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Article: Primers for 52 polymorphic regions in the Quercus rubra chloroplast, 47 of which amplify across 11 tracheophyte clades

Borkowski, Daniel S / McCleary, Tim / McAllister, Mary / Romero-Severson, Jeanne

Tree genetics & genomes. 2014 Aug., v. 10, no. 4

2014

Abstract: Postglacial migration studies in Quercus rubra L. (northern red oak) are hampered by low levels of population differentiation in the widely used universal chloroplast primers. We sequenced the large single copy (LSC) regions of the Q. rubra and Quercus ... ...

Abstract	Postglacial migration studies in Quercus rubra L. (northern red oak) are hampered by low levels of population differentiation in the widely used universal chloroplast primers. We sequenced the large single copy (LSC) regions of the Q. rubra and Quercus ellipsoidalis chloroplasts to enable us to query additional regions for future studies on migration and speciation. Using 454 sequencing of long-range PCR amplicons and Sanger sequencing for gap closure, we report 65 coding sequences from Q. rubra and 59 from Q. ellipsoidalis. Comparison of our de novo assembly of the LSC region sequence for Q. rubra to Q. rubra chloroplast sequence (NCBI Reference Sequence: NC_020152.1) from a different tree revealed 106 polymorphisms, all within intergenic regions, that can serve as tools for postglacial migration studies and taxonomic studies within the Lobatae. Sequence alignment for the 59 complete coding regions in common for theQ. rubrachloroplast reference sequence, our Q. rubra sequence and our Q. ellipsoidalis sequence revealed no sequence polymorphisms and no indels. We also report the 52 primer pairs we used for gap closure, including 53 new primer pairs not previously reported. We tested these 52 primer pairs against 11 species representing the Tracheophyta and detected 47 that produced amplicons in all 11 species. The new universal primers we have identified provide additional tools for resolving the taxonomic relationships among the congeneric taxa of forest trees in the temperate and subtropical forests of the Northern Hemisphere.
Keywords	Quercus ellipsoidalis ; Quercus rubra ; chloroplasts ; forest trees ; intergenic DNA ; polymerase chain reaction ; sequence alignment ; vascular plants
Language	English
Dates of publication	2014-08
Size	p. 885-893.
Publishing place	Springer-Verlag
Document type	Article
ZDB-ID	2180926-4
ISSN	1614-2950 ; 1614-2942
ISSN (online)	1614-2950
ISSN	1614-2942
DOI	10.1007/s11295-014-0729-x
Database	NAL-Catalogue (AGRICOLA)

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Article: EST-SSR markers reveal synonymies, homonymies and relationships inconsistent with putative pedigrees in chestnut cultivars

McCleary, Tim / McAllister, Mary / Coggeshall, Mark / Romero-Severson, Jeanne

Genetic resources and crop evolution. 2013 Apr., v. 60, no. 4

2013

Abstract: Over the last two centuries, chestnut breeding programs in Europe and Asia have generated an array of chestnut interspecific hybrids, primarily of European (Castanea sativa), Japanese (C. crenata) and Chinese (C. mollissima) ancestry. During this same ... ...

Abstract	Over the last two centuries, chestnut breeding programs in Europe and Asia have generated an array of chestnut interspecific hybrids, primarily of European (Castanea sativa), Japanese (C. crenata) and Chinese (C. mollissima) ancestry. During this same period, Europeans colonizing North America imported hybrid chestnuts and made interspecific hybrids with native chestnuts, primarily American chestnut (C. dentata). The importation of Chinese chestnut into the United States in the late 19th century also introduced chestnut blight, which triggered an additional interspecific hybridization effort in an attempt to develop blight resistant American chestnuts. Chestnut cultivars used for nut production in the United States and Canada have arisen against this background of non-native introductions and extensive hybridizing. The development of regionally adapted nut producing trees with dependable crops of high quality nuts requires sorting out the identities of existing cultivars. We chose 11 EST-SSR markers from C. mollissima for the initial task of genotyping 65 chestnut cultivars that grow well in the central United States. Many of these cultivars have interspecific pedigrees involving two or more species. We found extensive homonymies and synonymies, genetic groups inconsistent with published pedigrees, contradictory pedigrees and evidence for incorrect species assignments. Accurate inference of the interspecific ancestries of cultivars grown in the United States and Canada will require genotyping of species reference sets for C. sativa, C. crenata, C. mollissima, C. dentata and possibly C. pumila (the Ozark and Allegheny chinquapins).
Keywords	Castanea dentata ; Castanea mollissima ; Castanea sativa ; Cryphonectria parasitica ; Europeans ; ancestry ; blight ; chestnuts ; crops ; cultivars ; hybrids ; interspecific hybridization ; trees ; Asia ; Canada ; Europe ; United States
Language	English
Dates of publication	2013-04
Size	p. 1209-1222.
Publishing place	Springer-Verlag
Document type	Article
ZDB-ID	1134125-7
ISSN	0925-9864
ISSN	0925-9864
DOI	10.1007/s10722-012-9912-9
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Article: Development and Characterization of Genomic and Gene-Based Microsatellite Markers in North American Red Oak Species

Sullivan, Alexis R / Lind, Jennifer F / McCleary, Tim S / Romero-Severson, Jeanne / Gailing, Oliver

Plant molecular biology reporter. 2013 Feb., v. 31, no. 1

2013

Abstract: Oaks (Quercus: Fagaceae) are ecological and economic keystones of many forested ecosystems but effective genetic management strategies are hindered by high levels of phenotypic plasticity within species and frequent hybridization among them. These same ... ...

Abstract	Oaks (Quercus: Fagaceae) are ecological and economic keystones of many forested ecosystems but effective genetic management strategies are hindered by high levels of phenotypic plasticity within species and frequent hybridization among them. These same features, however, make oak communities suited for the study of speciation, hybridization, and genetic adaptation. Efforts to develop new and to adapt existing genomic resources to less-studied members of this genus should not only improve oak conservation and management but also aid the study of fundamental evolutionary processes. Here, we present a suite of 27 highly polymorphic simple sequence repeat (SSR) markers tested in four North American red oak (Quercus section Lobatae) species: Q. rubra, Q. ellipsoidalis, Q. coccinea, and Q. velutina. Five markers are genomic SSRs (gSSRs) — four novel and one previously transferred from Q. petraea — and 22 are gene-based SSRs derived from Q. robur and Q. petraea expressed sequence tags (EST-SSRs). Overall, levels of polymorphism detected with these primer pairs were high, with gene diversity (H ₑ) averaging 0.66 across all loci in natural populations. In addition, we show that EST-SSR markers may have the potential to detect divergent selection at stress-resistance candidate genes among closely related oak species.
Keywords	Quercus ; ecosystems ; expressed sequence tags ; genes ; hybridization ; loci ; microsatellite repeats ; phenotypic plasticity
Language	English
Dates of publication	2013-02
Size	p. 231-239.
Publishing place	Springer-Verlag
Document type	Article
ZDB-ID	2018592-3
ISSN	1572-9818 ; 0735-9640
ISSN (online)	1572-9818
ISSN	0735-9640
DOI	10.1007/s11105-012-0495-6
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Article ; Online: (with research data) Human-impacted landscapes facilitate hybridization between a native and an introduced tree.

Hoban, Sean M / McCleary, Tim S / Schlarbaum, Scott E / Anagnostakis, Sandra L / Romero-Severson, Jeanne

Evolutionary applications

2011 Volume 5, Issue 7, Page(s) 720–731

Abstract: Spatial and temporal dynamics of hybridization, in particular the influence of local environmental conditions, are well studied for sympatric species but less is known for native-introduced systems, especially for long-lived species. We used ... ...

Abstract	Spatial and temporal dynamics of hybridization, in particular the influence of local environmental conditions, are well studied for sympatric species but less is known for native-introduced systems, especially for long-lived species. We used microsatellite and chloroplast DNA markers to characterize the influence of anthropogenic landscapes on the extent, direction, and spatial distribution of hybridization between a native North American tree Juglans cinerea (butternut) and an introduced tree Juglans ailantifolia (Japanese walnut) for 1363 trees at 48 locations across the native range of butternut. Remarkably, admixture in anthropogenic sites reached nearly 70%, while fragmented and continuous forests showed minimal admixture (<8%). Furthermore, more hybrids in anthropogenic sites had J. ailantifolia seed parents (95%) than hybrids in fragmented and continuous forests (69% and 59%, respectively). Our results show a strong influence of landscape type on rate and direction of realized gene flow. While hybrids are common in anthropogenic landscapes, our results suggest that even small forested landscapes serve as substantial barriers to hybrid establishment, a key consideration for butternut conservation planning, a species already exhibiting severe decline, and for other North American forest trees that hybridize with introduced congeners.
Language	English
Publishing date	2011-10-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2405496-3
ISSN	1752-4571 ; 1752-4563 ; 1752-4571
ISSN (online)	1752-4571 ; 1752-4563
ISSN	1752-4571
DOI	10.1111/j.1752-4571.2012.00250.x
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Article: Geographically extensive hybridization between the forest trees American butternut and Japanese walnut.

Hoban, Sean M / McCleary, Tim S / Schlarbaum, Scott E / Romero-Severson, Jeanne

Biology letters

2009 Volume 5, Issue 3, Page(s) 324–327

Abstract: We investigate the question of naturally occurring interspecific hybrids between two forest trees: the native North American butternut (Juglans cinerea L.) and the introduced Japanese walnut (Juglans ailantifolia Carrière). Using nuclear and chloroplast ... ...

Abstract	We investigate the question of naturally occurring interspecific hybrids between two forest trees: the native North American butternut (Juglans cinerea L.) and the introduced Japanese walnut (Juglans ailantifolia Carrière). Using nuclear and chloroplast DNA markers, we provide evidence for 29 F(1) and 22 advanced generation hybrids in seven locations across the eastern and southern range of the native species. Two locations show extensive admixture (95% J. ailantifolia and hybrids) while other locations show limited admixture. Hybridization appears to be asymmetrical with 90.9 per cent of hybrids having J. ailantifolia as the maternal parent. This is, to our knowledge, the first genetic data supporting natural hybridization between these species. The long-term outcome of introgression could include loss of native diversity, but could also include transfer of useful traits from the introduced species.
MeSH term(s)	DNA, Plant/genetics ; Demography ; Genetic Markers ; Genotype ; Hybridization, Genetic ; Juglans/genetics ; United States
Chemical Substances	DNA, Plant ; Genetic Markers
Language	English
Publishing date	2009-03-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2135022-X
ISSN	1744-957X ; 1744-9561
ISSN (online)	1744-957X
ISSN	1744-9561
DOI	10.1098/rsbl.2009.0031
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Article: Evaluation of wet-prep motility test for presumptive identification of bacillus species.

Cleary, Tim / Miller, Nancimae / Martinez, Octavio V

Journal of clinical microbiology

2001 Volume 40, Issue 2, Page(s) 730

MeSH term(s)	Bacillus/classification ; Bacillus/physiology ; Bacterial Typing Techniques ; Culture Media ; Gram-Positive Bacterial Infections/microbiology ; Humans ; Movement ; Water
Chemical Substances	Culture Media ; Water (059QF0KO0R)
Language	English
Publishing date	2001-10-13
Publishing country	United States
Document type	Evaluation Study ; Letter
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/JCM.40.2.730.2002
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Article: Thirteen nuclear microsatellite loci for butternut (Juglans cinerea L.).

Hoban, Sean / Anderson, Robert / McCleary, Tim / Schlarbaum, Scott / Romero-Severson, Jeanne

Molecular ecology resources

2008 Volume 8, Issue 3, Page(s) 643–646

Abstract: Butternut (Juglans cinerea L.) is an eastern North American forest tree severely threatened by an exotic fungal pathogen, Sirococcus clavigignenti-juglandacearum. We report here 13 nuclear microsatellites for genetic evaluation of the remaining natural ... ...

Abstract	Butternut (Juglans cinerea L.) is an eastern North American forest tree severely threatened by an exotic fungal pathogen, Sirococcus clavigignenti-juglandacearum. We report here 13 nuclear microsatellites for genetic evaluation of the remaining natural populations. Summary statistics are reported for individuals from a population of butternuts in central Kentucky (N = 63). All markers were polymorphic, with an average of 13.7 alleles per locus observed. Four loci exhibited significantly fewer heterozygotes than expected under Hardy-Weinberg equilibrium (P < 0.05).
Language	English
Publishing date	2008-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2406816-0
ISSN	1471-8286 ; 1755-098X
ISSN (online)	1471-8286
ISSN	1755-098X
DOI	10.1111/j.1471-8286.2007.02030.x
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Article: Four cleaved amplified polymorphic sequence (CAPS) markers for the detection of the Juglans ailantifolia chloroplast in putatively native J. cinerea populations.

McCleary, Tim S / Robichaud, Rodney L / Nuanes, Steve / Anagnostakis, Sandra L / Schlarbaum, Scott E / Romero-Severson, Jeanne

Molecular ecology resources

2009 Volume 9, Issue 2, Page(s) 525–527

Abstract: Hybridization between butternut (Juglans cinerea), a forest tree native to eastern North America, and Japanese walnut (J. ailantifolia), a tree tolerant to the lethal fungal disease butternut canker, casts doubt on the genetic identity of the remaining ... ...

Abstract	Hybridization between butternut (Juglans cinerea), a forest tree native to eastern North America, and Japanese walnut (J. ailantifolia), a tree tolerant to the lethal fungal disease butternut canker, casts doubt on the genetic identity of the remaining butternuts. We report a diagnostic test to distinguish the J. cinerea chloroplast from the J. ailantifolia chloroplast using cleaved amplified polymorphic sequences resolvable in 1.5% agarose gels. J. ailantifolia maternal ancestry in naturally regenerated stands provides a site selection criterion for studies of introgression dynamics when the non-native parent and the hybrids tolerate a disease to which the native species is susceptible.
Language	English
Publishing date	2009-03
Publishing country	England
Document type	Journal Article
ZDB-ID	2406816-0
ISSN	1471-8286 ; 1755-098X
ISSN (online)	1471-8286
ISSN	1755-098X
DOI	10.1111/j.1755-0998.2008.02465.x
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Article ; Research data: (with research data) Range‐wide distribution of genetic diversity in the North American tree Juglans cinerea: a product of range shifts, not ecological marginality or recent population decline

Hoban, Sean M / Borkowski, Daniel S / Brosi, Sunshine L / McCleary, Tim S / Thompson, Laura M / McLachlan, Jason S / Pereira, Marie A / Schlarbaum, Scott E / Romero-Severson, Jeanne

Molecular ecology. 2010 Nov., v. 19, no. 22

2010

Abstract: The spatial distribution of genetic diversity is a product of recent and historical ecological processes, as well as anthropogenic activities. A current challenge in population and conservation genetics is to disentangle the relative effects of these ... ...

Abstract	The spatial distribution of genetic diversity is a product of recent and historical ecological processes, as well as anthropogenic activities. A current challenge in population and conservation genetics is to disentangle the relative effects of these processes, as a first step in predicting population response to future environmental change. In this investigation, we compare the influence of contemporary population decline, contemporary ecological marginality and postglacial range shifts. Using classical model comparison procedures and Bayesian methods, we have identified postglacial range shift as the clear determinant of genetic diversity, differentiation and bottlenecks in 29 populations of butternut, Juglans cinerea L., a North American outcrossing forest tree. Although butternut has experienced dramatic 20th century decline because of an introduced fungal pathogen, our analysis indicates that recent population decline has had less genetic impact than postglacial recolonization history. Location within the range edge vs. the range core also failed to account for the observed patterns of diversity and differentiation. Our results suggest that the genetic impact of large‐scale recent population losses in forest trees should be considered in the light of Pleistocene‐era large‐scale range shifts that may have had long‐term genetic consequences. The data also suggest that the population dynamics and life history of wind‐pollinated forest trees may provide a buffer against steep population declines of short duration, a result having important implications for habitat management efforts, ex situ conservation sampling and population viability analysis.
Keywords	Bayesian theory ; Juglans cinerea ; anthropogenic activities ; decline ; forest trees ; fungi ; genetic variation ; habitats ; history ; life history ; outcrossing ; pathogens ; population dynamics ; population genetics ; prediction ; viability
Language	English
Dates of publication	2010-11
Size	p. 4876-4891.
Publishing place	Blackwell Publishing Ltd
Document type	Article ; Research data
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083 ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/j.1365-294X.2010.04834.x
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Article: Rapid and specific detection of Mycobacterium tuberculosis from acid-fast bacillus smear-positive respiratory specimens and BacT/ALERT MP culture bottles by using fluorogenic probes and real-time PCR.

Miller, Nancimae / Cleary, Tim / Kraus, Günter / Young, Andrea K / Spruill, Gina / Hnatyszyn, H James

Journal of clinical microbiology

2001 Volume 40, Issue 11, Page(s) 4143–4147

Abstract: A real-time PCR assay using the LightCycler (LC) instrument for the specific identification of Mycobacterium tuberculosis complex (MTB) was employed to detect organisms in 135 acid-fast bacillus (AFB) smear-positive respiratory specimens and in 232 BacT/ ... ...

Abstract	A real-time PCR assay using the LightCycler (LC) instrument for the specific identification of Mycobacterium tuberculosis complex (MTB) was employed to detect organisms in 135 acid-fast bacillus (AFB) smear-positive respiratory specimens and in 232 BacT/ALERT MP (MP) culture bottles of respiratory specimens. The LC PCR assay was directed at the amplification of the internal transcribed spacer region of the Mycobacterium genome with real-time detection using fluorescence resonance energy transfer probes specific for MTB. The results from the respiratory specimens were compared to those from the Amplicor M. tuberculosis PCR test. Specimens from MP culture bottles were analyzed by Accuprobe and conventional identification methods. MTB was cultured from 105 (77.7%) respiratory AFB smear-positive specimens; 103 of these samples were positive by LC PCR and Amplicor PCR. Two samples negative in the LC assay contained rare numbers of organisms; both were positive in the Amplicor assay. Two separate samples negative by Amplicor PCR contained low and moderate numbers of AFB, respectively, and both of these were positive in the LC assay. There were 30 AFB smear-positive respiratory specimens that grew mycobacteria other than tuberculosis (MOTT), and all tested negative in both assays. Of the 231 MP culture bottles, 114 cultures were positive for MTB and all were positive by the LC assay. The remaining 117 culture bottles were negative in the LC assay and grew various MOTT. This real-time MTB assay is sensitive and specific; a result was available within 1 h of having a DNA sample available for testing.
MeSH term(s)	Bacterial Typing Techniques ; Culture Media ; Fluorescence Resonance Energy Transfer ; Fluorescent Dyes ; Humans ; Mycobacterium tuberculosis/genetics ; Mycobacterium tuberculosis/growth & development ; Mycobacterium tuberculosis/isolation & purification ; Polymerase Chain Reaction/methods ; Reagent Kits, Diagnostic ; Respiratory System/microbiology ; Sensitivity and Specificity ; Specimen Handling/methods ; Temperature ; Time Factors ; Tuberculosis, Pulmonary/microbiology
Chemical Substances	Culture Media ; Fluorescent Dyes ; Reagent Kits, Diagnostic
Language	English
Publishing date	2001-10-13
Publishing country	United States
Document type	Evaluation Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/JCM.40.11.4143-4147.2002
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