Publications by authors named "Luke R Tembrock"

22 Publications

  • Page 1 of 1

Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution.

Sci Rep 2021 May 4;11(1):9471. Epub 2021 May 4.

Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.

The chloroplast is one of two organelles containing a separate genome that codes for essential and distinct cellular functions such as photosynthesis. Given the importance of chloroplasts in plant metabolism, the genomic architecture and gene content have been strongly conserved through long periods of time and as such are useful molecular tools for evolutionary inferences. At present, complete chloroplast genomes from over 4000 species have been deposited into publicly accessible databases. Despite the large number of complete chloroplast genomes, comprehensive analyses regarding genome architecture and gene content have not been conducted for many lineages with complete species sampling. In this study, we employed the genus Populus to assess how more comprehensively sampled chloroplast genome analyses can be used in understanding chloroplast evolution in a broadly studied lineage of angiosperms. We conducted comparative analyses across Populus in order to elucidate variation in key genome features such as genome size, gene number, gene content, repeat type and number, SSR (Simple Sequence Repeat) abundance, and boundary positioning between the four main units of the genome. We found that some genome annotations were variable across the genus owing in part from errors in assembly or data checking and from this provided corrected annotations. We also employed complete chloroplast genomes for phylogenetic analyses including the dating of divergence times throughout the genus. Lastly, we utilized re-sequencing data to describe the variations of pan-chloroplast genomes at the population level for P. euphratica. The analyses used in this paper provide a blueprint for the types of analyses that can be conducted with publicly available chloroplast genomes as well as methods for building upon existing datasets to improve evolutionary inference.
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http://dx.doi.org/10.1038/s41598-021-88160-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8096831PMC
May 2021

Phylogeny and biogeography of the Japanese rhinoceros beetle, (Coleoptera: Scarabaeidae) based on SNP markers.

Ecol Evol 2021 Jan 22;11(1):153-173. Epub 2020 Dec 22.

School of Pharmaceutical Sciences Sun Yat-Sen University Guangzhou China.

The Japanese rhinoceros beetle is one of the largest beetle species in the world and is commonly used in traditional Chinese medicine. Ten subspecies of and a related species () have been described throughout Asia, but their taxonomic delimitations remain problematic. To clarify issues such as taxonomy, and the degree of genetic differentiation of populations, we investigated the genetic structure, genetic variability, and phylogeography of 53 specimens of species from 44 locations in five Asian countries (China, Japan, Korea, Thailand, and Myanmar). Using specific-locus amplified fragment sequencing (SLAF-seq) techniques, we developed 330,799 SLAFs over 114.16M reads, in turn yielding 46,939 high-resolution single nucleotide polymorphisms (SNPs) for genotyping. Phylogenetic analysis of SNPs indicated the presence of three distinct genetic groups, suggesting that the various subspecies could be treated as three groups of populations. PCA and ADMIXTURE analysis also identified three genetic clusters (North, South, West), which corresponded to their locations, suggesting that geographic factors were important in maintaining within population homogeneity and between population divergence. Analyses of SNP data confirmed the monophyly of certain subspecies on islands, while other subspecies (e.g., ) were found to be polyphyletic and nested in more than one lineage. AMOVA demonstrated high level of differentiation among populations/groups. Also, pairwise values revealed high differentiation, particularly between South and West, as well as between North and South. Despite the differentiation, measurable gene flow was inferred between genetic clusters but at varying rates and directions. Our study demonstrated that SLAF-seq derived markers outperformed 16S and COII sequences and provided improved resolution of the genetic differentiation of rhinoceros beetle populations from a large part of the species' range.
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http://dx.doi.org/10.1002/ece3.6982DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7790660PMC
January 2021

Comparative Analyses of Five Complete Chloroplast Genomes from the Genus (Fabacaeae).

Int J Mol Sci 2020 May 26;21(11). Epub 2020 May 26.

State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.

is a genus of trees mainly distributed in tropical Asia, Africa, and South America. Some species of are rosewood tree species, having important economic value for timber, and for some species, medicinal value as well. Up to now, information about this genus with regard to the genomic characteristics of the chloroplasts has been limited. Based on a combination of next-generation sequencing (Illumina Hiseq) and long-read sequencing (PacBio), the whole chloroplast genomes (cp genomes) of five species (rosewoods) in Pterocarpus (, , , , ) have been assembled. The cp genomes of five species in have similar structural characteristics, gene content, and sequence to other flowering plants. The cp genomes have a typical four-part structure, containing 110 unique genes (77 protein coding genes, 4 rRNAs, 29 tRNAs). Through comparative genomic analysis, abundant simple sequence repeat (SSR)loci (333-349) were detected in , among which A /T single nucleotide repeats accounted for the highest proportion (72.8-76.4%). In the five cp genomes of , eight hypervariable regions, including trnH-GUG_psbA, trnS-UGA_psbC, accD-psaI, ndhI-exon2_ndhI-exon1, ndhG_ndhi-exon2, rpoC2-exon2, ccsA, and trnfM-CAU, are proposed for use as DNA barcode regions. In the comparison of gene selection pressures ( as the reference genome), purifying selection was inferred as the primary mode of selection in maintaining important biological functions. Phylogenetic analysis shows that is a monophyletic group. The species is resolved as early diverging in the genus. was resolved as sister to the genus .
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http://dx.doi.org/10.3390/ijms21113758DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7312355PMC
May 2020

A Real-Time PCR Assay for Rapid Identification of Tuta absoluta (Lepidoptera: Gelechiidae).

J Econ Entomol 2020 06;113(3):1479-1485

USDA-APHIS-PPQ-Science & Technology, Identification Technology Program, Fort Collins, CO.

The tomato leafminer, Tuta absoluta (Meyrick), is a highly destructive pest of tomatoes, causing damage to leaves, stalks, buds, and fruits. Native to South America, T. absoluta is now found throughout Europe, South Asia, Africa, parts of Central America, and the Caribbean. Adults are small, with a wingspan of approximately one cm and lack distinctive markings, making morphological identification difficult. Larvae are also difficult to identify and resemble those of many other gelechiids. Due to the extensive time spent and expertise required for morphological identification, and the imminent threat to the North American tomato crop, we have developed a rapid molecular test for discriminating individual specimens of T. absoluta using a probe-based real-time polymerase chain reaction (PCR) assay. The assay is able to quickly distinguish T. absoluta from similar-sized moth specimens that are attracted to T. absoluta pheromone lures in the United States and is also able to identify larvae of T. absoluta. Decreased identification time for this critical pest will lead to more rapid identification at ports of entry and allow for more efficient trap screening for domestic monitoring programs.
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http://dx.doi.org/10.1093/jee/toaa040DOI Listing
June 2020

The Complete Chloroplast Genome of Heimia myrtifolia and Comparative Analysis within Myrtales.

Molecules 2018 Apr 8;23(4). Epub 2018 Apr 8.

Department of Biology, Colorado State University, Fort Collins, CO 80523, USA.

is an important medicinal plant with several pharmacologically active alkaloids and is also used as an ornamental landscape plant. The purpose of this study is to complete and characterize the chloroplast (cp) genome of and compare genomic features to other Myrtales species' cp genomes. The analysis showed that has a total length of 159,219 bp with a typical quadripartite structure containing two identical inverted repeats (IRs) of 25,643 bp isolated by one large single copy (LSC) of 88,571 bp and one small single copy (SSC) of 18,822 bp. The cp genome contains 129 genes with eight ribosomal RNAs, 30 transfer RNAs, and 78 protein coding genes, in which 17 genes are duplicated in two IR regions. The genome organization including gene type and number and guanine-cytosine (GC) content is analyzed among the 12 cp genomes in this study. Approximately 255 simple sequence repeats (SSRs) and 16 forward, two reverses, and two palindromic repeats were identified in the H. myrtifolia cp genome. By comparing the whole cp genome with 11 other Myrtales species, the results showed that the sequence similarity was high between coding regions while sequence divergence was high between intergenic regions. By employing the full cp genomes for phylogenetic analysis, structural and sequence differences were characterized between and 11 Myrtales species illustrating what patterns are common in the evolution of cp genomes within the Myrtales. The first entire cp genome in the genus provides a valuable resource for further studies in these medicinally and ornamentally important taxa.
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http://dx.doi.org/10.3390/molecules23040846DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6017443PMC
April 2018

A ddPCR Assay for Identification of Autographa gamma (Noctuidae: Plusiinae) in Bulk Trap Samples.

J Econ Entomol 2018 05;111(3):1490-1495

USDA-APHIS-PPQ-Science & Technology, Identification Technology Program, Fort Collins, CO.

The silver Y moth [Autographa gamma (Linneaus) (Noctuidae: Plusiinae)] is a pervasive crop pest in its native range but has not been found in moth surveys in the United States. Specimens of A. gamma are often intercepted at U.S. ports of entry, so the risk of introduction of this invasive species is high. Currently, identification of Plusiinae adults captured in domestic surveys is done by morphlogical comparison; however, this method is time consuming and misidentifications have occurred in the past. A recent study outlined a real-time PCR assay capable of rapidly identifying individual A. gamma specimens using CO1. This same study provided preliminary data for a droplet digital PCR (ddPCR) assay capable of processing bulk trap samples. Here, we develop and test a ddPCR assay for detecting a single A. gamma in a trap sample of 200 individual moths. This assay will drastically reduce the time and cost needed to screen domestic trap samples for A. gamma.
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http://dx.doi.org/10.1093/jee/toy052DOI Listing
May 2018

The Complete Chloroplast Genome of Catha edulis: A Comparative Analysis of Genome Features with Related Species.

Int J Mol Sci 2018 Feb 9;19(2). Epub 2018 Feb 9.

Department of Ecology, Evolution, and Organismal Biology, Ames, IA 50011, USA.

Qat (, Celastraceae) is a woody evergreen species with great economic and cultural importance. It is cultivated for its stimulant alkaloids cathine and cathinone in East Africa and southwest Arabia. However, genome information, especially DNA sequence resources, for are limited, hindering studies regarding interspecific and intraspecific relationships. Herein, the complete chloroplast (cp) genome of is reported. This genome is 157,960 bp in length with 37% GC content and is structurally arranged into two 26,577 bp inverted repeats and two single-copy areas. The size of the small single-copy and the large single-copy regions were 18,491 bp and 86,315 bp, respectively. The cp genome consists of 129 coding genes including 37 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes, and 84 protein coding genes. For those genes, 112 are single copy genes and 17 genes are duplicated in two inverted regions with seven tRNAs, four rRNAs, and six protein coding genes. The phylogenetic relationships resolved from the cp genome of qat and 32 other species confirms the monophyly of Celastraceae. The cp genomes of , and seven Celastraceae species lack the intron, which indicates an intron loss took place among an ancestor of this family. The cp genome of provides a highly valuable genetic resource for further phylogenomic research, barcoding and cp transformation in Celastraceae.
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http://dx.doi.org/10.3390/ijms19020525DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5855747PMC
February 2018

A Real-Time PCR Assay for the Separation of Autographa gamma (Noctuidae: Plusiinae) From Morphologically Similar Species in North America.

J Econ Entomol 2017 12;110(6):2609-2617

USDA-APHIS-PPQ-Science & Technology, Identification Technology Program.

The silver Y moth, Autographa gamma L. (Noctuidae: Plusiinae), is a pest of major economic importance in its native range of Europe, Asia, and North Africa. Although not present in North America, larvae of A. gamma are commonly intercepted in commodity shipments at U.S. ports, and adult surveys are conducted each year in more than 20 states. Because of the similarity of A. gamma to several native North American species that are attracted to the same pheromone lure, morphological identification of adults is difficult and requires dissection. In 2010, a specimen of Autographa californica (Speyer, 1875) (Lepidoptera: Noctuidae) from Pennsylvania was incorrectly identified as A. gamma, signaling the need for an alternative method of rapid identification. Here we detail a real-time PCR assay capable of identifying A. gamma specimens in approximately 45 min using extracted DNA. The assay uses a hydrolysis probe that targets a species-specific segment of the CO1 DNA barcode region, while a control probe targets a conserved region of 18S rDNA. The assay was tested with two independent runs of 452 specimens of Plusiinae representing 23 different species. The assay provided unambiguous data 99.7% of the time and did not result in any false positives; these data were used to develop a rule set for interpreting the real-time PCR results. In addition, the same diagnostic probe was tested in bulk sample simulations using real-time PCR and droplet digital PCR where A. gamma could be detected in concentrations as low as 1:1,000,000 (gamma:californica). These experiments provide baseline data for developing a bulk sample assay.
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http://dx.doi.org/10.1093/jee/tox256DOI Listing
December 2017

A droplet digital PCR (ddPCR) assay to detect Helicoverpa armigera (Lepidoptera: Noctuidae) in bulk trap samples.

PLoS One 2017 31;12(5):e0178704. Epub 2017 May 31.

USDA-APHIS-PPQ-Science & Technology, Identification Technology Program, Fort Collins, Colorado, United States of America.

Moths in the genus Helicoverpa are some of the most important agricultural pests in the world. Two species, H. armigera (Hübner) and H. zea (Boddie), cause the majority of damage to crops and millions of dollars are spent annually on control of these pests. The recent introduction of H. armigera into the New World has prompted extensive survey efforts for this species in the United States. Surveys are conducted using bucket traps baited with H. armigera pheromone, and, because the same pheromone compounds attract both species, these traps often capture large numbers of the native H. zea. Adult H. armigera and H. zea are very similar and can only be separated morphologically by minor differences in the genitalia. Thus, a time consuming genitalic dissection by a trained specialist is necessary to reliably identify either species, and every specimen must be dissected. Several molecular methods are available for differentiating and identifying H. armigera and H. zea, including two recently developed rapid protocols using real-time PCR. However, none of the published methods are capable of screening specimens in large batches. Here we detail a droplet digital PCR (ddPCR) assay that is capable of detecting a single H. armigera in a background of up to 999 H. zea. The assay has been tested using bulk extractions of 1,000 legs from actual trap samples and is effective even when using poor quality samples. This study provides an efficient, rapid, reproducible, and scalable method for processing H. armigera survey trap samples in the U.S. and demonstrates the potential for applying ddPCR technology to screen and diagnose invasive species.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0178704PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451079PMC
September 2017

Characterization of the whole chloroplast genome of Chikusichloa mutica and its comparison with other rice tribe (Oryzeae) species.

PLoS One 2017 24;12(5):e0177553. Epub 2017 May 24.

State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.

Chloroplast genomes are a significant genomic resource in plant species and have been used in many research areas. The complete genomic information from wild crop species could supply a valuable genetic reservoir for breeding. Chikusichloa mutica is one of the most important wild distant relatives of cultivated rice. In this study, we sequenced and characterized its complete chloroplast (cp) genome and compared it with other species in the same tribe. The whole cp genome sequence is 136,603 bp in size and exhibits a typical quadripartite structure with large and small single-copy regions (LSC, 82,327 bp; SSC, 12,598 bp) separated by a pair of 20,839-bp inverted repeats (IRA, B). A total of 110 unique genes are annotated, including 76 protein-coding genes, 4 ribosomal RNA genes and 30 tRNA genes. The genome structure, gene order, GC content, and other features are similar to those of other angiosperm cp genomes. When comparing the cp genomes between Oryzinae and Zizaniinae subtribes, the main differences were found between the junction regions and distribution of simple sequence repeats (SSRs). In comparing the two Chikusichloa species, the genomes were only 40 bp different in length and 108 polymorphic sites, including 83 single nucleotide substitutions (SNPs) and 25 insertion-deletions (Indels), were found between the whole cp genomes. The complete cp genome of C. mutica will be an important genetic tool for future breeding programs and understanding the evolution of wild rice relatives.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0177553PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5443529PMC
September 2017

Phylogeography of the wild and cultivated stimulant plant qat (, Celastraceae) in areas of historical cultivation.

Am J Bot 2017 Apr 14;104(4):538-549. Epub 2017 Apr 14.

Center for Humanities and Social Sciences, Qatar University, Doha, Qatar.

Premise Of The Study: Qat (, Celastraceae) is a woody plant species cultivated for its stimulant alkaloids. Qat is important to the economy and culture in large regions of Ethiopia, Kenya, and Yemen. Despite the importance of this species, the wild origins and dispersal of cultivars have only been described in often contradictory historical documents. We examined the wild origins, human-mediated dispersal, and genetic divergence of cultivated qat compared to wild qat.

Methods: We sampled 17 SSR markers and 1561 wild and cultivated individuals across the historical areas of qat cultivation.

Key Results: On the basis of genetic structure inferred using Bayesian and nonparametric methods, two centers of origin in Kenya and one in Ethiopia were found for cultivated qat. The centers of origin in Ethiopia and northeast of Mt. Kenya are the primary sources of cultivated qat genotypes. Qat cultivated in Yemen is derived from Ethiopian genotypes rather than Yemeni wild populations. Cultivated qat with a wild Kenyan origin has not spread to Ethiopia or Yemen, whereas a small minority of qat cultivated in Kenya originated in Ethiopia. Hybrid genotypes with both Ethiopian and Kenyan parentage are present in northern Kenya.

Conclusions: Ethiopian cultivars have diverged from their wild relatives, whereas Kenyan qat has diverged less. This pattern of divergence could be caused by the extinction of the wild-source qat populations in Ethiopia due to deforestation, undersampling, and/or artificial selection for agronomically important traits.
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http://dx.doi.org/10.3732/ajb.1600437DOI Listing
April 2017

Employing Two-stage Derivatisation and GC-MS to Assay for Cathine and Related Stimulant Alkaloids across the Celastraceae.

Phytochem Anal 2017 Jul 26;28(4):257-266. Epub 2017 Jan 26.

Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA.

Introduction: Catha edulis (qat, khat, mirra) is a woody plant species that is grown and consumed in East Africa and Yemen for its stimulant alkaloids cathinone, cathine and norephedrine. Two Celastraceae species, in addition to qat, have been noted for their stimulant properties in ethnobotanical literature. Recent phylogenetic reconstructions place four genera in a clade sister to Catha edulis, and these genera are primary candidates to search for cathine and related alkaloids.

Objective: Determine if cathine or related alkaloids are present in species of Celastraceae other than Catha edulis.

Methods: Leaf samples from 43 Celastraceae species were extracted in water followed by basification of the aqueous extract and partitioning with methyl-t-butyl ether to provide an alkaloid-enriched fraction. The extract was derivatised in a two-stage process and analysed using GC-MS for the presence of cathine. Related alkaloids and other metabolites in this alkaloid-enriched fraction were tentatively identified.

Results: Cathinone, cathine and norephedrine were not detected in any of the 43 Celastraceae species assayed other than Catha edulis. However, the phenylalanine- or tyrosine-derived alkaloid phenylethylamine was identified in five species. Nine species were found to be enriched for numerous sterol- and terpene-like compounds.

Conclusion: These results indicate that cathine is unique to Catha edulis, and not the compound responsible for the stimulant properties reported in related Celastraceae species. Copyright © 2017 John Wiley & Sons, Ltd.
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http://dx.doi.org/10.1002/pca.2671DOI Listing
July 2017

The complete chloroplast genome of queen's crape-myrtle().

Mitochondrial DNA B Resour 2016 Jun 20;1(1):408-409. Epub 2016 Jun 20.

Department of Biology, Colorado State University, Fort Collins, CO, USA.

The whole complete chloroplast genome of was assembled in this study. Total genome is 152,472 bp in length consisting of two inverted repeats of 17,562 bp separated by a large single-copy region and a small single-copy region of 84,050 bp and 33,295 bp, respectively. This genome contains 112 unique genes including 78 protein-coding genes, 4 ribosomal RNA genes and 30 transfer RNA genes. In 78 protein-coding genes, 8 genes (, , , , , , , ) contain one intron and three genes with two introns each (, and ). This newly sequenced chloroplast genome supply highly variable information of polymorphisms within species.
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http://dx.doi.org/10.1080/23802359.2016.1176879DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7799958PMC
June 2016

Chloroplast Genome Sequence of Lagerstroemia guilinensis (Lythraceae, Myrtales), a Species Endemic to the Guilin Limestone Area in Guangxi Province, China.

Genome Announc 2016 May 19;4(3). Epub 2016 May 19.

Department of Biology, Colorado State University, Fort Collins, Colorado, USA

We announce here the first complete chloroplast genome sequence of Lagerstroemia guilinensis (Lythraceae, Myrtales), a species endemic to the Guilin limestone area, along with its genome structure and functional gene annotations. The plant was collected from Guilin, Guangxi, China, and deposited as a germplasm accession of the Zhejiang Agriculture and Forestry University Collection (ZAFU 1507144). This genome will provide valuable information for future research of the Lagerstroemia genus and its relatives.
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http://dx.doi.org/10.1128/genomeA.00341-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4889003PMC
May 2016

Cadmium accumulation and tolerance of Lagerstroemia indica and Lagerstroemia fauriei (Lythraceae) seedlings for phytoremediation applications.

Int J Phytoremediation 2016 Nov;18(11):1104-12

c Department of Biology, Colorado State University , Fort Collins , Colorado , USA.

Contamination by heavy metals is one of the most serious environmental problems generated from human activities. Because phytoremediation utilizes plants to uptake contaminants, it could potentially be used to remediate metal-contaminated areas. A pot culture experiment with four levels of cadmium (Cd) (0, 20, 40, and 80 mg of Cd/kg dry soil) was conducted to investigate Cd accumulation and tolerance of roots, shoots, and leaves of Lagerstroemia indica and Lagerstroemia fauriei as well as their potential for phytoremediation. Experimental results indicated that Cd inhibited seedling growth only at the higher Cd exposure concentration (40 and 80 mg/kg). The tolerance index revealed that on average L. indica is more tolerant of Cd than L. fauriei. Moreover, plants in the experiment accumulated Cd differentially. In comparisons between L. indica and L. fauriei, the leaves of the former had higher concentrations of Cd, while the roots of latter had higher concentrations of Cd. Furthermore, the roots, shoots, and leaves had very high bioaccumulation factors that markedly exceeded 1.0 (exceptional only in shoots of 80 mg/kg for L. fauriei), indicating that the seedlings extracted Cd from the soil. The leaves' translocation factor of L. indica was greater than 1.0, being significantly higher than that of L. fauriei. Chlorophyll a, Chlorophyll b and total declined in both species significantly as Cd concentrations exceeded 40 mg/kg in the soil. In contrast, lipid peroxidation and proline content was found to increase with increasing Cd concentration. From the assessments of biomass production, Cd tolerance and uptake L. indica and L. fauriei could stand as excellent species for remediating Cd-contaminated soils.
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http://dx.doi.org/10.1080/15226514.2016.1183581DOI Listing
November 2016

The complete chloroplast genome of .

Mitochondrial DNA B Resour 2016 Apr 18;1(1):291-292. Epub 2016 Apr 18.

Key Laboratory of Pollinating Insect Biology of the Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China.

We report the complete chloroplast DNA (cpDNA) of (Brassicaceae), a less studied relative of by employing next-generation sequencing reads and assembly. The length of the closed circular cpDNA is 154,604 bp with a typical quadripartite structure. The genome is composed of one large single copy and one small single copy regions of 84,209 bp and 17,871 bp, respectively, and separated by a pair of inverted repeats of 26,262 bp in length. The overall GC content is 36.35% and the GC content of the LSC, IRs and SSC regions are 34.12%, 42.30% and 29.38%, separately. The gene content and the number for are the same as other published species in Brassicaceae with 112 annotated known unique genes including 78 protein-coding genes, 30 tRNA genes and four rRNA genes. The complete cpDNA of will provide valuable molecular resources for further phylogenetic and evolutionary analysis in the model genus.
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http://dx.doi.org/10.1080/23802359.2016.1166082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7871834PMC
April 2016

The complete plastid genome of the wild rice species (Poaceae).

Mitochondrial DNA B Resour 2016 Apr 11;1(1):218-219. Epub 2016 Apr 11.

Department of Biology, Colorado State University, Fort Collins, CO, USA.

The whole plastid genome of wild rice () is characterized in this study. The genome is 134 604 bp in length and is arranged in a typical circular structure, including a pair of inverted repeats (IRs) of 20 832 bp in size separated by a large single-copy region (LSC) of 80 411 bp in length and a small single-copy region (SSC) of 12 529 bp in length. The overall GC content of the genome is 38.98%. One hundred and ten unique genes were annotated from the chloroplast genome, including 76 protein-coding genes, 4 ribosomal RNA genes and 30 tRNA genes. A total of 20 of these genes are duplicated in the IR regions, 13 genes contain 1 intron and 2 genes ( and ) have 2 introns.
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http://dx.doi.org/10.1080/23802359.2016.1155093DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7871827PMC
April 2016

The Complete Plastid Genome of Lagerstroemia fauriei and Loss of rpl2 Intron from Lagerstroemia (Lythraceae).

PLoS One 2016 7;11(3):e0150752. Epub 2016 Mar 7.

Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America.

Lagerstroemia (crape myrtle) is an important plant genus used in ornamental horticulture in temperate regions worldwide. As such, numerous hybrids have been developed. However, DNA sequence resources and genome information for Lagerstroemia are limited, hindering evolutionary inferences regarding interspecific relationships. We report the complete plastid genome of Lagerstroemia fauriei. To our knowledge, this is the first reported whole plastid genome within Lythraceae. This genome is 152,440 bp in length with 38% GC content and consists of two single-copy regions separated by a pair of 25,793 bp inverted repeats. The large single copy and the small single copy regions span 83,921 bp and 16,933 bp, respectively. The genome contains 129 genes, including 17 located in each inverted repeat. Phylogenetic analysis of genera sampled from Geraniaceae, Myrtaceae, and Onagraceae corroborated the sister relationship between Lythraceae and Onagraceae. The plastid genomes of L. fauriei and several other Lythraceae species lack the rpl2 intron, which indicating an early loss of this intron within the Lythraceae lineage. The plastid genome of L. fauriei provides a much needed genetic resource for further phylogenetic research in Lagerstroemia and Lythraceae. Highly variable markers were identified for application in phylogenetic, barcoding and conservation genetic applications.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0150752PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4780714PMC
August 2016

Two complete chloroplast genomes of white campion (Silene latifolia) from male and female individuals.

Mitochondrial DNA A DNA Mapp Seq Anal 2017 05 29;28(3):375-376. Epub 2015 Dec 29.

a Department of Biology , Colorado State University , Fort Collins , CO , USA.

In this study, we assembled two individuals' complete chloroplast genomes with one male and one female from the dioecious plant species white campion (Silene latifolia). The two chloroplast genomes have an identical composition with each other as a circular molecule of 150 931 bp in length, with an overall GC content of 36.4%. The genomes consist of a pair of inverted repeats (IRs) of 25 503 bp, separated by a large single-copy (LSC) region and a small single-copy (SSC) region of 82 708 and 17 217 bp, respectively. The genomes contain 111 single copy genes, including 77 protein-coding genes, 4 ribosomal RNA genes and 30 transfer RNA genes. In these protein-coding genes, eight genes (rpl16, rpoC1, rps16, petD, petB, ndhB, ndhA and atpF) contain a single intron and three genes (rps12, clpP and ycf3) contain two introns. The two newly sequenced chloroplast genomes provide valuable information for detecting polymorphisms within species and between sexes.
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http://dx.doi.org/10.3109/19401736.2015.1126829DOI Listing
May 2017

A Multiplex Real-Time PCR Assay to Diagnose and Separate Helicoverpa armigera and H. zea (Lepidoptera: Noctuidae) in the New World.

PLoS One 2015 11;10(11):e0142912. Epub 2015 Nov 11.

National Plant Protection Organization, Netherlands Food and Consumers Product Safety Authority, Ministry of Economic Affairs, Wageningen, The Netherlands.

The Old World bollworm, Helicoverpa armigera (Hübner), and the corn earworm, H. zea (Boddie), are two of the most important agricultural pests in the world. Diagnosing these two species is difficult-adults can only be separated with a complex dissection, and larvae cannot be identified to species using morphology, necessitating the use of geographic origin for identification in most instances. With the discovery of H. armigera in the New World, identification of immature Helicoverpa based on origin is no longer possible because H. zea also occurs in all of the geographic regions where H. armigera has been discovered. DNA barcoding and restriction fragment length polymorphism (RFLP) analyses have been reported in publications to distinguish these species, but these methods both require post-PCR processing (i.e., DNA sequencing or restriction digestion) to complete. We report the first real-time PCR assay to distinguish these pests based on two hydrolysis probes that bind to a segment of the internal transcribed spacer region 2 (ITS2) amplified using a single primer pair. One probe targets H. armigera, the second probe targets H. zea, and a third probe that targets a conserved segment of 18S rDNA is used as a control of DNA quality. The assay can be completed in 50 minutes when using isolated DNA and is successfully tested on larvae intercepted at ports of entry and adults captured during domestic surveys. We demonstrate that the assay can be run in triplex with no negative effects on sensitivity, can be run using alternative real-time PCR reagents and instruments, and does not cross react with other New World Heliothinae.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142912PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4641610PMC
June 2016

Multilocus analysis of nucleotide variation and speciation in three closely related Populus (Salicaceae) species.

Mol Ecol 2015 Oct;24(19):4994-5005

State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.

Historical tectonism and climate oscillations can isolate and contract the geographical distributions of many plant species, and they are even known to trigger species divergence and ultimately speciation. Here, we estimated the nucleotide variation and speciation in three closely related Populus species, Populus tremuloides, P. tremula and P. davidiana, distributed in North America and Eurasia. We analysed the sequence variation in six single-copy nuclear loci and three chloroplast (cpDNA) fragments in 497 individuals sampled from 33 populations of these three species across their geographic distributions. These three Populus species harboured relatively high levels of nucleotide diversity and showed high levels of nucleotide differentiation. Phylogenetic analysis revealed that P. tremuloides diverged earlier than the other two species. The cpDNA haplotype network result clearly illustrated the dispersal route from North America to eastern Asia and then into Europe. Molecular dating results confirmed that the divergence of these three species coincided with the sundering of the Bering land bridge in the late Miocene and a rapid uplift of the Qinghai-Tibetan Plateau around the Miocene/Pliocene boundary. Vicariance-driven successful allopatric speciation resulting from historical tectonism and climate oscillations most likely played roles in the formation of the disjunct distributions and divergence of these three Populus species.
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http://dx.doi.org/10.1111/mec.13368DOI Listing
October 2015

Are differences in genomic data sets due to true biological variants or errors in genome assembly: an example from two chloroplast genomes.

PLoS One 2015 6;10(2):e0118019. Epub 2015 Feb 6.

State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.

DNA sequencing has been revolutionized by the development of high-throughput sequencing technologies. Plummeting costs and the massive throughput capacities of second and third generation sequencing platforms have transformed many fields of biological research. Concurrently, new data processing pipelines made rapid de novo genome assemblies possible. However, high quality data are critically important for all investigations in the genomic era. We used chloroplast genomes of one Oryza species (O. australiensis) to compare differences in sequence quality: one genome (GU592209) was obtained through Illumina sequencing and reference-guided assembly and the other genome (KJ830774) was obtained via target enrichment libraries and shotgun sequencing. Based on the whole genome alignment, GU592209 was more similar to the reference genome (O. sativa: AY522330) with 99.2% sequence identity (SI value) compared with the 98.8% SI values in the KJ830774 genome; whereas the opposite result was obtained when the SI values in coding and noncoding regions of GU592209 and KJ830774 were compared. Additionally, the junctions of two single copies and repeat copies in the chloroplast genome exhibited differences. Phylogenetic analyses were conducted using these sequences, and the different data sets yielded dissimilar topologies: phylogenetic replacements of the two individuals were remarkably different based on whole genome sequencing or SNP data and insertions and deletions (indels) data. Thus, we concluded that the genomic composition of GU592209 was heterogeneous in coding and non-coding regions. These findings should impel biologists to carefully consider the quality of sequencing and assembly when working with next-generation data.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118019PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4320078PMC
October 2015