scholarly journals Elevational Zonation and the Phylogenetic Relationships of the Henicorhina Wood-Wrens

The Auk ◽  
2006 ◽  
Vol 123 (1) ◽  
pp. 119-134 ◽  
Author(s):  
Caroline Dingle ◽  
Irby J. Lovette ◽  
Chris Canaday ◽  
Thomas B. Smith
Keyword(s):  
Central America ◽  
Dna Sequences ◽  
Genetic Relationships ◽  
Elevational Gradient ◽  
Species Status ◽  
Ecological Diversification ◽  
Evolutionary Origins ◽  
The Andes

Abstract The Henicorhina wood-wren complex consists of three taxonomic species. Two of these, the Gray-breasted Wood-Wren (Henicorhina leucophrys) and the White-breasted Wood-Wren (H. leucosticta), are widespread throughout Central America and northern South America, with leucophrys occurring at higher elevations in regions where both occur. A third, recently described, species—the Bar-winged Wood-Wren (H. leucoptera)—occurs only in several isolated cordilleras in southeastern Ecuador and northeastern Peru, where it replaces the Gray-breasted Wood-Wren at the highest elevations. We used mitochondrial DNA sequences to explore the phylo-genetic relationships among populations of these taxa and to draw inferences about the evolutionary origins of elevational zonation. We found substantial mitochondrial diversity within both leucophrys and leucosticta. Differentiation across the Andes in leucophrys was negligible, but populations from Central America and from northwestern Ecuador showed substantial differentiation. Three highly differentiated haplotype groups were also present in leucosticta, corresponding to populations in the eastern Andean lowlands, Central America, and the Chocó region of northwestern Ecuador; these populations may each warrant taxonomic species status. Bar-winged haplo-types nested within the mitochondrially diverse leucosticta group, where they were most closely allied to the geographically distant Chocó haplotypes. This leucoptera-leucosticta affinity is not consistent with previous inferences, based on plumage and behavioral similarities, that grouped leucoptera and leucophrys as sister species. These reconstructions refute the hypothesis that elevational zonation in this clade originated from in situ speciation along an elevational gradient, and instead highlight the role of complex changes in geographic distributions in fostering phylogenetic and ecological diversification. Reemplazos Altitudinales y Relaciones Filogenéticas en el Género Henicorhina (Troglodytidae)

Inheritance of Chromosomally Integrated Human Herpesvirus 6 DNA

Blood ◽  
1999 ◽  
Vol 94 (5) ◽  
pp. 1545-1549 ◽  
Author(s):  
Masanori Daibata ◽  
Takahiro Taguchi ◽  
Yuiko Nemoto ◽  
Hirokuni Taguchi ◽  
Isao Miyoshi
Keyword(s):  
Dna Sequences ◽  
Viral Genome ◽  
Family Members ◽  
Human Herpesvirus ◽  
Single Step ◽  
Human Herpesvirus 6 ◽  
Viral Genomes ◽  
Herpesvirus 6

Abstract Human herpesvirus 6 (HHV-6) genome has been detected in several human lymphoproliferative disorders with no signs of active viral infection, and found to be integrated into chromosomes in some cases. We previously reported a woman with HHV-6–infected Burkitt’s lymphoma. Fluorescence in situ hybridization showed that the viral genome was integrated into the long arm of chromosome 22 (22q13). The patient’s asymptomatic husband also carried HHV-6 DNA integrated at chromosome locus 1q44. To assess the possibility of chromosomal transmission of HHV-6 DNA, we looked for HHV-6 DNA in the peripheral blood of their daughter. She had HHV-6 DNA on both chromosomes 22q13 and 1q44, identical to the site of viral integration of her mother and father, respectively. The findings suggested that her viral genomes were inherited chromosomally from both parents. The 3 family members were all seropositive for HHV-6, but showed no serological signs of active infection. To confirm the presence of HHV-6 DNA sequences, we performed polymerase chain reaction (PCR) with 7 distinct primer pairs that target different regions of HHV-6. The viral sequences were consistently detected by single-step PCR in all 3 family members. We propose a novel latent form for HHV-6, in which integrated viral genome can be chromosomally transmitted. The possible role of the chromosomally integrated HHV-6 in the pathogenesis of lymphoproliferative diseases remains to be explained.

Inheritance of Chromosomally Integrated Human Herpesvirus 6 DNA

Blood ◽  
1999 ◽  
Vol 94 (5) ◽  
pp. 1545-1549 ◽  
Author(s):  
Masanori Daibata ◽  
Takahiro Taguchi ◽  
Yuiko Nemoto ◽  
Hirokuni Taguchi ◽  
Isao Miyoshi
Keyword(s):  
Dna Sequences ◽  
Viral Genome ◽  
Family Members ◽  
Human Herpesvirus ◽  
Single Step ◽  
Human Herpesvirus 6 ◽  
Viral Genomes ◽  
Herpesvirus 6

Human herpesvirus 6 (HHV-6) genome has been detected in several human lymphoproliferative disorders with no signs of active viral infection, and found to be integrated into chromosomes in some cases. We previously reported a woman with HHV-6–infected Burkitt’s lymphoma. Fluorescence in situ hybridization showed that the viral genome was integrated into the long arm of chromosome 22 (22q13). The patient’s asymptomatic husband also carried HHV-6 DNA integrated at chromosome locus 1q44. To assess the possibility of chromosomal transmission of HHV-6 DNA, we looked for HHV-6 DNA in the peripheral blood of their daughter. She had HHV-6 DNA on both chromosomes 22q13 and 1q44, identical to the site of viral integration of her mother and father, respectively. The findings suggested that her viral genomes were inherited chromosomally from both parents. The 3 family members were all seropositive for HHV-6, but showed no serological signs of active infection. To confirm the presence of HHV-6 DNA sequences, we performed polymerase chain reaction (PCR) with 7 distinct primer pairs that target different regions of HHV-6. The viral sequences were consistently detected by single-step PCR in all 3 family members. We propose a novel latent form for HHV-6, in which integrated viral genome can be chromosomally transmitted. The possible role of the chromosomally integrated HHV-6 in the pathogenesis of lymphoproliferative diseases remains to be explained.

scholarly journals Transcriptomic analysis of diplomonad parasites reveals a trans-spliced intron in a helicase gene in Giardia

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2861 ◽  
Author(s):  
Scott William Roy
Keyword(s):  
Dna Sequences ◽  
Molecular Mechanisms ◽  
Transcriptomic Data ◽  
Coding Regions ◽  
Evolutionary Origins ◽  
Helicase Gene ◽  
Trans Splicing ◽  
High Degree ◽  
Future Work

Background The mechanisms by which DNA sequences are expressed is the central preoccupation of molecular genetics. Recently, ourselves and others reported that in the diplomonad protist Giardia lamblia, the coding regions of several mRNAs are produced by ligation of independent RNA species expressed from distinct genomic loci. Such trans-splicing of introns was found to affect nearly as many genes in this organism as does classical cis-splicing of introns. These findings raised questions about the incidence of intron trans-splicing both across the G. lambliatranscriptome and across diplomonad diversity in general, however a dearth of transcriptomic data at the time prohibited systematic study of these questions. Methods I leverage newly available transcriptomic data from G. lamblia and the related diplomonad Spironucleus salmonicidato search for trans-spliced introns. My computational pipeline recovers all four previously reported trans-spliced introns in G. lamblia, suggesting good sensitivity. Results Scrutiny of thousands of potential cases revealed only a single additional trans-spliced intron in G. lamblia, in the p68 helicase gene, and no cases in S. salmonicida. The p68 intron differs from the previously reported trans-spliced introns in its high degree of streamlining: the core features of G. lamblia trans-spliced introns are closely packed together, revealing striking economy in the implementation of a seemingly inherently uneconomical molecular mechanism. Discussion These results serve to circumscribe the role of trans-splicing in diplomonads both in terms of the number of genes effected and taxonomically. Future work should focus on the molecular mechanisms, evolutionary origins and phenotypic implications of this intriguing phenomenon.

scholarly journals Unveiling the Organisms behind Novel Eukaryotic Ribosomal DNA Sequences from the Ocean

2002 ◽  
Vol 68 (9) ◽  
pp. 4554-4558 ◽  
Author(s):  
Ramon Massana ◽  
Laure Guillou ◽  
Beatriz Díez ◽  
Carlos Pedrós-Alió
Keyword(s):  
Dna Sequences ◽  
Heterotrophic Flagellates ◽  
Marine Food Webs ◽  
Field Samples ◽  
Marine Food ◽  
Phylogenetic Lineages ◽  
One Year ◽  
Total Stock

ABSTRACT Despite the fact that the smallest eukaryotes (cells less than 5 μm in diameter) play key roles in marine food webs, particularly in open oligotrophic areas, the study of their in situ diversity started just one year ago. Perhaps the most remarkable finding of the most recent studies has been the discovery of completely new phylogenetic lineages, such as novel clades belonging to the stramenopile and alveolate phyla. The two new groups account for a significant fraction of clones in genetic libraries from North Atlantic, equatorial Pacific, Antarctic, and Mediterranean Sea waters. However, the identities and ecological relevance of these organisms remain unknown. Here we investigate the phylogenetic relationships, morphology, in situ abundance, and ecological role of novel stramenopiles. They form at least eight independent clades within the stramenopile basal branches, indicating a large phylogenetic diversity within the group. Two lineages were visualized and enumerated in field samples and enrichments by fluorescent in situ hybridization using specific rRNA-targeted oligonucleotide probes. The targeted organisms were 2- to 3-μm-diameter, round-shaped, nonpigmented flagellates. Further, they were found to be bacterivorous. One lineage accounted for up to 46% (average during an annual cycle, 19%) of heterotrophic flagellates in a coastal environment, providing evidence that novel stramenopiles are important and unrecognized components of the total stock of bacterial grazers.

Rubiacearum Americanarum Magna Hama Pars XLVIII: A New View of Palicourea sect. Axillares and Description of Some New Species (Palicoureeae)

2021 ◽  
Vol 29 ◽  
pp. 85-111
Author(s):  
Charlotte M. Taylor
Keyword(s):  
New Species ◽  
South America ◽  
Central America ◽  
Species Status ◽  
The Andes ◽  
Southern Ecuador ◽  
Center Of Diversity ◽  
Infraspecific Taxa ◽  
Southern Central ◽  
Molecular Characters

Many of the species classified in Psychotria L. subg. Heteropsychotria Steyerm. (Rubiaceae), including the species of Psychotria ser. Axillares (Hook. f.) Steyerm., have been shown to belong to Palicourea Aubl. based on morphological and molecular characters. This section is now treated as Palicourea sect. Axillares (Hook. f.) Borhidi, and includes 14 species found from southern Central America through the Andes of northwestern and western South America with a center of diversity in eastern Colombia and western Venezuela. This section is characterized by the combination of laminar, well-developed, bilobed stipules and mostly capitate, pseudoaxillary or sometimes terminal, mostly sessile inflorescences with numerous well-developed bracts that enclose the flowers but without enlarged involucral bracts. It is circumscribed differently here than it is by Borhidi. The nomenclatural summary, key, and diagnostic discussions that separate the species included here are based on several new taxonomic circumscriptions. No infraspecific taxa are recognized in Pal. axillaris (Sw.) Borhidi, but one of its varieties from Venezuela is raised to species status as Pal. villipila (Steyerm.) C. M. Taylor. The circumscription of Pal. rosacea (Steyerm.) Borhidi is expanded, and four species are newly described here: Pal. aristata C. M. Taylor from the Andes of southern Ecuador, Pal. quibdoana C. M. Taylor from northwestern Colombia, Pal. santanderiana C. M. Taylor from the Andes of eastern Colombia, and Pal. winfriedii C. M. Taylor from northern Venezuela.

Genome analysis of seven species of Kengyilia (Triticeae: Poaceae) with FISH and GISH

Genome ◽  
2013 ◽  
Vol 56 (11) ◽  
pp. 641-649 ◽  
Author(s):  
Quanwen Dou ◽  
Richard R.-C. Wang ◽  
Yuting Lei ◽  
Feng Yu ◽  
Yuan Li ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Genetic Relationships ◽  
5S Rdna ◽  
Common Species ◽  
Genomic In Situ Hybridization ◽  
Genetic Groups ◽  
Molecular Karyotype ◽  
Species Specific

The genome compositions and genetic relationships of seven species of Kengyilia were assessed using a sequential fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) technique. Five species, K. kokonorica, K. rigidula, K. hirsuta, K. grandiglumis, and K. thoroldiana, are native to Qinghai (China). The other two, K. alatavica and K. batalinii, are distributed in Xinjiang (China) and Kyrgyzstan, respectively. Each chromosome could be easily identified using chromosome markers (45S rDNA, 5S rDNA, pAs1, and AAG repeats) by FISH and allocated to the St, P, or Y genome by GISH. Molecular karyotype comparison indicated that K. alatavica and K. batalinii were distinct from the Qinghai species in all three genomes. These results support that the species of Kengyilia from Central Asia and the Qinghai–Tibetan plateau have independent origins. Genomic differentiation was still detected among the species of Kengyilia from Qinghai. Specifically, a common species-specific pericentric inversion was identified in both K. grandiglumis and K. thoroldiana, and an identical St-P non-Robertsonian translocation was frequently detected in K. hirsuta. The Qinghai species formed three genetic groups, K. kokonorica–K. rigidula, K. hirsuta, and K. grandiglumis–K. thoroldiana. The possible role of species-specific inversions and translocations in the evolution of StPY species is discussed.

scholarly journals Retrotransposon-Related DNA Sequences in the Centromeres of Grass Chromosomes

Genetics ◽  
1998 ◽  
Vol 150 (4) ◽  
pp. 1615-1623 ◽  
Author(s):  
Joseph T Miller ◽  
Fenggao Dong ◽  
Scott A Jackson ◽  
Junqi Song ◽  
Jiming Jiang
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequences ◽  
Blot Hybridization ◽  
Artificial Chromosome ◽  
Fish Analysis ◽  
Sequence Identity ◽  
Centromere Function ◽  
Eukaryotic Species

Abstract Several distinct DNA fragments were subcloned from a sorghum (Sorghum bicolor) bacterial artificial chromosome clone 13I16 that was derived from a centromere. Three fragments showed significant sequence identity to either Ty3/gypsy- or Ty1/copia-like retrotransposons. Fluorescence in situ hybridization (FISH) analysis revealed that the Ty1/copia-related DNA sequences are not specific to the centromeric regions. However, the Ty3/gypsy-related sequences were present exclusively in the centromeres of all sorghum chromosomes. FISH and gel-blot hybridization showed that these sequences are also conserved in the centromeric regions of all species within Gramineae. Thus, we report a new retrotransposon that is conserved in specific chromosomal regions of distantly related eukaryotic species. We propose that the Ty3/gypsy-like retrotransposons in the grass centromeres may be ancient insertions and are likely to have been amplified during centromere evolution. The possible role of centromeric retrotransposons in plant centromere function is discussed.

scholarly journals A CR1 element is embedded in a novel tandem repeat (HinfI repeat) within the chicken genome

Genome ◽  
2006 ◽  
Vol 49 (2) ◽  
pp. 97-103 ◽  
Author(s):  
Juan Li ◽  
Frederick C Leung
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Chicken Genome ◽  
Unique Region ◽  
Pericentric Region ◽  
Evolutionary Origins ◽  
Highly Repetitive Dna ◽  
Chicken Repeat ◽  
Eukaryotic Genomes

Highly repetitive DNA sequences constitute a significant portion of most eukaryotic genomes, raising questions about their evolutionary origins and amplification dynamics. In this study, a novel chicken repetitive DNA family, the HinfI repeat, was characterized. The basic repeating unit of this family displays a uniform length of 770 bp, which was defined by the recognition site of HinfI. The HinfI repeat was specifically localized in the pericentric region of chromosome 4 by fluorescence in situ hybridization and constitutes 0.51% of the chicken genome. Interestingly, a chicken repeat 1 (CR1) element has been identified within this basic repeating unit. Like other CR1 elements, this CR1 element also displays typical retrotransposition characteristics, including a highly conserved 3′ region and a badly truncated 5′ end. This direct evidence from sequence analysis, together with our Southern blot results, suggests that the HinfI repeat may originate from a unique region containing a retrotransposed CR1 element.Key words: satellite DNA, CR1 retrotransposon, HinfI repeat, Gallus gallus.

Rubiacearum Americanarum Magna Hama Pars XLIX: Overview of the Neotropical Genus Tournefortiopsis (Guettardeae), With Some New Species and Subspecies

2021 ◽  
Vol 29 ◽  
pp. 227-265
Author(s):  
Charlotte M. Taylor ◽  
Andreas Berger
Keyword(s):  
New Species ◽  
South America ◽  
Central America ◽  
Lesser Antilles ◽  
Species Status ◽  
Southern Mexico ◽  
Molecular Analyses ◽  
The Andes ◽  
Center Of Diversity ◽  
Andean South America

Guettarda L. (Rubiaceae) as traditionally circumscribed has been found to be polyphyletic in molecular analyses. Tournefortiopsis Rusby has been separated from it based on details of inflorescence arrangement, pyrene shape, and molecular analyses. We here find additional characters that distinguish this genus: valvate-induplicate corolla lobes and apical horns on the pyrenes. Some features that are usually consistent within species and often genera of Rubiaceae vary within some species of Tournefortiopsis, especially pubescence form and number of corolla lobes and locules. Our taxonomic review of this genus recognizes 12 species found in Central America and perhaps southern Mexico, the Lesser Antilles, and northern and Andean South America, and finds its center of diversity in the Andes of Colombia. Chomelia torrana C. M. Taylor is here transferred to Tournefortiopsis, and four species are newly described here plus one recently recognized variety is raised to species status, all in South America: T. crassifolia (Standl. ex Steyerm.) C. M. Taylor & A. C. Berger, T. deviana C. M. Taylor, T. robusta C. M. Taylor, T. sopkinii C. M. Taylor, and T. tamboana C. M. Taylor. Tournefortiopsis crispiflora (Vahl) Borhidi is here treated as widespread and morphologically variable, with a complex of forms that are not distinctive but completely separable and with notable diversification in Central America and the northern Andes. Four subspecies of T. crispiflora are recognized, with one circumscribed differently than previously and one newly described, T. crispiflora subsp. delicatula C. M. Taylor & A. C. Berger. The identity and characters of T. dependens (Ruiz & Pav.) Borhidi are clarified, and it is more widely distributed than previously noted. Six names are lectotypified.

DNA sequence mapping in interphase and metaphase chromosomes by fluorescence in situ hybridization

1992 ◽  
Vol 50 (1) ◽  
pp. 496-497
Author(s):  
Barbara Trask ◽  
Susan Allen ◽  
Anne Bergmann ◽  
Mari Christensen ◽  
Anne Fertitta ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Dual Band ◽  
Nick Translation ◽  
Metaphase Chromosomes ◽  
Band Pass ◽  
Texas Red ◽  
Fluorescent Spot

Using fluorescence in situ hybridization (FISH), the positions of DNA sequences can be discretely marked with a fluorescent spot. The efficiency of marking DNA sequences of the size cloned in cosmids is 90-95%, and the fluorescent spots produced after FISH are ≈0.3 μm in diameter. Sites of two sequences can be distinguished using two-color FISH. Different reporter molecules, such as biotin or digoxigenin, are incorporated into DNA sequence probes by nick translation. These reporter molecules are labeled after hybridization with different fluorochromes, e.g., FITC and Texas Red. The development of dual band pass filters (Chromatechnology) allows these fluorochromes to be photographed simultaneously without registration shift.

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