Characterization and assessment of an avian repetitive DNA sequence as an icterid phylogenetic marker

Genome ◽  
1992 ◽  
Vol 35 (1) ◽  
pp. 155-162 ◽  
Author(s):  
J. S. Quinn ◽  
E. Guglich ◽  
G. Seutin ◽  
R. Lau ◽  
J. Marsolais ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Restriction Enzymes ◽  
Repeated Sequence ◽  
Passerine Bird ◽  
Anser Anser ◽  
Closely Related Species ◽  
Phylogenetic Studies ◽  
Repeated Structure ◽  
Amazona Vittata ◽  
Puerto Rican Parrot

The first tandemly repeated sequence examined in a passerine bird, a 431-bp PstI fragment named pMAT1, has been cloned from the genome of the brown-headed cowbird (Molothrus ater). The sequence represents about 5–10% of the genome (about 4 × 105 copies) and yields prominent ethidium bromide stained bands when genomic DNA cut with a variety of restriction enzymes is electrophoresed in agarose gels. A particularly striking ladder of fragments is apparent when the DNA is cut with HinfI, indicative of a tandem arrangement of the monomer. The cloned PstI monomer has been sequenced, revealing no internal repeated structure. There are sequences that hybridize with pMAT1 found in related nine-primaried oscines but not in more distantly related oscines, suboscines, or nonpasserine species. Little sequence similarity to tandemly repeated PstI cut sequences from the merlin (Falco columbarius), saurus crane (Grus antigone), or Puerto Rican parrot (Amazona vittata) or to HinfI digested sequence from the Toulouse goose (Anser anser) was detected. The isolated sequence was used as a probe to examine DNA samples of eight members of the tribe Icterini. This examination revealed phylogenetically informative characters. The repeat contains cutting sites from a number of restriction enzymes, which, if sufficiently polymorphic, would provide new phylogenetic characters. Sequences like these, conserved within a species, but variable between closely related species, may be very useful for phylogenetic studies of closely related taxa.Key words: tandemly repeated sequences, satellite DNA, tribe Icterini.

scholarly journals Variable evolutionary stability of Y chromosomal repeated sequences in the genus Mus

1989 ◽  
Vol 53 (2) ◽  
pp. 87-93 ◽  
Author(s):  
Timothy H. K. Platt ◽  
Michael J. Dewey
Keyword(s):  
Restriction Enzyme ◽  
Species Distributions ◽  
Restriction Enzymes ◽  
Evolutionary Stability ◽  
Repeated Sequences ◽  
Closely Related Species ◽  
Phylogenetic Studies ◽  
Length Polymorphisms ◽  
Associated Sequences ◽  
Restriction Fragment Length

SummaryThe study reported here is an examination of the organization and evolution of three Y chromosomal repeated sequences, designated pBC10–0.6, pBC15–1.1, and pBA33–1.8, in five closely related species of the genus Mus. The species distributions of major restriction fragment length polymorphisms produced with a panel of restriction enzymes is used to develop the phylogenetic relationships between the five species studied. However, the apparent degree of relatedness among these species varied a great deal with each of the three probes and was also highly dependent on the particular restriction enzyme used. The usefulness for phylogenetic studies of closely associated sequences varying in evolutionary stability is discussed.

scholarly journals Minimizing Potential Allee Effects in Psittacine Reintroductions: An Example from Puerto Rico

Diversity ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 13
Author(s):  
Thomas H. White ◽  
Wilfredo Abreu ◽  
Gabriel Benitez ◽  
Arelis Jhonson ◽  
Marisel Lopez ◽  
...  
Keyword(s):  
Puerto Rico ◽  
Site Fidelity ◽  
Conservation Strategies ◽  
Allee Effects ◽  
Species Reintroduction ◽  
Social Species ◽  
Potential Applicability ◽  
Amazona Vittata ◽  
Puerto Rican Parrot ◽  
Release Strategy

The family Psittacidae is comprised of over 400 species, an ever-increasing number of which are considered threatened with extinction. In recent decades, conservation strategies for these species have increasingly employed reintroduction as a technique for reestablishing populations in previously extirpated areas. Because most Psittacines are highly social and flocking species, reintroduction efforts may face the numerical and methodological challenge of overcoming initial Allee effects during the critical establishment phase of the reintroduction. These Allee effects can result from failures to achieve adequate site fidelity, survival and flock cohesion of released individuals, thus jeopardizing the success of the reintroduction. Over the past 20 years, efforts to reestablish and augment populations of the critically endangered Puerto Rican parrot (Amazona vittata) have periodically faced the challenge of apparent Allee effects. These challenges have been mitigated via a novel release strategy designed to promote site fidelity, flock cohesion and rapid reproduction of released parrots. Efforts to date have resulted in not only the reestablishment of an additional wild population in Puerto Rico, but also the reestablishment of the species in the El Yunque National Forest following its extirpation there by the Category 5 hurricane Maria in 2017. This promising release strategy has potential applicability in reintroductions of other psittacines and highly social species in general.

scholarly journals Nonomuraea solani sp. nov., an actinomycete isolated from eggplant root (Solanum melongena L.)

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2418-2423 ◽  
Author(s):  
Xiangjing Wang ◽  
Junwei Zhao ◽  
Chongxi Liu ◽  
Jidong Wang ◽  
Yue Shen ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Solanum Melongena ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Phenotypic Differentiation ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

A novel actinomycete, designated strain NEAU-Z6T, was isolated from eggplant (Solanum melongena L.) root. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain NEAU-Z6T belonged to the genus Nonomuraea , with highest sequence similarity to Nonomuraea monospora PT 708T (98.83 %), Nonomuraea rosea GW 12687T (98.55 %) and Nonomuraea rhizophila YIM 67092T (98.02 %). Sequence similarities between strain NEAU-Z6T and other species of the genus Nonomuraea ranged from 97.94 % ( Nonomuraea candida HMC10T) to 96.30 % ( Nonomuraea wenchangensis 210417T). Key morphological, physiological and chemotaxonomic characteristics of strain NEAU-Z6T were congruent with the description of the genus Nonomuraea . The G+C content of the genomic DNA was 64.51 mol%. DNA–DNA relatedness and comparative analysis of physiological, biochemical and chemotaxonomic data allowed genotypic and phenotypic differentiation of strain NEAU-Z6T from closely related species. Thus, strain NEAU-Z6T represents a novel species of the genus Nonomuraea , for which the name Nonomuraea solani sp. nov. is proposed. The type strain is NEAU-Z6T ( = CGMCC 4.7037T = DSM 45729T).

scholarly journals Molecular Characterisation of a Novel and Highly Divergent Passerine Adenovirus 1

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 1036
Author(s):  
Ajani Athukorala ◽  
Jade K. Forwood ◽  
David N. Phalen ◽  
Subir Sarker
Keyword(s):  
Complete Genome ◽  
Sequence Similarity ◽  
Evolutionary Relationship ◽  
Passerine Bird ◽  
The Novel ◽  
Transmembrane Helices ◽  
Novel Genes ◽  
Separate Species ◽  
Natural Host Species ◽  
Genes Encoding

Wild birds harbour a large number of adenoviruses that remain uncharacterised with respect to their genomic organisation, diversity, and evolution within complex ecosystems. Here, we present the first complete genome sequence of an atadenovirus from a passerine bird that is tentatively named Passerine adenovirus 1 (PaAdV-1). The PaAdV-1 genome is 39,664 bp in length, which was the longest atadenovirus to be sequenced, to the best of our knowledge, and contained 42 putative genes. Its genome organisation was characteristic of the members of genus Atadenovirus; however, the novel PaAdV-1 genome was highly divergent and showed the highest sequence similarity with psittacine adenovirus-3 (55.58%). Importantly, PaAdV-1 complete genome was deemed to contain 17 predicted novel genes that were not present in any other adenoviruses sequenced to date, with several of these predicted novel genes encoding proteins that harbour transmembrane helices. Subsequent analysis of the novel PaAdV-1 genome positioned phylogenetically to a distinct sub-clade with all others sequenced atadenoviruses and did not show any obvious close evolutionary relationship. This study concluded that the PaAdV-1 complete genome described here is not closely related to any other adenovirus isolated from avian or other natural host species and that it should be considered a separate species.

Using artificial canopy gaps to restore Puerto Rican Parrot (Amazona vittata) habitat in tropical timber plantations

2007 ◽  
Vol 243 (2-3) ◽  
pp. 169-177 ◽  
Author(s):  
Faith M. Inman ◽  
Thomas R. Wentworth ◽  
Martha Groom ◽  
Cavell Brownie ◽  
Russ Lea
Keyword(s):  
Puerto Rican ◽  
Canopy Gaps ◽  
Tropical Timber ◽  
Timber Plantations ◽  
Amazona Vittata ◽  
Puerto Rican Parrot

Ferrimonas pelagia sp. nov., isolated from seawater

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3175-3179 ◽  
Author(s):  
Kyung June Yim ◽  
Myunglip Lee ◽  
Hae-Won Lee ◽  
Kil-Nam Kim ◽  
Hye-Mi Yang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Isoprenoid Quinones

A Gram-stain-negative bacterium, designated strain CBA4601T, was isolated from a seawater sample obtained off the coast of Jeju Island, Korea. The organism grew in the presence of 0–4 % (w/v) NaCl and at 20–35 °C and pH 7.0–9.0, with optimal growth in 2 % NaCl, and at 25 °C and pH 8.0. Phylogenetic trees based on 16S rRNA gene sequences showed that strain CBA4601T was related to the genus Ferrimonas within the class Gammaproteobacteria . 16S rRNA gene sequence similarity between strain CBA4601T and Ferrimonas marina A4D-4T, the most closely related species, was 96.9 %. The G+C content of the genomic DNA from strain CBA4601T was 54.2 mol%, and the isoprenoid quinones menaquinone 7 (MK-7), ubiquinone 7 (Q-7) and ubiquinone 8 (Q-8) were detected. The major fatty acids were C17 : 1ω8c, C18 : 1ω9c and C16 : 0, and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified ninhydrin-positive phospholipid. On the basis of this taxonomic study using a polyphasic approach, strain CBA4601T represents a novel species of the genus Ferrimonas , for which the name Ferrimonas pelagia sp. nov. is proposed. The type strain is CBA4601T ( = KACC 16695T = KCTC 32029T = JCM 18401T).

Actinoplanes couchii sp. nov.

2007 ◽  
Vol 57 (4) ◽  
pp. 721-724 ◽  
Author(s):  
Peter Kämpfer ◽  
Birgit Huber ◽  
Kathrin Thummes ◽  
Iris Grün-Wollny ◽  
Hans-Jürgen Busse
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Closely Related Species ◽  
Bacterium Strain

A Gram-positive bacterium, strain GW8-1761T, was isolated from soil close to the Marmore waterfalls, Terni, Italy. 16S rRNA gene sequence similarity studies showed that strain GW8-1761T belonged to the genus Actinoplanes, being most closely related to Actinoplanes italicus JCM 3165T (98.9 %), A. rectilineatus IFO 13941T (98.5 %), A. palleronii JCM 7626T (97.8 %), A. utahensis IFO 13244T (97.6 %) and A. cyaneus DSM 46137T (97.6 %). Strain GW8-1761T could be distinguished from any other Actinoplanes species with validly published names by 16S rRNA gene sequence similarity values of less than 97.5 %. Chemotaxonomic data [major menaquinone MK-9(H4); major polar lipids diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol, with phosphatidylcholine and aminoglycolipids absent; major fatty acids C15 : 0, C16 : 0, C16 : 0 iso, C17 : 1 ω8c and summed feature 3 (C16 : 1 ω7c and/or C15 : 0 iso 2-OH)] supported the affiliation of strain GW8-1761T to the genus Actinoplanes. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain GW8-1761T from the most closely related species. Strain GW8-1761T therefore merits species status, and we propose the name Actinoplanes couchii sp. nov., with the type strain GW8-1761T (=DSM 45050T=CIP 109316T).

scholarly journals Brevibacterium sandarakinum sp. nov., isolated from a wall of an indoor environment

2010 ◽  
Vol 60 (4) ◽  
pp. 909-913 ◽  
Author(s):  
Peter Kämpfer ◽  
Jenny Schäfer ◽  
Nicole Lodders ◽  
Hans-Jürgen Busse
Keyword(s):  
Indoor Environment ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Polar Lipid Profile ◽  
Closely Related Species ◽  
Phenotypic Differentiation ◽  
Diamino Acid ◽  
Type Strains

A Gram-stain-positive, rod-shaped, non-endospore-forming, orange-pigmented (coloured) actinobacterium (01-Je-003T) was isolated from the wall of an indoor environment primarily colonized with moulds. On the basis of 16S rRNA gene sequence similarity studies, strain 01-Je-003T was shown to belong to the genus Brevibacterium and was most similar to the type strains of Brevibacterium picturae (98.8 % similarity), Brevibacterium marinum (97.3 %) and Brevibacterium aurantiacum (97.2 %). Chemotaxonomic data [predominant quinone menaquinone MK-8(H2); polar lipid profile consisting of major compounds diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid; characteristic cell-wall diamino acid meso-diaminopimelic acid; polyamine pattern showing major compounds putrescine and cadaverine; major fatty acids anteiso-C15 : 0 and anteiso-C17 : 0] supported the affiliation of strain 01-Je-003T to the genus Brevibacterium. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 01-Je-003T from the two most closely related species, B. picturae and B. marinum. Strain 01-Je-003T therefore represents a novel species, for which the name Brevibacterium sandarakinum sp. nov. is proposed, with the type strain 01-Je-003T (=DSM 22082T =CCM 7649T).

scholarly journals Sphingomonas hengshuiensis sp. nov., isolated from lake wetland

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4644-4649 ◽  
Author(s):  
Shuzhen Wei ◽  
Tingting Wang ◽  
Hongliang Liu ◽  
Caifeng Zhang ◽  
Jiping Guo ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Optimal Growth ◽  
Northern China ◽  
Rrna Gene ◽  
The Novel ◽  
Respiratory Quinone ◽  
Closely Related Species ◽  
Novel Bacterium ◽  
The Status ◽  
Type Strains

A polyphasic taxonomic study was undertaken to establish the status of a novel bacterium, designated strain WHSC-8T, which was isolated from soil of Hengshui Lake Wetland Reserve in Hebei province, northern China. Colonies of this strain were yellow and cells were rod-shaped, polar-flagellated and obligately aerobic, exhibiting negative Gram reaction. The strain was able to grow at 0–1 % (w/v) NaCl, pH 5–10 and 20–35 °C, with optimal growth occurring at pH 7.0 and 28 °C without NaCl. Chemotaxonomic data revealed that strain WHSC-8T possesses ubiquinone Q-10 as the predominant respiratory quinone, C18 : 1ω7c, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids, and sym-homospermidine as the major polyamine. Sphingomonadaceae-specific sphingoglycolipid was detected in the polar lipid patterns. The G+C content of the genomic DNA was 68.7 mol%. All of the above characters corroborated the assignment of the novel strain to the genus Sphingomonas. Strain WHSC-8T shared less than 97.0 % 16S rRNA gene sequence similarity with the type strains of other species of the genus Sphingomonas, except for Sphingomonas asaccharolytica DSM 10564T (97.5 %). The low DNA–DNA relatedness value and distinct phenotypic and chemotaxonomic characteristics distinguished strain WHSC-8T from closely related species of the genus Sphingomonas. Therefore, strain WHSC-8T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas hengshuiensis sp. nov. is proposed. The type strain is WHSC-8T ( = KCTC 42455T = CCTCC AB 2015265T).

scholarly journals A Sida sp. Is a New Host for “Candidatus Phytoplasma brasiliense” in Brazil

Plant Disease ◽  
2011 ◽  
Vol 95 (3) ◽  
pp. 363-363 ◽  
Author(s):  
B. Eckstein ◽  
J. C. Barbosa ◽  
J. A. M. Rezende ◽  
I. P. Bedendo
Keyword(s):  
16S Rdna ◽  
Sequence Similarity ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Sao Paulo ◽  
São Paulo ◽  
New Host ◽  
Nucleotide Sequence Alignment ◽  
Pcr Products

Sida is a genus of flowering herbs in the family Malvaceae, which includes several species that are weeds in Brazil. Plants of a Sida sp. exhibiting symptoms characterized by stunting, chlorosis, small leaves, and witches'-broom, indicative of infection by phytoplasmas, were found in a field previously cultivated with tomato, located in the region of Campinas, State of São Paulo, in December 2008. To demonstrate the presence of phytoplasmas in diseased tissues, DNA was extracted from shoots and leaves from three symptomatic and eight asymptomatic plants. Nested PCR was performed using primers P1/Tint followed by primer pair R16F2n/R16R2 (1). DNA fragments of 1.2 kb, corresponding to 16S rDNA, were amplified only for DNA from two symptomatic samples. Phytoplasma identification was initially carried out by restriction fragment length polymorphism (RFLP) analysis through digesting the PCR products with the restriction enzymes AluI, HhaI, HaeIII, HpaII, MseI, and RsaI. The two phytoplasma isolates found to be infecting a Sida sp. showed identical RFLP patterns, which were indistinguishable from the phytoplasma previously reported in association with hibiscus (Hibiscus rosa-sinensis) witches'-broom in Brazil (2). Nucleotide sequence alignment revealed that 16S rDNA of both phytoplasma isolates found in a Sida sp. (GenBank Accession No. HQ230579) shared 99.9% sequence similarity with 16S rDNA from hibiscus witches'-broom phytoplasma (HibWB) (GenBank Accession No. AF147708). HibWB is the representative of the 16SrXV group and it was proposed as a putative species nominated “Candidatus Phytoplasma brasiliense” (2). The disease is frequently observed in hibiscus plants used as ornamentals in the states of São Paulo (4) and Rio de Janeiro (2). “Ca. Phytoplasma brasiliense” has only been reported in Brazil to be infecting hibiscus (2,4) and periwinkle (Catharanthus roseus) (3). The presence of a phytoplasma belonging to group 16SrXV in a Sida sp. expands its natural host range. The role of this weed as a potential source of inoculum for crops should be investigated. References: (1) I. M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998. (2) H. G. Montano et al. Int. J. Syst. Evol. Microbiol. 51:1109, 2001. (3) H. G. Montano et al. Plant Dis. 85:1209, 2001. (4) E. G. Silva et al. Summa Phytopathol. 35:234, 2009.

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