scholarly journals Genome comparisons indicate recent transfer of wRi-like Wolbachia between sister species Drosophila suzukii and D. subpulchrella

2017 ◽  
Author(s):  
William R. Conner ◽  
Mark L. Blaxter ◽  
Gianfranco Anfora ◽  
Lino Ometto ◽  
Omar Rota-Stabelli ◽  
...  
Keyword(s):  
Relative Frequency ◽  
Cytoplasmic Incompatibility ◽  
Single Copy ◽  
Sister Species ◽  
Published Data ◽  
Drosophila Suzukii ◽  
Closely Related Species ◽  
Coding Sequences ◽  
Genome Comparisons ◽  
Rates Of Molecular Evolution

AbstractWolbachia endosymbionts may be acquired by horizontal transfer, by introgression through hybridization between closely related species, or by cladogenic retention during speciation. All three modes of acquisition have been demonstrated, but their relative frequency is largely unknown. Drosophila suzukii and its sister species D. subpulchrella harbor Wolbachia, denoted wSuz and wSpc, very closely related to wRi, identified in California populations of D. simulans. However, these variants differ in their induced phenotypes: wRi causes significant cytoplasmic incompatibility (CI) in D. simulans, but CI has not been detected in D. suzukii or D. subpulchrella. Our draft genomes of wSuz and wSpc contain full-length copies of 703 of the 734 single-copy genes found in wRi. Over these coding sequences, wSuz and wSpc differ by only 0.004% (i.e., 28 of 704,883 bp); they are sisters relative to wRi, from which each differs by 0.014-0.015%. Using published data from D. melanogaster, Nasonia wasps and Nomada bees to calibrate relative rates of Wolbachia versus host nuclear divergence, we conclude that wSuz and wSpc are too similar - by at least a factor of 100 - to be plausible candidates for cladogenic transmission. These three wRi-like Wolbachia, which differ in CI phenotype in their native hosts, have different numbers of orthologs of genes postulated to contribute to CI; and the CI loci differ at several nucleotides that may account for the CI difference. We discuss the general problem of distinguishing alternative modes of Wolbachia acquisition, focusing on the difficulties posed by limited knowledge of variation in absolute and relative rates of molecular evolution for host nuclear genomes, mitochondria and Wolbachia.

scholarly journals Gene decay in archaea

Archaea ◽  
2007 ◽  
Vol 2 (2) ◽  
pp. 137-143 ◽  
Author(s):  
M. W. J. van Passel ◽  
C. S. Smillie ◽  
H. Ochman
Keyword(s):  
Related Species ◽  
Whole Genome ◽  
Genome Sequences ◽  
Closely Related Species ◽  
Coding Sequences ◽  
Frameshift Mutations ◽  
Large Numbers ◽  
Inactivating Mutation ◽  
Gene Decay ◽  
Genome Comparisons

The gene-dense chromosomes of archaea and bacteria were long thought to be devoid of pseudogenes, but with the massive increase in available genome sequences, whole genome comparisons between closely related species have identified mutations that have rendered numerous genes inactive. Comparative analyses of sequenced archaeal genomes revealed numerous pseudogenes, which can constitute up to 8.6% of the annotated coding sequences in some genomes. The largest proportion of pseudogenes is created by gene truncations, followed by frameshift mutations. Within archaeal genomes, large numbers of pseudogenes contain more than one inactivating mutation, suggesting that pseudogenes are deleted from the genome more slowly in archaea than in bacteria. Although archaea seem to retain pseudogenes longer than do bacteria, most archaeal genomes have unique repertoires of pseudogenes.

scholarly journals Genome comparisons indicate recent transfer of w Ri-like Wolbachia between sister species Drosophila suzukii and D. subpulchrella

2017 ◽  
Vol 7 (22) ◽  
pp. 9391-9404 ◽  
Author(s):  
William R. Conner ◽  
Mark L. Blaxter ◽  
Gianfranco Anfora ◽  
Lino Ometto ◽  
Omar Rota-Stabelli ◽  
...  
Keyword(s):  
Sister Species ◽  
Drosophila Suzukii ◽  
Genome Comparisons

scholarly journals SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: Secale) Species

2020 ◽  
Vol 21 (24) ◽  
pp. 9421
Author(s):  
Lidia Skuza ◽  
Ewa Filip ◽  
Izabela Szućko ◽  
Jan Bocianowski
Keyword(s):  
Mitochondrial Dna ◽  
Molecular Markers ◽  
Related Species ◽  
Economic Importance ◽  
Closely Related Species ◽  
Coding Sequences ◽  
Coding Regions ◽  
Genomic Regions ◽  
Tribe Triticeae

Secale is a small but very diverse genus from the tribe Triticeae (family Poaceae), which includes annual, perennial, self-pollinating and open-pollinating, cultivated, weedy and wild species of various phenotypes. Despite its high economic importance, classification of this genus, comprising 3–8 species, is inconsistent. This has resulted in significantly reduced progress in the breeding of rye which could be enriched with functional traits derived from wild rye species. Our previous research has suggested the utility of non-coding sequences of chloroplast and mitochondrial DNA in studies on closely related species of the genus Secale. Here we applied the SPInDel (Species Identification by Insertions/Deletions) approach, which targets hypervariable genomic regions containing multiple insertions/deletions (indels) and exhibiting extensive length variability. We analysed a total of 140 and 210 non-coding sequences from cpDNA and mtDNA, respectively. The resulting data highlight regions which may represent useful molecular markers with respect to closely related species of the genus Secale, however, we found the chloroplast genome to be more informative. These molecular markers include non-coding regions of chloroplast DNA: atpB-rbcL and trnT-trnL and non-coding regions of mitochondrial DNA: nad1B-nad1C and rrn5/rrn18. Our results demonstrate the utility of the SPInDel concept for the characterisation of Secale species.

scholarly journals Rates and patterns of molecular evolution in marine animals following the Isthmian emergence

1992 ◽  
Vol 6 ◽  
pp. 68-68
Author(s):  
Timothy Collins
Keyword(s):  
Molecular Evolution ◽  
Time Scale ◽  
Published Data ◽  
Rate Variation ◽  
Marine Animals ◽  
Sequence Comparisons ◽  
Western Atlantic ◽  
Taxonomic Groups ◽  
A Site ◽  
Rates Of Molecular Evolution

The marine vicariant event resulting from the Pliocene emergence of the Central American Isthmus presents a unique opportunity for calibrating rates of molecular evolution. The synchronous fragmentation of the ranges of previously widespread taxa into Western Atlantic and Eastern Pacific components (geminates) enables one to make comparisons of rates among higher taxa on the same time scale and to evaluate the regularity of rates of molecular evolution among all species sampled. Other advantages of this approach are that the time scale (approximately 3 Ma) is one of particular interest for evolutionary biologists concerned with speciation and one that minimizes the ambiguities associated with augmentation of divergence values to account for multiple hits at a site. The divergence values derived for geminate pairs are independent, allowing statistical evaluation of variance in rates.The current popularity of the relative rates test as the final arbiter of questions regarding rates and rate variation is primarily a matter of convenience and not a reflection of methodological superiority. A review of the commonly used techniques for calibrating rates of molecular evolution shows that each approach has limitations. Temporally based calibrations of rates are necessary complements to time-independent comparisons.Interpretation of transisthmian molecular comparisons in the literature have in many cases been unduly influenced and confused by molecular clock assumptions and the restriction of studies to single higher-level taxa. Analysis of the apparently contradictory published data as well as new results from sequence comparisons of fishes, urchins and snails suggests a synthesis: taxon specific rates of molecular evolution, with reduced variance within taxonomic groups and great variance among all groups sampled.

scholarly journals Characterization of the genome of the mealybug Planococcus lilacinus, a model organism for studying whole-chromosome imprinting and inactivation

2002 ◽  
Vol 79 (2) ◽  
pp. 111-118 ◽  
Author(s):  
K. NAGA MOHAN ◽  
PARAMITA RAY ◽  
H. SHARAT CHANDRA
Keyword(s):  
Drosophila Melanogaster ◽  
Repetitive Sequences ◽  
Gc Content ◽  
Model Organism ◽  
Fruit Fly ◽  
Single Copy ◽  
Coding Sequences ◽  
Repeat Sequences ◽  
Chromosome Imprinting

The co-occurrence of three chromosome-wide phenomena – imprinting, facultative heterochromatization and diffuse centromere – in the mealybug Planococcus lilacinus makes investigation of the genomics of this species an attractive prospect. In order to estimate the complexity of the genome of this species, 300 random stretches of its DNA, constituting ∼0·1% of the genome, were sequenced. Coding sequences appear to constitute ∼53·5%, repeat sequences ∼44·5% and non-coding single-copy sequences ∼2% of the genome. The proportion of repetitive sequences in the mealybug is higher than that in the fruit fly Drosophila melanogaster (∼30%). The mealybug genome (∼220 Mb) is about 1·3 times the size of the fly genome (∼165 Mb) and its GC content (∼35%) less than that of the fly genome (∼40%). The relative abundance of various dinucleotides, as analysed by the method of Gentles and Karlin, shows that the dinucleotide signatures of the two species are moderately similar and that in the mealybug there is neither over-representation nor under-representation of any dinucleotide.

Locus control region activity by 5′HS3 requires a functional interaction with β-globin gene regulatory elements: expression of novel β/γ-globin hybrid transgenes

Blood ◽  
2000 ◽  
Vol 95 (10) ◽  
pp. 3242-3249 ◽  
Author(s):  
Joel E. Rubin ◽  
Peter Pasceri ◽  
Xiumei Wu ◽  
Philippe Leboulch ◽  
James Ellis
Keyword(s):  
Gene Therapy ◽  
Transgenic Mice ◽  
Control Region ◽  
Globin Gene ◽  
Single Copy ◽  
Gene Sequences ◽  
Coding Sequences ◽  
Globin Promoter ◽  
Intron 2 ◽  
Chromatin Opening

Abstract The human β-globin locus control region (LCR) contains chromatin opening and transcriptional enhancement activities that are important to include in β-globin gene therapy vectors. We previously used single-copy transgenic mice to map chromatin opening activity to the 5′HS3 LCR element. Here, we test novel hybrid globin genes to identify β-globin gene sequences that functionally interact with 5′HS3. First, we show that an 850-base pair (bp) 5′HS3 element activates high-level β-globin gene expression in fetal livers of 17 of 17 transgenic mice, including 3 single-copy animals, but fails to reproducibly activate Aγ-globin transgenes. To identify the β-globin gene sequences required for LCR activity by 5′HS3, we linked the 815-bp β-globin promoter to Aγ-globin coding sequences (BGT34), together with either the β-globin intron 2 (BGT35), the β-globin 3′ enhancer (BGT54), or both intron 2 and the 3′ enhancer (BGT50). Of these transgenes, only BGT50 reproducibly expresses Aγ-globin RNA (including 7 of 7 single-copy animals, averaging 71% per copy). Modifications to BGT50 show that LCR activity is detected after replacing the β-globin promoter with the 700-bp Aγ-globin promoter, but is abrogated when an AT-rich region is deleted from β-globin intron 2. We conclude that LCR activity by 5′HS3 on globin promoters requires the simultaneous presence of β-globin intron 2 sequences and the 260-bp 3′ β-globin enhancer. The BGT50 construct extends the utility of the 5′HS3 element to include erythroid expression of nonadult β-globin coding sequences in transgenic animals and its ability to express antisickling γ-globin coding sequences at single copy are ideal characteristics for a gene therapy cassette.

DNA-DNA Hybridization, Phylogenetic Reconstruction and the Fossil Record

1988 ◽  
Vol 1 ◽  
pp. 75-88 ◽  
Author(s):  
Charles R. Marshall
Keyword(s):  
Dna Hybridization ◽  
Nuclear Dna ◽  
Phylogenetic Reconstruction ◽  
Cost Effective ◽  
Single Copy ◽  
Molecular Techniques ◽  
Phylogenetic Information ◽  
Molecular Approaches ◽  
Molecular Characters ◽  
Rates Of Molecular Evolution

In 1962 Zuckerkandl & Pauling suggested that the amino acid sequence of proteins might evolve in a clock-like fashion and thus may be useful for phylogenetic reconstruction. Since then, many different molecular approaches to phylogenetic reconstruction have been proposed (Wilson et al., 1977). Enthusiasm for the clock hypothesis was dampened by the discovery that rates of molecular evolution for many macromolecules have been highly variable through time (Romero-Herrera et al., 1979). However, the contribution of molecular characters to the study of phylogeny is not necessarily dependent on the notion of a molecular clock and molecular approaches continue to be an important source of phylogenetic information. One of the more powerful and cost-effective molecular techniques for phylogenetic purposes is DNA-DNA hybridization, which measures the single-copy nuclear DNA sequence divergences between species.

Description of ten tadpoles in the genus Boophis from Madagascar

Zootaxa ◽  
2010 ◽  
Vol 2694 (1) ◽  
pp. 1 ◽  
Author(s):  
TAHIRY RASOLONJATOVO HIOBIARILANTO ◽  
ROGER-DANIEL RANDRIANIAINA ◽  
JULIAN GLOS ◽  
AXEL STRAUß ◽  
MIGUEL VENCES
Keyword(s):  
Dna Barcoding ◽  
Related Species ◽  
Lower Number ◽  
Sister Species ◽  
Morphological Similarity ◽  
Additional Species ◽  
Closely Related Species ◽  
Species Groups ◽  
First Time

We provide morphological descriptions of the tadpoles of ten species of Malagasy treefrogs of the genus Boophis (family Mantellidae). Based on individuals determined by DNA barcoding, the larvae of eight species are described for the first time: B. anjanaharibeensis, B. axelmeyeri, B. elenae, B. englaenderi, B. luciae, B. rhodoscelis, B. roseipalmatus, and B. vittatus. For two additional species, B. andreonei and B. microtympanum, we provide descriptions from other localities than the previously known larvae. All tadpoles described herein are stream-adapted, exotrophic, and of a relatively generalized morphology. In general, we found a morphological similarity of larvae belonging to phenetic species groups of Boophis, but more detailed analyses showed several differences between taxa that are known to be sister species or closely related to each other: B. luciae has a much higher number of oral papillae than B. sibilans, B. roseipalmatus has a slightly lower number of papillae and possibly a stronger caudal musculature than B. madagascariensis, and B. elenae has a distinctly lower number of oral papillae and keratodonts in the first upper keratodont row than B. sandrae. This indicates that tadpole characters might, in some cases, provide good taxonomic characters in Boophis, a genus in which adults of closely related species are often morphologically extremely similar.

Phylogeny of Pnyxiopalpus Vilkamaa & Hippa, with the description of P. persimplex sp. n. (Diptera, Sciaridae)

Zootaxa ◽  
2011 ◽  
Vol 2743 (1) ◽  
pp. 56 ◽  
Author(s):  
PEKKA VILKAMAA ◽  
HEIKKI HIPPA
Keyword(s):  
New Species ◽  
Basic Structure ◽  
Sister Group ◽  
Sister Species ◽  
Data Matrix ◽  
Published Data ◽  
Congeneric Species ◽  
Related Genus ◽  
Parsimony Analysis ◽  
A New Species

Phylogeny of the Oriental genus Pnyxiopalpus Vilkamaa & Hippa, 1999 was re-studied in the light of the recently described, putatively related genus Vulagisciara Evenhuis, 2007, from Fiji, and a new species of Pnyxiopalpus, P. persimplex sp. n. from Selangor, Malaysia. Characters of these taxa were added to a previously published data matrix . The parsimony analysis yields two most parsimonious cladograms. In the strict concensus cladogram, Vulagisciara appears as the sister group of a monophyletic Pnyxiopalpus. Pnyxiopalpus persimplex sp. n. is described. The new species shares the basic structure of Pnyxiopalpus, but lacks some of the unique morphological modifications present in congeneric species. P. persimplex appears as the sister species to P. simplex, these two species together appearing as the sister group to all other Pnyxiopalpus.

scholarly journals Complete Chloroplast Genome of Michelia shiluensis and a Comparative Analysis with Four Magnoliaceae Species

Forests ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 267 ◽  
Author(s):  
Yanwen Deng ◽  
Yiyang Luo ◽  
Yu He ◽  
Xinsheng Qin ◽  
Chonggao Li ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Single Copy ◽  
Closely Related Species ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Phylogenetic Studies ◽  
Natural Reproduction ◽  
Rare And Endangered ◽  
Landscape Gardening

Michelia shiluensis is a rare and endangered magnolia species found in South China. This species produces beautiful flowers and is thus widely used in landscape gardening. Additionally, its timber is also used for furniture production. As a result of low rates of natural reproduction and increasing levels of human impact, wild M. shiluensis populations have become fragmented. This species is now classified as endangered by the IUCN. In the present study, we characterized the complete chloroplast genome of M. shiluensis and found it to be 160,075 bp in length with two inverted repeat regions (26,587 bp each), a large single-copy region (88,105 bp), and a small copy region (18,796 bp). The genome contained 131 genes, including 86 protein-coding genes, 37 tRNAs, and 8 rRNAs. The guanine-cytosine content represented 39.26% of the overall genome. Comparative analysis revealed high similarity between the M. shiluensis chloroplast genome and those of four closely related species: Michelia odora, Magnolia laevifolia, Magnolia insignis, and Magnolia cathcartii. Phylogenetic analysis shows that M. shiluensis is most closely related to M. odora. The genomic information presented in this study is valuable for further classification, phylogenetic studies, and to support ongoing conservation efforts.

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