Publications by authors named "Tongming Yin"

70 Publications

Fine mapping of the sex locus in Salix triandra confirms a consistent sex determination mechanism in genus Salix.

Hortic Res 2020 May 1;7(1):64. Epub 2020 May 1.

The Key Lab of Cultivar Innovation and Germplasm Improvement of Salicaceae, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.

Salix triandra belongs to section Amygdalinae in genus Salix, which is in a different section from the willow species in which sex determination has been well studied. Studying sex determination in distantly related willow species will help to clarify whether the sexes of different willows arise through a common sex determination system. For this purpose, we generated an intraspecific full-sib F population for S. triandra and constructed high-density genetic linkage maps for the crossing parents using restriction site-associated DNA sequencing and following a two-way pseudo-testcross strategy. With the established maps, the sex locus was positioned in linkage group XV only in the maternal map, and no sex linkage was detected in the paternal map. Consistent with previous findings in other willow species, our study showed that chromosome XV was the incipient sex chromosome and that females were the heterogametic sex in S. triandra. Therefore, sex in this willow species is also determined through a ZW sex determination system. We further performed fine mapping in the vicinity of the sex locus with SSR markers. By comparing the physical and genetic distances for the target interval encompassing the sex determination gene confined by SSRs, severe recombination repression was revealed in the sex determination region in the female map. The recombination rate in the confined interval encompassing the sex locus was approximately eight-fold lower than the genome-wide average. This study provides critical information relevant to sex determination in S. triandra.
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http://dx.doi.org/10.1038/s41438-020-0289-1DOI Listing
May 2020

Design, synthesis and biological evaluation of anilide (dicarboxylic acid) shikonin esters as antitumor agents through targeting PI3K/Akt/mTOR signaling pathway.

Bioorg Chem 2021 Mar 29;111:104872. Epub 2021 Mar 29.

State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China. Electronic address:

Triple-negative breast cancer (TNBC) has an unfavorable prognosis attribute to its low differentiation, rapid proliferation and high distant metastasis rate. PI3K/Akt/mTOR as an intracellular signaling pathway plays a key role in the cell proliferation, migration, invasion, metabolism and regeneration. In this work, we designed and synthesized a series of anilide (dicarboxylic acid) shikonin esters targeting PI3K/Akt/mTOR signaling pathway, and assessed their antitumor effects. Through three rounds of screening by computer-aided drug design method (CADD), we preliminarily obtained sixteen novel anilide (dicarboxylic acid) shikonin esters and identified them as excellent compounds. CCK-8 assay results demonstrated that compound M9 exhibited better antiproliferative activities against MDA-MB-231, A549 and HeLa cell lines than shikonin (SK), especially for MDA-MB-231 (M9: IC = 4.52 ± 0.28 μM; SK: IC = 7.62 ± 0.26 μM). Moreover, the antiproliferative activity of M9 was better than that of paclitaxel. Further pharmacological studies showed that M9 could induce apoptosis of MDA-MB-231 cells and arrest the cell cycle in G2/M phase. M9 also inhibited the migration of MDA-MB-231 cells by inhibiting Wnt/β-catenin signaling pathway. In addition, western blot results showed that M9 could inhibit cell proliferation and migration by down-regulating PI3K/Akt/mTOR signaling pathway. Finally, a three-dimensional quantitative structure-activity relationship (3D-QSAR) model was also constructed to provide a basis for further development of shikonin derivatives as potential antitumor drugs through structure-activity relationship analysis. To sum up, M9 could be a potential candidate for TNBC therapy.
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http://dx.doi.org/10.1016/j.bioorg.2021.104872DOI Listing
March 2021

The chromosome-scale assembly of the willow genome provides insight into Salicaceae genome evolution.

Hortic Res 2020 Apr 1;7(1):45. Epub 2020 Apr 1.

Key Laboratory for Tree Breeding and Germplasm Improvement, Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.

Salix suchowensis is an early-flowering shrub willow that provides a desirable system for studies on the basic biology of woody plants. The current reference genome of S. suchowensis was assembled with 454 sequencing reads. Here, we report a chromosome-scale assembly of S. suchowensis generated by combining PacBio sequencing with Hi-C technologies. The obtained genome assemblies covered a total length of 356 Mb. The contig N50 of these assemblies was 263,908 bp, which was ~65-fold higher than that reported previously. The contiguity and completeness of the genome were significantly improved. By applying Hi-C data, 339.67 Mb (95.29%) of the assembled sequences were allocated to the 19 chromosomes of haploid willow. With the chromosome-scale assembly, we revealed a series of major chromosomal fissions and fusions that explain the genome divergence between the sister genera of Salix and Populus. The more complete and accurate willow reference genome obtained in this study provides a fundamental resource for studying many genetic and genomic characteristics of woody plants.
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http://dx.doi.org/10.1038/s41438-020-0268-6DOI Listing
April 2020

Sex determination through X-Y heterogamety in Salix nigra.

Heredity (Edinb) 2021 Apr 28;126(4):630-639. Epub 2021 Jan 28.

Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409-3131, USA.

The development of non-recombining sex chromosomes has radical effects on the evolution of discrete sexes and sexual dimorphism. Although dioecy is rare in plants, sex chromosomes have evolved repeatedly throughout the diversification of angiosperms, and many of these sex chromosomes are relatively young compared to those found in vertebrates. In this study, we designed and used a sequence capture array to identify a novel sex-linked region (SLR) in Salix nigra, a basal species in the willow clade, and demonstrated that this species has XY heterogamety. We did not detect any genetic overlap with the previously characterized ZW SLRs in willows, which map to a different chromosome. The S. nigra SLR is characterized by strong recombination suppression across a 2 MB region and an excess of low-frequency alleles, resulting in a low Tajima's D compared to the remainder of the genome. We speculate that either a recent bottleneck in population size or factors related to positive or background selection generated this differential pattern of Tajima's D on the X and autosomes. This discovery provides insights into factors that may influence the evolution of sex chromosomes in plants and contributes to a large number of recent observations that underscore their dynamic nature.
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http://dx.doi.org/10.1038/s41437-020-00397-3DOI Listing
April 2021

Differential relieving effects of shikonin and its derivatives on inflammation and mucosal barrier damage caused by ulcerative colitis.

PeerJ 2021 7;9:e10675. Epub 2021 Jan 7.

State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, China.

Background: Ulcerative colitis (UC) is one of the most challenging human diseases. Natural shikonin (SK) and its derivatives (with have higher accumulation) isolated from the root of have numerous beneficial effects, such as wound healing and anti-inflammatory activities. Some researchers have reported that hydroxynaphthoquinone mixture (HM) and SK attenuate the acute UC induced by dextran sulfate sodium (DSS). However, no existing study has systemically investigated the effectiveness of SK and other hydroxynaphthoquinone natural derivative monomers on UC.

Methods: In this study, mice were treated with SK and its derivatives (25 mg/kg) and mesalazine (200 mg/kg) after DSS administration daily for one week. Disease progression was monitored daily by observing the changes in clinical signs and body weight.

Results: Intragastric administration natural single naphthoquinone attenuated the malignant symptoms induced by DSS. SK or its derivatives remarkably suppressed the serum levels of pro-inflammatory cytokines while increasing the inflammatory cytokine interleukin (IL)-10 . Additionally, both SK and alkanin restrained the activities of cyclooxygenase-2 (COX-2), myeloperoxidase (MPO) and inducible nitric oxide synthase (iNOS) in serum and colonic tissues. SK and its derivatives inhibited the activation of nucleotide binding oligomerization domain-like receptors (NLRP3) inflammasome and NF-κB signaling pathway, thereby relieving the DSS-induced disruption of epithelial tight junction (TJ) in colonic tissues.

Conclusions: Our findings shed more lights on the pharmacological efficacy of SK and its derivatives in UC against inflammation and mucosal barrier damage.
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http://dx.doi.org/10.7717/peerj.10675DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7797173PMC
January 2021

Evidences for a role of two Y-specific genes in sex determination in Populus deltoides.

Nat Commun 2020 11 18;11(1):5893. Epub 2020 Nov 18.

The Key Laboratory of Tree Genetic Improvement and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, 200137, Nanjing, China.

Almost all plants in the genus Populus are dioecious (i.e. trees are either male or female), but it is unknown whether dioecy evolved in a common ancestor or independently in different subgenera. Here, we sequence the small peritelomeric X- and Y-linked regions of P. deltoides chromosome XIX. Two genes are present only in the Y-linked region. One is a duplication of a non-Y-linked, female-specifically expressed response regulator, which produces siRNAs that block this gene's expression, repressing femaleness. The other is an LTR/Gypsy transposable element family member, which generates long non-coding RNAs. Overexpression of this gene in A. thaliana promotes androecium development. We also find both genes in the sex-determining region of P. simonii, a different poplar subgenus, which suggests that they are both stable components of poplar sex-determining systems. By contrast, only the duplicated response regulator gene is present in the sex-linked regions of P. davidiana and P. tremula. Therefore, findings in our study suggest dioecy may have evolved independently in different poplar subgenera.
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http://dx.doi.org/10.1038/s41467-020-19559-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7674411PMC
November 2020

Impact of a G2-EPSPS & GAT Dual Transgenic Glyphosate-Resistant Soybean Line on the Soil Microbial Community under Field Conditions Affected by Glyphosate Application.

Microbes Environ 2020 ;35(4)

Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University.

In the past thirty years, the biosafety of the aboveground part of crops, including horizontal gene transferal through pollen dispersal and hybridization, has been the focus of research; however, microbial communities in the underground part are attracting increasing attention. In the present study, the soybean root-associated bacterial communities of the G2-EPSPS plus GAT transgenic soybean line Z106, its recipient variety ZH10, and Z106 treated with glyphosate (Z106J) were compared at the seedling, flowering, and seed filling stages by high-throughput sequencing of the V4 hypervariable regions of 16S rRNA gene amplicons using Illumina MiSeq. The results obtained showed no significant differences in the alpha/beta diversities of root-associated bacterial communities at the three stages among ZH10, Z106, and Z106J under field growth conditions; however, the relative abundance of four main nitrogen-fixing bacterial genera significantly differed among ZH10, Z106, and Z106J. Ternary plot results indicated that in the root compartment, the proportional contributions of rhizobial nitrogen-fixing Ensifer fredii and Bradyrhizobium elkanii, which exhibit an extremely broad nodulation host range, markedly differed among the three treatments at the three stages. Thus, the present results indicate that transgenic G2-EPSPS and GAT soybean may induce different changes in functional bacterial species in soil, such as E. fredii and B. elkanii, from ZH10, which were compensated for/enriched at the flowering and seed filling stages, respectively, to some extent through as of yet unknown mechanisms by transgenic soybean treated with glyphosate.
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http://dx.doi.org/10.1264/jsme2.ME20056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7734404PMC
January 2020

A General Model to Explain Repeated Turnovers of Sex Determination in the Salicaceae.

Mol Biol Evol 2021 03;38(3):968-980

Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.

Dioecy, the presence of separate sexes on distinct individuals, has evolved repeatedly in multiple plant lineages. However, the specific mechanisms by which sex systems evolve and their commonalities among plant species remain poorly understood. With both XY and ZW sex systems, the family Salicaceae provides a system to uncover the evolutionary forces driving sex chromosome turnovers. In this study, we performed a genome-wide association study to characterize sex determination in two Populus species, P. euphratica and P. alba. Our results reveal an XY system of sex determination on chromosome 14 of P. euphratica, and a ZW system on chromosome 19 of P. alba. We further assembled the corresponding sex-determination regions, and found that their sex chromosome turnovers may be driven by the repeated translocations of a Helitron-like transposon. During the translocation, this factor may have captured partial or intact sequences that are orthologous to a type-A cytokinin response regulator gene. Based on results from this and other recently published studies, we hypothesize that this gene may act as a master regulator of sex determination for the entire family. We propose a general model to explain how the XY and ZW sex systems in this family can be determined by the same RR gene. Our study provides new insights into the diversification of incipient sex chromosomes in flowering plants by showing how transposition and rearrangement of a single gene can control sex in both XY and ZW systems.
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http://dx.doi.org/10.1093/molbev/msaa261DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7947767PMC
March 2021

The genomic architecture of the sex-determining region and sex-related metabolic variation in Ginkgobiloba.

Plant J 2020 12 27;104(5):1399-1409. Epub 2020 Oct 27.

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.

Sex differences and evolutionary differences are critical biological issues. Ginkgo is an ancient lineage of dioecious gymnosperms with special value for studying the mechanism of sex determination in plants. However, the major genetic basic underlying sex chromosomes remains to be uncovered. In this study, we identify the sex-determining region of Ginkgo and locate it to the area from megabases 48 to 75 on chromosome 2. We find that the male sex-determining region of Ginkgo contains more than 200 genes, including four MADS-box genes, demonstrating that the Ginkgo sex determination system is of the XY type. We also find that genetic sex differences result in specialized flavonoid metabolism and regulation in each sex. These findings establish a foundation for revealing the molecular mechanism of sexual dimorphism and promoting the development of the Ginkgo industry.
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http://dx.doi.org/10.1111/tpj.15009DOI Listing
December 2020

PreLnc: An Accurate Tool for Predicting lncRNAs Based on Multiple Features.

Genes (Basel) 2020 08 23;11(9). Epub 2020 Aug 23.

College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China.

Accumulating evidence indicates that long non-coding RNAs (lncRNAs) have certain similarities with messenger RNAs (mRNAs) and are associated with numerous important biological processes, thereby demanding methods to distinguish them. Based on machine learning algorithms, a variety of methods are developed to identify lncRNAs, providing significant basic data support for subsequent studies. However, many tools lack certain scalability, versatility and balance, and some tools rely on genome sequence and annotation. In this paper, we propose a convenient and accurate tool "PreLnc", which uses high-confidence lncRNA and mRNA transcripts to build prediction models through feature selection and classifiers. The false discovery rate (FDR) adjusted P-value and Z-value were used for analyzing the tri-nucleotide composition of transcripts of different species. Conclusions can be drawn from the experiment that there were significant differences in RNA transcripts among plants, which may be related to evolutionary conservation and the fact that plants are under evolutionary pressure for a longer time than animals. Combining with the Pearson correlation coefficient, we use the incremental feature selection (IFS) method and the comparison of multiple classifiers to build the model. Finally, the balanced random forest was used to construct the classifier, and PreLnc obtained 91.09% accuracy for 349,186 transcripts of animals and plants. In addition, by comparing standard performance measurements, PreLnc performed better than other prediction tools.
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http://dx.doi.org/10.3390/genes11090981DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7563287PMC
August 2020

The Acer truncatum genome provides insights into nervonic acid biosynthesis.

Plant J 2020 11 2;104(3):662-678. Epub 2020 Oct 2.

Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, China.

Acer truncatum (purpleblow maple) is a woody tree species that produces seeds with high levels of valuable fatty acids (especially nervonic acid). However, the lack of a complete genome sequence has limited both basic and applied research on A. truncatum. We describe a high-quality draft genome assembly comprising 633.28 Mb (contig N50 = 773.17 kb; scaffold N50 = 46.36 Mb) with at least 28 438 predicted genes. The genome underwent an ancient triplication, similar to the core eudicots, but there have been no recent whole-genome duplication events. Acer yangbiense and A. truncatum are estimated to have diverged about 9.4 million years ago. A combined genomic, transcriptomic, metabonomic, and cell ultrastructural analysis provided new insights into the biosynthesis of very long-chain monounsaturated fatty acids. In addition, three KCS genes were found that may contribute to regulating nervonic acid biosynthesis. The KCS paralogous gene family expanded to 28 members, with 10 genes clustered together and distributed in the 0.27-Mb region of pseudochromosome 4. Our chromosome-scale genomic characterization may facilitate the discovery of agronomically important genes and stimulate functional genetic research on A. truncatum. Furthermore, the data presented also offer important foundations from which to study the molecular mechanisms influencing the production of nervonic acids.
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http://dx.doi.org/10.1111/tpj.14954DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7702125PMC
November 2020

Efficient CRISPR/Cas9-Mediated Gene Editing in an Interspecific Hybrid Poplar With a Highly Heterozygous Genome.

Front Plant Sci 2020 3;11:996. Epub 2020 Jul 3.

Key Laboratory for Tree Breeding and Germplasm Improvement, Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, China.

Although the CRISPR/Cas9 system has been widely used for crop breeding, its application for the genetic improvement of trees has been limited, partly because of the outcrossing nature and substantial genomic heterozygosity of trees. Shanxin yang ( × ), is a commercially important poplar clone that is widely grown in northern China. An established transformation protocol for this interspecific hybrid enables researchers to simultaneously investigate the efficiency and specificity of the CRISPR/Cas9-mediated manipulation of a highly heterozygous genome. Using the phytoene desaturase gene () as an example, we revealed that the CRISPR/Cas9 system could efficiently edit the Shanxin yang genome. Two sgRNAs were designed and incorporated into a single binary vector containing the Cas9 expression cassette. Among 62 independent transgenic lines, 85.5% exhibited an exclusively albino phenotype, revealing the total loss of PDS function. The Illumina sequencing results confirmed the targeted mutation of homologs induced by CRISPR/Cas9, and small insertions/deletions were the most common mutations. Biallelic and homozygous knockout mutations were detected at both target sites of the T transformants. Off-target activity was detected for sgRNA2 with a frequency of 3.2%. Additionally, the SNP interference of targeting specificity was assessed based on the sequence variation among homologs. A single mismatch at 19- or 10-bp from the PAM was tolerated by the CRISPR/Cas9 system. Therefore, multiple homologous genes were simultaneously edited despite the presence of a mismatch between the sgRNA and the target site. The establishment of a viable CRISPR/Cas9-based strategy for editing the Shanxin yang genome will not only accelerate the breeding process, but may also be relevant for other economically or scientifically important non-model plants species.
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http://dx.doi.org/10.3389/fpls.2020.00996DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7347981PMC
July 2020

Fine mapping of the sex locus in confirms a consistent sex determination mechanism in genus .

Hortic Res 2020 1;7:64. Epub 2020 May 1.

The Key Lab of Cultivar Innovation and Germplasm Improvement of Salicaceae, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China.

belongs to section in genus , which is in a different section from the willow species in which sex determination has been well studied. Studying sex determination in distantly related willow species will help to clarify whether the sexes of different willows arise through a common sex determination system. For this purpose, we generated an intraspecific full-sib F population for and constructed high-density genetic linkage maps for the crossing parents using restriction site-associated DNA sequencing and following a two-way pseudo-testcross strategy. With the established maps, the sex locus was positioned in linkage group XV only in the maternal map, and no sex linkage was detected in the paternal map. Consistent with previous findings in other willow species, our study showed that chromosome XV was the incipient sex chromosome and that females were the heterogametic sex in . Therefore, sex in this willow species is also determined through a ZW sex determination system. We further performed fine mapping in the vicinity of the sex locus with SSR markers. By comparing the physical and genetic distances for the target interval encompassing the sex determination gene confined by SSRs, severe recombination repression was revealed in the sex determination region in the female map. The recombination rate in the confined interval encompassing the sex locus was approximately eight-fold lower than the genome-wide average. This study provides critical information relevant to sex determination in .
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http://dx.doi.org/10.1038/s41438-020-0289-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7193568PMC
May 2020

The chromosome-scale assembly of the willow genome provides insight into Salicaceae genome evolution.

Hortic Res 2020 1;7:45. Epub 2020 Apr 1.

1Key Laboratory for Tree Breeding and Germplasm Improvement, Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China.

is an early-flowering shrub willow that provides a desirable system for studies on the basic biology of woody plants. The current reference genome of was assembled with 454 sequencing reads. Here, we report a chromosome-scale assembly of generated by combining PacBio sequencing with Hi-C technologies. The obtained genome assemblies covered a total length of 356 Mb. The contig N50 of these assemblies was 263,908 bp, which was ~65-fold higher than that reported previously. The contiguity and completeness of the genome were significantly improved. By applying Hi-C data, 339.67 Mb (95.29%) of the assembled sequences were allocated to the 19 chromosomes of haploid willow. With the chromosome-scale assembly, we revealed a series of major chromosomal fissions and fusions that explain the genome divergence between the sister genera of and . The more complete and accurate willow reference genome obtained in this study provides a fundamental resource for studying many genetic and genomic characteristics of woody plants.
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http://dx.doi.org/10.1038/s41438-020-0268-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7109076PMC
April 2020

Characterization, Expression Profiling, and Functional Analysis of , a Defensin-Encoding Gene From .

Front Microbiol 2020 7;11:106. Epub 2020 Feb 7.

Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and Environment, Nanjing Forestry University, Nanjing, China.

PtDef cloned from contained eight cysteine domains specific to defensins. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis showed that was expressed in all tissues tested, with lower expression in leaves and higher expression in petioles, stems, and roots. Purified fused PtDef inhibited , , , , sp., and . PtDef also inhibited the growth of by triggering autolysis. overexpression in Nanlin895 poplar ( × cv. Nanlin895) enhanced the level of resistance to qRT-PCR analysis also showed that the expression of 13 genes related to salicylic acid (SA) and jasmonic acid (JA) signal transduction differed between transgenic and wild-type (WT) poplars before and after inoculation, and that (12-72 h), , , and expression was higher in transgenic poplars than in WT. During the hypersensitivity response (HR), large amounts of HO were produced by the poplar lines, particularly 12-24 h after inoculation; the rate and magnitude of the HO concentration increase were greater in transgenic lines than in WT. Overall, our findings suggest that , a defensin-encoding gene of , could be used for genetic engineering of woody plants for enhanced disease resistance.
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http://dx.doi.org/10.3389/fmicb.2020.00106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7018670PMC
February 2020

Pathways to sex determination in plants: how many roads lead to Rome?

Curr Opin Plant Biol 2020 04 25;54:61-68. Epub 2020 Feb 25.

Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA. Electronic address:

The presence of thousands of independent origins of dioecy in angiosperms provides a unique opportunity to address the parallel evolution of the molecular pathways underlying unisexual flowers. Recent progress towards identifying sex determination genes has identified hormone response pathways, mainly associated with cytokinin and ethylene response pathways, as having been recruited multiple times independently to control unisexuality. Moreover, transcriptomics has begun to identify commonalities among intermediate sections of signal transduction pathways. These recent advances set the stage for development of a comparative evolutionary development research program to identify the shared and unique aspects of the genetic pathways of unisexual flower development in angiosperms.
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http://dx.doi.org/10.1016/j.pbi.2020.01.004DOI Listing
April 2020

Identification of Genes Underlying the Resistance to in an Gene Supercluster of the Genome.

Plant Dis 2020 Apr 12;104(4):1133-1143. Epub 2020 Feb 12.

The Key Laboratory for Poplar Breeding and Germplasm Improvement, The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing 210037, China.

Identification of the particular genes in an genes supercluster underlying resistance to the rust fungus in poplar genome remains challenging. Based on the de novo assembly of the genome, all of the detected major genetic loci conferring resistance to were confined to a 3.5-Mb region on chromosome 19. The transcriptomes of the resistant and susceptible genotypes were sequenced for a timespan from 0 to 168 hours postinoculation. By mapping the differentially expressed genes to the target genomic region, we identified two constitutive expression genes and one inducible expression gene that might confer resistance to . Nucleotide variations were predicted based on the reconstructed haplotypes for each allele of the candidate genes. We also confirmed that salicylic acid was the phytohormone mediating signal transduction pathways, and was identified as a key gene inhibiting rust reproduction. Finally, quantitative reverse transcription PCR assay revealed consistent expressions with the RNA-sequencing data for the detected key genes. This study presents an efficient approach for the identification of particular genes underlying phenotype of interest by the combination of genetic mapping, transcriptome profiling, and candidate gene sequences dissection. The identified key genes would be useful for host resistance diagnosis and for molecular breeding of elite poplar cultivars exhibiting resistance to infection. The detected genes are also valuable for testing whether the combination of individual genes can induce durable quantitative resistance.
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http://dx.doi.org/10.1094/PDIS-08-19-1699-REDOI Listing
April 2020

Genome-wide identification and characterization of the MADS-box gene family in .

PeerJ 2019 7;7:e8019. Epub 2019 Nov 7.

Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.

MADS-box genes encode transcription factors that participate in various plant growth and development processes, particularly floral organogenesis. To date, MADS-box genes have been reported in many species, the completion of the sequence of the willow genome provides us with the opportunity to conduct a comprehensive analysis of the willow MADS-box gene family. Here, we identified 60 willow MADS-box genes using bioinformatics-based methods and classified them into 22 M-type (11 Mα, seven Mβ and four Mγ) and 38 MIKC-type (32 MIKCc and six MIKC*) genes based on a phylogenetic analysis. Fifty-six of the 60 SsMADS genes were randomly distributed on 19 putative willow chromosomes. By combining gene structure analysis with evolutionary analysis, we found that the MIKC-type genes were more conserved and played a more important role in willow growth. Further study showed that the MIKC* type was a transition between the M-type and MIKC-type. Additionally, the number of MADS-box genes in gymnosperms was notably lower than that in angiosperms. Finally, the expression profiles of these willow MADS-box genes were analysed in five different tissues (root, stem, leave, bud and bark) and validated by RT-qPCR experiments. This study is the first genome-wide analysis of the willow MADS-box gene family, and the results establish a basis for further functional studies of willow MADS-box genes and serve as a reference for related studies of other woody plants.
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http://dx.doi.org/10.7717/peerj.8019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6842560PMC
November 2019

Phylogenomics of the genus Populus reveals extensive interspecific gene flow and balancing selection.

New Phytol 2020 02 31;225(3):1370-1382. Epub 2019 Oct 31.

Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.

Phylogenetic analysis is complicated by interspecific gene flow and the presence of shared ancestral polymorphisms, particularly those maintained by balancing selection. In this study, we aimed to examine the prevalence of these factors during the diversification of Populus, a model tree genus in the Northern Hemisphere. We constructed phylogenetic trees of 29 Populus taxa using 80 individuals based on re-sequenced genomes. Our species tree analyses recovered four main clades in the genus based on consensus nuclear phylogenies, but in conflict with the plastome phylogeny. A few interspecific relationships remained unresolved within the multiple-species clade because of inconsistent gene trees. Our results indicated that gene flow has been widespread within each clade and also occurred among the four clades during their early divergence. We identified 45 candidate genes with ancient polymorphisms maintained by balancing selection. These genes were mainly associated with mating compatibility, growth and stress resistance. Both gene flow and selection-mediated ancient polymorphisms are prevalent in the genus Populus. These are potentially important contributors to adaptive variation. Our results provide a framework for the diversification of model tree genus that will facilitate future comparative studies.
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http://dx.doi.org/10.1111/nph.16215DOI Listing
February 2020

Evaluation, characterization, expression profiling, and functional analysis of DXS and DXR genes of Populus trichocarpa.

Plant Physiol Biochem 2019 Sep 10;142:94-105. Epub 2019 Jun 10.

Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University. Nanjing, 210037, China. Electronic address:

1-Deoxy-D-xylulose-5-phosphate synthasse (DXS) and 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) are key enzymes in terpenoid biosynthesis. DXS catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate (DXP) from pyruvate and D-glyceraldehyde-3-phosphate. DXR catalyzes the formation of 2-C-methyl-D-erythritol 4-phosphate (MEP) from DXP. Previous studies of the DXS and DXR genes have focused on herbs, such as Arabidopsis thaliana, Salvia miltiorrhiza, and Amomum villosum, but few studies have been conducted on woody plants. For that reason, we chose Populus trichocarpa as a model woody plant for investigating the DXS and DXR genes. PtDXS exhibited the highest expression level in leaves and the lowest expression in roots. PtDXR showed maximum expression in young leaves, and the lowest expression in mature leaves. The expression profiles revealed by RT-PCR following different elicitor treatments such as abscisic acid, NaCl, PEG, HO, and cold stress showed that PtDXS and PtDXR were elicitor-responsive genes. Our results showed that the PtDXS gene exhibited diurnal changes, but PtDXR did not. Moreover, overexpression of PtDXR in transgenic poplars improved tolerance to abiotic and biotic stresses. Those results showed that the PtDXR encoded a functional protein, and widely participates in plant growth and development, stress physiological process.
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http://dx.doi.org/10.1016/j.plaphy.2019.05.034DOI Listing
September 2019

Corrigendum #2 to "VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity".

Biomed Res Int 2019 30;2019:2150291. Epub 2019 May 30.

The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, Jiangsu 210037, China.

[This corrects the article DOI: 10.1155/2016/7823429.].
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http://dx.doi.org/10.1155/2019/2150291DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582879PMC
May 2019

Optimization of the Sequence Enhances the Hyper-Resistance of Transgenic Poplars to .

Front Plant Sci 2019 26;10:335. Epub 2019 Mar 26.

Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China.

Increased expression of the insect control protein genes of in has been critical to the development of genetically improved plants with agronomically acceptable levels of insect resistance. () proteins with highly specific toxicity against were screened using an indoor bioactivity assay to obtain hyper-resistant transgenic poplars. Then, the sequence was optimized and transformed according to the optimal codon in poplar using software of our own design (http://120.79.60.226:8080/u/chen/w/codonpoplar). A vector was constructed to transform poplar NL895. The gene was transformed to poplar NL895 and six transgenic lines were obtained. The expression and insecticidal effect of the gene in transgenic poplar were evaluated by PCR and ELISA, and the specific indoor activity and field insecticidal activity against . were compared with a control. We concluded that the insecticidal activity of the transgenic NL895 was significantly better against lower instar larvae of than against higher instar larvae. The mortality and pupation rates clearly differed among the various instar larvae and between transgenic and non-transgenic poplar. We obtained poplar seedlings with hyper-resistance to . by screening Bt genes and optimizing their genetic sequence.
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http://dx.doi.org/10.3389/fpls.2019.00335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6443852PMC
March 2019

Uneven selection pressure accelerating divergence of and .

Hortic Res 2019 6;6:37. Epub 2019 Apr 6.

The Key Laboratory for Cultivar Innovation and Germplasm Improvement for Salicaceae Species, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China.

(poplars) and (willows) are sister genera in the Salicaceae family that arise from a common tetraploid ancestor. The karyotypes of these two lineages are distinguished by two major interchromosomal and some minor intrachromosomal rearrangements, but which one is evolutionarily more primitive remains debatable. In this study, we compare the selection pressure acting on the paralogous genes resulting from salicoid duplication (PGRS) within and between the genomes of the two lineages. Purifying selection was determined to act more strongly on the PGRS in willow than on those in poplar, which would cause a faster loss of paralogous duplicates in willow. Therefore, species are supposed to evolve faster than species, which is consistent with the observation that the former are taxonomically and morphologically more diverse than the latter. In these two lineages, different autosomes were found to have been evolving into sex chromosomes. Examining the ω ratio and the PGRS in the sex determination regions in willow and poplar revealed higher convergent selection pressure and a faster loss of PGRS in the sex determination regions of both lineages. At the chromosome level, the sex chromosome in poplar is characterized by the lowest gene density among all chromosome members, while this feature is not observed on the sex chromosome in willow, suggesting that species may inherit the more incipient sex chromosome from their progenitor. Taken together, is supposed to be the nascent lineage arising from the additional round of genome reorganization that distinguishes the karyotypes of the two sister genera. In this study, assessment of ω ratios also detected a list of paralogous genes under unusual selection pressure, which could have special consequences for the adaptive evolution of Salicaceae species. In conclusion, the results of this study provide unique information for better understanding the genetic mechanism accelerating the divergence of these two closely related lineages.
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http://dx.doi.org/10.1038/s41438-019-0121-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450953PMC
April 2019

Hardwood Tree Genomics: Unlocking Woody Plant Biology.

Front Plant Sci 2018 17;9:1799. Epub 2018 Dec 17.

Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States.

Woody perennial angiosperms (i.e., hardwood trees) are polyphyletic in origin and occur in most angiosperm orders. Despite their independent origins, hardwoods have shared physiological, anatomical, and life history traits distinct from their herbaceous relatives. New high-throughput DNA sequencing platforms have provided access to numerous woody plant genomes beyond the early reference genomes of and , references that now include willow and oak, with pecan and chestnut soon to follow. Genomic studies within these diverse and undomesticated species have successfully linked genes to ecological, physiological, and developmental traits directly. Moreover, comparative genomic approaches are providing insights into speciation events while large-scale DNA resequencing of native collections is identifying population-level genetic diversity responsible for variation in key woody plant biology across and within species. Current research is focused on developing genomic prediction models for breeding, defining speciation and local adaptation, detecting and characterizing somatic mutations, revealing the mechanisms of gender determination and flowering, and application of systems biology approaches to model complex regulatory networks underlying quantitative traits. Emerging technologies such as single-molecule, long-read sequencing is being employed as additional woody plant species, and genotypes within species, are sequenced, thus enabling a comparative ("evo-devo") approach to understanding the unique biology of large woody plants. Resource availability, current genomic and genetic applications, new discoveries and predicted future developments are illustrated and discussed for poplar, eucalyptus, willow, oak, chestnut, and pecan.
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http://dx.doi.org/10.3389/fpls.2018.01799DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6304363PMC
December 2018

GEsture: an online hand-drawing tool for gene expression pattern search.

PeerJ 2018 20;6:e4927. Epub 2018 Jun 20.

College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu, China.

Gene expression profiling data provide useful information for the investigation of biological function and process. However, identifying a specific expression pattern from extensive time series gene expression data is not an easy task. Clustering, a popular method, is often used to classify similar expression genes, however, genes with a 'desirable' or 'user-defined' pattern cannot be efficiently detected by clustering methods. To address these limitations, we developed an online tool called GEsture. Users can draw, or graph a curve using a mouse instead of inputting abstract parameters of clustering methods. GEsture explores genes showing similar, opposite and time-delay expression patterns with a gene expression curve as input from time series datasets. We presented three examples that illustrate the capacity of GEsture in gene hunting while following users' requirements. GEsture also provides visualization tools (such as expression pattern figure, heat map and correlation network) to display the searching results. The result outputs may provide useful information for researchers to understand the targets, function and biological processes of the involved genes.
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http://dx.doi.org/10.7717/peerj.4927DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6015481PMC
June 2018

Functional analyses of PtRDM1 gene overexpression in poplars and evaluation of its effect on DNA methylation and response to salt stress.

Plant Physiol Biochem 2018 Jun 10;127:64-73. Epub 2018 Mar 10.

Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China. Electronic address:

Epigenetic modification by DNA methylation is necessary for all cellular processes, including genetic expression events, DNA repair, genomic imprinting and regulation of tissue development. It occurs almost exclusively at the C5 position of symmetric CpG and asymmetric CpHpG and CpHpH sites in genomic DNA. The RNA-directed DNA methylation (RDM1) gene is crucial for heterochromatin and DNA methylation. We overexpressed PtRDM1 gene from Populus trichocarpa to amplify transcripts of orthologous RDM1 in 'Nanlin895' (P. deltoides × P. euramericana 'Nanlin895'). This overexpression resulted in increasing RDM1 transcript levels: by ∼150% at 0 mM NaCl treatment and by ∼300% at 60 mM NaCl treatment compared to WT (control) poplars. Genomic cytosine methylation was monitored within 5.8S rDNA and histone H3 loci by bisulfite sequencing. In total, transgenic poplars revealed more DNA methylation than WT plants. In our results, roots revealed more methylated CG contexts than stems and leaves whereas, histone H3 presented more DNA methylation than 5.8S rDNA in both WT and transgenic poplars. The NaCl stresses enhanced more DNA methylation in transgenic poplars than WT plants through histone H3 and 5.8 rDNA loci. Also, the overexpression of PtRDM1 resulted in hyper-methylation, which affected plant phenotype. Transgenic poplars revealed significantly more regeneration of roots than WT poplars via NaCl treatments. Our results proved that RDM1 protein enhanced the DNA methylation by chromatin remodeling (e.g. histone H3) more than repetitive DNA sequences (e.g. 5.8S rDNA).
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http://dx.doi.org/10.1016/j.plaphy.2018.03.011DOI Listing
June 2018

Organellar genome assembly methods and comparative analysis of horticultural plants.

Hortic Res 2018 10;5. Epub 2018 Jan 10.

1College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu China.

Although organellar genomes (including chloroplast and mitochondrial genomes) are smaller than nuclear genomes in size and gene number, organellar genomes are very important for the investigation of plant evolution and molecular ecology mechanisms. Few studies have focused on the organellar genomes of horticultural plants. Approximately 1193 chloroplast genomes and 199 mitochondrial genomes of land plants are available in the National Center for Biotechnology Information (NCBI), of which only 39 are from horticultural plants. In this paper, we report an innovative and efficient method for high-quality horticultural organellar genome assembly from next-generation sequencing (NGS) data. Sequencing reads were first assembled by Newbler, Amos, and Minimus software with default parameters. The remaining gaps were then filled through BLASTN search and PCR. The complete DNA sequence was corrected based on Illumina sequencing data using BWA (Burrows-Wheeler Alignment tool) software. The advantage of this approach is that there is no need to isolate organellar DNA from total DNA during sample preparation. Using this procedure, the complete mitochondrial and chloroplast genomes of an ornamental plant, , and a fruit tree, , were identified. This study shows that horticultural plants have similar mitochondrial and chloroplast sequence organization to other seed plants. Most horticultural plants demonstrate a slight bias toward A+T rich features in the mitochondrial genome. In addition, a phylogenetic analysis of 39 horticultural plants based on 15 protein-coding genes showed that some mitochondrial genes are horizontally transferred from chloroplast DNA. Our study will provide an important reference for organellar genome assembly in other horticultural plants. Furthermore, phylogenetic analysis of the organellar genomes of horticultural plants could accurately clarify the unanticipated relationships among these plants.
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http://dx.doi.org/10.1038/s41438-017-0002-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798811PMC
January 2018

L1-Norm Distance Minimization-Based Fast Robust Twin Support Vector $k$ -Plane Clustering.

IEEE Trans Neural Netw Learn Syst 2018 09 3;29(9):4494-4503. Epub 2017 Oct 3.

Twin support vector clustering (TWSVC) is a recently proposed powerful k-plane clustering method. It, however, is prone to outliers due to the utilization of squared L2-norm distance. Besides, TWSVC is computationally expensive, attributing to the need of solving a series of constrained quadratic programming problems (CQPPs) in learning each clustering plane. To address these problems, this brief first develops a new k-plane clustering method called L1-norm distance minimization-based robust TWSVC by using robust L1-norm distance. To achieve this objective, we propose a novel iterative algorithm. In each iteration of the algorithm, one CQPP is solved. To speed up the computation of TWSVC and simultaneously inherit the merit of robustness, we further propose Fast RTWSVC and design an effective iterative algorithm to optimize it. Only a system of linear equations needs to be computed in each iteration. These characteristics make our methods more powerful and efficient than TWSVC. We also conduct some insightful analysis on the existence of local minimum and the convergence of the proposed algorithms. Theoretical insights and effectiveness of our methods are further supported by promising experimental results.
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http://dx.doi.org/10.1109/TNNLS.2017.2749428DOI Listing
September 2018

A Highly Dense Genetic Map for Constructed Using Sequence-Based Markers.

Front Plant Sci 2017 15;8:1041. Epub 2017 Jun 15.

Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry UniversityNanjing, China.

L. is a well-known living gymnosperm fossil that has medicinal and ornamental value. In this study, a high density genetic map was constructed with megagametophytes of 94 seeds from a single tree by employing the specific-locus amplified fragment (SLAF) sequencing technique. The average sequencing depth was 11.20×, which yielded 538,031 high-quality SLAFs. Among these SLAFs, 204,361 were heterozygous in the maternal tree and segregated in the progeny. The established map contained 12,263 SLAFs that were assigned to 12 linkage groups (LGs). The number of LGs on this map equaled the number of chromosomes in . The total map length was 1,671.77 cM, with an average distance of 0.89 cM between adjacent marker bins. Map evaluation based on the haplotype map and the heat map validated the high quality of the established map. Because is an economically and biologically important tree, strenuous efforts have been exerted to sequence its genome. This new map, built using sequence-based markers, will serve in the future as a fundamental platform for anchoring sequence assemblies along chromosomes. This map also provides a desirable platform for various genetic studies of , including gene/quantitative trait locus mapping and marker-aided selection.
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http://dx.doi.org/10.3389/fpls.2017.01041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5471298PMC
June 2017

Detecting the Candidate Gender Determinants by Bioinformatic Prediction of miRNAs and Their Targets from Transcriptome Sequences of the Male and Female Flowers in .

Biomed Res Int 2017 30;2017:9614596. Epub 2017 May 30.

Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.

MicroRNAs (miRNAs) belong to a class of small, noncoding, and endogenous single-stranded RNAs that negatively regulate gene expression at the posttranscriptional level. Potential miRNAs can be identified based on sequence homology since miRNAs are highly conserved in plants. In this study, we aligned the expressed sequence tags derived from flower buds of male and female to miRNAs in the miRBase, which enable us to identify 34 potential miRNAs from flower buds of the alternate sexes. Among them, 11 were from the female and 23 were from the male. Analyzing sequence complementarity led to identification of 124 and 55 miRNA targets in the male and female flower buds, respectively. By mapping the target genes of the predicted miRNAs to the sequence assemblies of , a miR156 mediated gene was detected at the gender locus of willow, which was a transcription factor involved in flower development. It is noteworthy that this target is not expressed in male flower, while it is expressed fairly highly in female flower based on the transcriptome data derived from the alternate sexes of willows. This study provides new bioinformatic clue for further exploring the genetic mechanism underlying gender determination in willows.
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http://dx.doi.org/10.1155/2017/9614596DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5468582PMC
September 2018