the number of repeats is low, e.g., 5, the mycoplasma is killed by complement when the cells are dispersed but has the capacity to form a biofilm that resists complement. Here, we examine the role of the Vsa proteins in the avoidance of phagocytosis and find that cells producing a protein with many tandem repeats are relatively resistant to killing by macrophages. These results may be pertinent to understanding the functions of similar proteins that have extensive repeat regions in other microbes.

The complete mitochondrial genome sequence of the planthopper, Sivaloka damnosus.

The complete mitochondrial genome (mitogenome) sequence was determined from the plant hopper, Sivaloka damnosus Chow and Lu (Hemiptera: Issidae), a representative of the insect family Issidae. The genome is a circular molecule of 15,287 bp with a total A+T content of 76.5%. The gene content, order, and structure are identical to that in Drosophila melanogaster, which is considered ancestral for insects. All 13 protein-coding genes of the S. damnosus mitogenome have a putative inframe ATR methionine or ATT isoleucine codons as start signals. The usual termination codons (TAA and TAG) were found in 11 protein-coding genes. However, atp6, and nad4 have incomplete termination codons. All tRNAs show stable canonical clover-leaf structures similar to other insect mitochondrial tRNAs, except for tRNASer(AGN), which has a reduced DHU arm. The A+T-rich region or putative control region includes two extensive repeat regions. The first repeat region is composed of two sets of complicated repeat units, and these repetitive sequences are arranged alternately; the second contains ten 20 bp tandemly repetitive sequences. In the phylogenetic analyses based on protein-coding genes, Cicadomorpha is a sister to Fulgoromorpha+Sternorrhyncha, and Heteroptera is a sister to all other Hemiptera.

Complete mitochondrial genome of brown marmorated stink bug Halyomorpha halys (Hemiptera: Pentatomidae), and phylogenetic relationships of hemipteran suborders.

The newly sequenced complete mitochondrial genome of the brown marmorated stink bug, Halyomorpha halys (Stål) (Hemiptera: Pentatomidae), is a circular molecule of 16,518 bp with a total A+T content of 76.4% and two extensive repeat regions in A+T rich region. Nucleotide composition and codon usage of H. halys are about average when compared with values observed in 19 other published hemipteran mitochondrial genomes. Phylogenetic analyses using these 20 hemipteran mitochondrial genomes support the currently accepted hypothesis that suborders Heteroptera and Auchenorrhyncha form a monophyletic group. The mitochondrial gene arrangements of the 20 genomes=are also consistent with our results.

The Complete Mitochondrial Genome of the Bristletail Pedetontus silvestrii (Archaeognatha: Machilidae) and an Examination of Mitochondrial Gene Variability within Four Bristletails

Abstract The entire mitochondrial genome of the bristletail Pedetontus silvestrii (Mendes) (Archaeognatha: Machilidae) was sequenced. The genome is 15,879 bp and bears the standard set of genes common to all arthropods. Genome features like nucleotide composition and codon use are compared with three other bristletails. The gene trnQ was inverted compared with the order in other hexapods. The major noncoding region (the A+T-rich region or control region) between the small ribosomal subunit (rrnS) and the trnI gene includes one extensive repeat region, which has two tandem repeats of a 128-bp sequence. A+T content is higher than in other known species of Archaeognatha and Zygentoma but is similar to that in Collembola and Pterygota.

Insect mitochondrial genomics: the complete mitochondrial genome sequence of the meadow spittlebugPhilaenus spumarius(Hemiptera: Auchenorrhyncha: Cercopoidae)

We present the complete mitochondrial genome sequence of the meadow spittlebug Philaenus spumarius (Auchenorrhyncha: Cercopoidae). This contribution represents the second mitochondrial genome from the Hemiptera and the second of the three hemipteran suborders sampled. The genome is a circular molecule of 16 324 bp with a total A+T content of 77.0% and 76.7% for coding regions only. The gene content, order, and structure are consistent with the Drosophila yakuba genome structure (Clary and Wolstenholme 1985) and the hypothesized ancestral arthropod genome arrangement (Crease 1999). Nucleotide composition and codon usage are near the means observed in other insect mitochondria sequenced to date but have a higher A+T richness compared with the other hemipteran example, the kissing bug Triatoma dimidiata (Dotson and Beard. 2001. Insect Mol. Biol. 10: 205-215). The major noncoding region (the A+T rich region or putative control region) between the small ribosomal subunit and the tRNAIle gene includes two extensive repeat regions. The first repeat region includes 19 tandem repeats of a 46-bp sequence, whereas the second contains a longer sequence (146 bp) tandemly repeated four times.

Identification of Xenorhabdus nematophila genes required for mutualistic colonization of Steinernema carpocapsae nematodes.

One stage in the symbiotic interaction between the bacterium Xenorhabdus nematophila and its nematode host, Steinernema carpocapsae, involves the species-specific colonization of the nematode intestinal vesicle by the bacterium. To characterize the bacterial molecular determinants that are essential for vesicle colonization, we adapted and applied a signature-tagged mutagenesis (STM) screen to this system. We identified 15 out of 3000 transposon mutants of X. nematophila with at least a 15-fold reduction in average vesicle colonization. These 15 mutants harbour disruptions in nine separate loci. Three of these loci have predicted open reading frames (ORFs) with similarity to genes (rpoS, rpoE, lrp) encoding regulatory proteins; two have predicted ORFs with similarity to genes (aroA, serC) encoding amino acid biosynthetic enzymes; one, designated nilB (nematode intestine localization), has an ORF with similarity to a gene encoding a putative outer membrane protein (OmpU) in Neisseria; and three, nilA, nilC and nilD, have no apparent homologues in the public database. nilA, nilB and nilC are linked on a single 4 kb locus. nilB and nilC are > 104-fold reduced in their ability to colonize the nematode vesicle and are predicted to encode membrane-localized proteins. The nilD locus contains an extensive repeat region and several small putative ORFs. Other than reduced colonization, the nilB, nilC and nilD mutants did not display alterations in any other phenotype tested, suggesting a specific role for these genes in allowing X. nematophila to associate with the nematode host.

Common Sequence Elements in Structurally Unrelated Genomes of Defective Interfering Semliki Forest Virus

The polymerase chain reaction was used to amplify defective interfering (DI) Semliki Forest virus (SFV) genomes from tissue culture preparations which had in vitro interfering and in vivo mouse-protecting activity. The products were molecularly cloned and sequenced (pSFVDI-6, 2146 nt and pSFVDI-19, 1244 nt). Comparison with the sequence of the SFV genome showed that both were derived from three noncontiguous regions: the 5′ terminus including the start of the nsP1 coding region, part of the nsP2 coding region, and the 3′ untranslated region. Both clones possessed open reading frames, including one with the potential of encoding truncated versions of nsP1. Transcribed RNAs from pSFVDI-6 and pSFVDI-19 were translated in an in vitro system into polypeptides of M r 27,000 and 25,000, respectively. Although pSFVDI-6 and pSFVDI-19 did not possess the rearranged sequences or extensive repeat regions of previously cloned DI SFV genomes (Lehtovaara et al., Proc. Natl. Acad. Sci. USA 78, 5353-5357, 1981; Lehtovaara et al., J. Mol. Biol. 156, 731-748, 1982), they were derived from similar regions of the SFV genome, suggesting a common sequence requirement for DI SFV particles.