The application of microwave denaturation in comparative genomic hybridization

AnWRKY29 and AnHSP90 synergistically modulate trehalose levels in a desert shrub leaves during osmotic stress

Trehalose, a biological macromolecule with osmotic adjustment properties, plays a crucial role during osmotic stress. As a psammophyte, Ammopiptanthus nanus relies on the accumulation of organic solutes to respond to osmotic stress. We utilized virus-induced gene silencing technology for the first time in the desert shrub A. nanus to confirm the central regulatory role of AnWRKY29 in osmotic stress, as it controls the transcription of AnTPS11 (trehalose-6-phosphate synthase 11). Further investigation has shown that AnHSP90 may interact with AnWRKY29. The AnHSP90 gene is sensitive to osmotic stress, underscoring its pivotal role in orchestrating the response to such adverse conditions. By directly targeting the W-box element within the AnTPS11 promoter, AnWRKY29 effectively enhances the transcriptional activity of AnTPS11, which is facilitated by AnHSP90. This discovery highlights the critical role of AnWRKY29 and AnHSP90 in enabling organisms to adapt to and cope effectively with osmotic stress, which can be a crucial factor in A. nanus survival and overall ecological resilience. Collectively, uncovering the molecular mechanisms underlying the osmotic responses of A. nanus is paramount for comprehending and augmenting the osmotic tolerance mechanisms of psammophyte shrub plants.

Signal and regulatory mechanisms involved in spore development of Phytophthora and Peronophythora

Oomycetes cause hundreds of destructive plant diseases, threatening agricultural production and food security. These fungus-like eukaryotes show multiple sporulation pattern including the production of sporangium, zoospore, chlamydospore and oospore, which are critical for their survival, dispersal and infection on hosts. Recently, genomic and genetic technologies have greatly promoted the study of molecular mechanism of sporulation in the genus Phytophthora and Peronophythora. In this paper, we characterize the types of asexual and sexual spores and review latest progress of these two genera. We summarize the genes encoding G protein, mitogen-activated protein kinase (MAPK) cascade, transcription factors, RNA-binding protein, autophagy-related proteins and so on, which function in the processes of sporangium production and cleavage, zoospore behaviors and oospore formation. Meanwhile, various molecular, chemical and electrical stimuli in zoospore behaviors are also discussed. Finally, with the molecular mechanism of sporulation in Phytophthora and Peronophythora is gradually being revealed, we propose some thoughts for the further research and provide the alternative strategy for plant protection against phytopathogenic oomycetes.

Phylogeography of Amygdalus mongolica in relation to Quaternary climatic aridification and oscillations in northwestern China

Quaternary period geological events and climatic oscillations significantly affect the geographic structure and genetic diversity of species distribution in arid northwestern China. Amygdalus mongolica is a relict and endangered shrub that occurs primarily in arid areas of northwestern China. Based on variation patterns present at three cpDNA regions (psbK-psbI, trnL-trnF and trnV) and in one nDNA sequence (ITS1-ITS4) in 174 individuals representing 15 populations, the spatial genetic structure and demographic history of A. mongolica was examined across its entire geographic range. The 17 different haplotypes and 10 ribotypes showed two lineages, distributed across the Western (Mazong Mountains, Hexi Corridor, and Alxa Left Banner) and Eastern regions (Urad Houqi, Yinshan Mountains, Urad Zhongqi, and Daqing Mountains) according to the median-joining network and the BI (Bayesian inference) and ML (Maximum likelihood) trees. AMOVA analysis demonstrated that over 65% of the observed genetic variation was related to this lineage split. The expansions of the Ulanbuhe and Tengger deserts and the eastward extension of the Yinshan Mountains since the Quaternary period likely interrupted gene flow and triggered the observed divergence in the two allopatric regions; arid landscape fragmentation accompanied by local environmental heterogeneity further increased local adaptive differentiation between the Western and Eastern groups. Based on the evidence from phylogeographical patterns and the distribution of genetic variation, A. mongolica distributed in the eastern and western regions are speculated to have experienced eastward migration along the southern slopes of the Lang Mountains and westward migration along the margins of the Ulanbuhe and Tengger deserts to the Hexi Corridor, respectively. For setting a conservation management plan, it is recommended that the south slopes of the Lang Mountains and northern Helan Mountains be identified as the two primary conservation areas, as they have high genetic variation and habitats that are more suitable.

Dispersal into the Qinghai-Tibet plateau: evidence from the genetic structure and demography of the alpine plant Triosteum pinnatifidum

Triosteum pinnatifidum Maxim., an alpine plant, is traditionally used for several medicinal purposes. Here, both chloroplast DNA sequences and nuclear low copy sequence markers were used to investigate the genetic diversity and population structure of T. pinnatifidum. Materials were collected from thirteen localities in the northeast Qinghai-Tibet Plateau (QTP) and adjacent highlands and advanced analytical toolkits were used to access their origin and range shifts. The results revealed a higher level of population differentiation based on chloroplast DNA (cpDNA) concatenated sequences compared with the nuclear DNA sequences (F _ST = 0.654 for cpDNA, F _ST = 0.398 for AT103), indicating that pollen flow was still extensive in T. pinnatifidum. A decline in haplotype variation was observed from the plateau edge and adjoining highlands toward the platform of the QTP. The hypothesis "dispersal into the QTP," proposing that T. pinnatifidum experienced migration from the plateau edge and adjacent highlands to the platform, was supported. These results were in line with the hypothesis that multiple refugia exist on the plateau edge and adjacent highlands rather than on the plateau platform. Our unimodal mismatch distribution, star-like network supported a recent expansion in T. pinnatifidum.

Phylogeography of Prunus armeniaca L. revealed by chloroplast DNA and nuclear ribosomal sequences

To clarify the phytogeography of Prunus armeniaca L., two chloroplast DNA fragments (trnL-trnF and ycf1) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to assess genetic variation across 12 P. armeniaca populations. The results of cpDNA and ITS sequence data analysis showed a high the level of genetic diversity (cpDNA: H_T = 0.499; ITS: H_T = 0.876) and a low level of genetic differentiation (cpDNA: F_ST = 0.1628; ITS: F_ST = 0.0297) in P. armeniaca. Analysis of molecular variance (AMOVA) revealed that most of the genetic variation in P. armeniaca occurred among individuals within populations. The value of interpopulation differentiation (N_ST) was significantly higher than the number of substitution types (G_ST), indicating genealogical structure in P. armeniaca. P. armeniaca shared genotypes with related species and may be associated with them through continuous and extensive gene flow. The haplotypes/genotypes of cultivated apricot populations in Xinjiang, North China, and foreign apricot populations were mixed with large numbers of haplotypes/genotypes of wild apricot populations from the Ili River Valley. The wild apricot populations in the Ili River Valley contained the ancestral haplotypes/genotypes with the highest genetic diversity and were located in an area considered a potential glacial refugium for P. armeniaca. Since population expansion occurred 16.53 kyr ago, the area has provided a suitable climate for the population and protected the genetic diversity of P. armeniaca.

Effects of Mountain Uplift and Climatic Oscillations on Phylogeography and Species Divergence of Chamaesium (Apiaceae)

Exploring the effects of orographic events and climatic shifts on the geographic distribution of organisms in the Himalayas-Hengduan Mountains (HHM) region and Qinghai-Tibetan Plateau (QTP) is crucial to understand the impact of environmental changes on organism evolution. To gain further insight into these processes, we reconstructed the evolutionary history of nine Chamaesium species distributed across the HHM and QTP regions. In total, 525 individuals from 56 populations of the nine species were analyzed based on three maternally inherited chloroplast fragments (rpl16, trnT-trnL, and trnQ-rps16) and one nuclear DNA region (internal transcribed spacer, ITS). Fifty-two chloroplast DNA (cpDNA) and 47 ITS haplotypes were identified in nine species. All of the cpDNA and ITS haplotypes were species-specific. Phylogenetic analysis suggested that all nine species form a monophyletic clade with high support. Dating analysis and ancestral area reconstruction revealed that the ancestral group of Chamaesium originated in the southern Himalayan region at the beginning of the Paleogene (60.85 Ma). The nine species of Chamaesium then separated well during the last 25 million years started in Miocene. Our maxent modeling indicated the broad-scale distributions of all nine species remained fairly stable from LIG to the present and predicted that it will remain stable into the future. The initial split of Chamaesium was triggered by climate changes following the collision of the Indian plate with the Eurasia plate during the Eocene. Subsequently, divergences within Chamaesium may have been induced by the intense uplift of the QTP, the onset of the monsoon system, and Central Asian aridification. Long evolutionary history, sexual reproduction, and habitat fragmentation could contribute to the high level of genetic diversity of Chamaesium. The higher genetic differentiation among Chamaesium populations may be related to the drastic changes of the external environment in this region and limited seed/pollen dispersal capacity.

Molecular Phylogeography and Evolutionary History of the Endemic Species Corydalis hendersonii (Papaveraceae) on the Tibetan Plateau Inferred From Chloroplast DNA and ITS Sequence Variation

In response to past climatic changes, the species with different habits or adaptive traits likely have experienced very different evolutionary histories, especially for species that restricted to high mountain areas. In order to trace how Quaternary climatic oscillations affected range distributions and intraspecific divergence of such alpine plants on the Tibetan Plateau, here, we investigated maternally inherited chloroplast DNA (cpDNA) markers and biparentally inherited nuclear ribosomal internal transcribed spacer (ITS) DNA variations and aimed to explore the phylogeographic history of the endemic alpine species Corydalis hendersonii Hemsl. (Papaveraceae). We sequenced four cpDNA fragments (trnS-trnG, trnT-trnL, atpH-atpI, and psbE-petL) and also the nuclear (ITS) region in 368 individuals from 30 populations across the species' range. The network and phylogenetic analysis based on cpDNA variations identified 15 chlorotypes that cluster into three distinct clades. However, our nuclear DNA results demonstrated that there were four genetic/geographical groups within C. hendersonii. Some common and highly divergent cpDNA and ITS haplotypes were distributed in the populations of central and northeastern Tibetan Plateau, and the highest nucleotide diversity and genetic differentiation were detected in the central region. Demographic tests further indicated that the populations of southwestern and western Tibet may have experienced recent range expansion, which most likely occurred during the last glacial maximum (LGM) and continued its expansion after the beginning of the Holocene. These two different groups of this species may have derived from potential refugia that existed in the central and/or northeastern regions of Tibet during recent interglacial periods. In addition, our AMOVA analyses detected high genetic differentiation along with the whole sampling range. Also, distinct phylogeographic structures were detected among populations of C. hendersonii based on both of cpDNA and ITS variation. These findings shed new light on the importance of climatic oscillations during Quaternary and complex local topography as causes of intraspecific diversification and demographic changes within cold-tolerant herbs in the Tibetan Plateau biodiversity hotspot.

Population Differentiation and Demographic History of the Cycas taiwaniana Complex (Cycadaceae) Endemic to South China as Indicated by DNA Sequences and Microsatellite Markers

Historical geology, climatic oscillations, and seed dispersal capabilities are thought to influence the population dynamics and genetics of plants, especially for distribution-restricted and threatened species. Investigating the genetic resources within and among taxa is a prerequisite for conservation management. The Cycas taiwaniana complex consists of six endangered species that are endemic to South China. In this study, we investigated the relationship between phylogeographic history and the genetic structure of the C. taiwaniana complex. To estimate the phylogeographic history of the complex, we assessed the genetic structure and divergence time, and performed phylogenetic and demographic historical analyses. Two chloroplast DNA intergenic regions (cpDNA), two single-copy nuclear genes (SCNGs), and six microsatellite loci (SSR) were sequenced for 18 populations. The SCNG data indicated a high genetic diversity within populations, a low genetic diversity among populations, and significant genetic differentiation among populations. Significant phylogeographical structure was detected. Structure and phylogenetic analyses both revealed that the 18 populations of the C. taiwaniana complex have two main lineages, which were estimated to diverge in the Middle Pleistocene. We propose that Cycas fairylakea was incorporated into Cycas szechuanensis and that the other populations, which are mainly located on Hainan Island, merged into one lineage. Bayesian skyline plot analyses revealed that the C. taiwaniana complex experienced a recent decline, suggesting that the complex probably experienced a bottleneck event. We infer that the genetic structure of the C. taiwaniana complex has been affected by Pleistocene climate shifts, sea-level oscillations, and human activities. In addition to providing new insights into the evolutionary legacy of the genus, the genetic characterizations will be useful for the conservation of Cycas species.

High Genetic Diversity With Weak Phylogeographic Structure of the Invasive Spartina alterniflora (Poaceae) in China

Biological invasion represents a global issue of concern due to its large negative impacts on native ecosystems and society. Elucidating the evolutionary history and genetic basis underpinning invasiveness is critical to understanding how alien species invade and adapt to novel environments. Smooth cordgrass (Spartina alterniflora, 2n = 6x = 62) is a notorious invasive species that causes heavily negative effects on native ecosystems worldwide. Here we addressed the evolutionary mechanisms underlying the invasion and dispersal history of this species along the China coast in the past decades. We employed nine microsatellites and three chloroplast fragments to investigate phylogeographic structure and genetic diversity of 11 native US and 11 invasive Chinese S. alterniflora populations. Demographic history simulation was also performed for both the native and invasive populations, respectively. Comparative genetic analyses of these natural populations revealed that although all the Chinese populations were introduced only once, high level of genetic diversity with weak geographic structure was observed. In particular, both the genetic features and mathematical simulation illustrated very recent population expansion in the Chinese populations. We found that genetic variants identified in native US populations were mixed in the Chinese populations, suggesting the recombination of these original variants during the invasion process. These genetic attributes indicate that Chinese populations might not have experienced a genetic bottleneck during the invasion process. High genetic diversity and genetic admixture might have contributed to the success of invasion of S. alterniflora in China. Our study provides a framework of how the smooth cordgrass spreads along the China coast as well as its potential genetic mechanisms underlying the invasion.

Microwaves for chromogenic in situ hybridization

In situ hybridization can be employed in formalin-fixed, paraffin-embedded tissue sections (FFPT) and allows direct visualization of amplified genes and chromosomes in individual cell nuclei. Fluorescence in situ hybridization (FISH) is the most widely employed method, but the fluorescence preparations suffer from the main disadvantages of fading over time and poor visualization, the latter making it difficult to accurately separate invasive from in situ cancer cells. Chromogenic in situ hybridization (CISH) is a viable alternative to FISH in FFPT as it employs a peroxidase reaction to visualize the chromogen thus allowing the convenience of bright field microscopy and the correlation of the visualized gene amplification with cytomorphology. It is relatively less expensive and allows a permanent record, with several studies attesting to its validity. As with FISH, heat pretreatment and enzyme digestion are two critical components of the protocol. We describe a protocol for CISH in which a microwave-induced target retrieval step is introduced as a replacement for heat pretreatment. The same procedure is performed following enzyme digestion to produce consistent signals in amplified and nonamplified cells that are both larger in size and numbers when compared with those produced by the conventional protocol.

The effect of microwave irradiation on DNA hybridization

The effect of microwave irradiation on DNA/DNA hybridization has been studied under controlled power and temperature conditions. It was discovered that microwave irradiation led to the melting of double-stranded deoxyoligonucleotides well below their thermal melting temperature and independent of the length of the deoxyoligonucleotides. These observations indicate a specific interaction of microwaves with DNA, and have important implications in the chemical or enzymatic processing of DNA under microwave heating.

FISHing in the microwave: the easy way to preserve proteins. I. Colocalization of DNA probes and surface antigens in human leukocytes

Most of the techniques for simultaneous visualization of proteic cell components and DNA probes are difficult to carry out. We have developed an alternative protocol for simultaneous visualization of DNA probes and cell surface antigens in human cells. The method exploits microwave energy to denature DNA and to anneal the probe after antigen fluorescent detection of unfixed cells previously embedded in a microgel. CD3 antigens and whole genome DNA probes or specific repetitive DNA sequences were colocalized in peripheral blood samples. The results show a strong, specific and consistent hybridization pattern in each cell that allowed correlation between cell subtype (PROTEINS) and nuclear phenotype (DNA).

Comparative genomic hybridisation

Comparative genomic hybridisation (CGH) is a technique that permits the detection of chromosomal copy number changes without the need for cell culturing. It provides a global overview of chromosomal gains and losses throughout the whole genome of a tumour. Tumour DNA is labelled with a green fluorochrome, which is subsequently mixed (1:1) with red labelled normal DNA and hybridised to normal human metaphase preparations. The green and red labelled DNA fragments compete for hybridisation to their locus of origin on the chromosomes. The green to red fluorescence ratio measured along the chromosomal axis represents loss or gain of genetic material in the tumour at that specific locus. In addition to a fluorescence microscope, the technique requires a computer with dedicated image analysis software to perform the analysis. This review aims to provide a detailed discussion of the CGH technique, and to provide a protocol with an emphasis on crucial steps.

Progression from colorectal adenoma to carcinoma is associated with non-random chromosomal gains as detected by comparative genomic hybridisation

AIMS

Chromosomal gains and losses were surveyed by comparative genomic hybridisation (CGH) in a series of colorectal adenomas and carcinomas, in search of high risk genomic changes involved in colorectal carcinogenesis.

METHODS

Nine colorectal adenomas and 14 carcinomas were analysed by CGH, and DNA ploidy was assessed with both flow and image cytometry.

RESULTS

In the nine adenomas analysed, an average of 6.6 (range 1 to 11) chromosomal aberrations were identified. In the 14 carcinomas an average of 11.9 (range 5 to 17) events were found per tumour. In the adenomas the number of gains and losses was in balance (3.6 v 3.0) while in carcinomas gains occurred more often than losses (8.2 v 3.7). Frequent gains involved 13q, 7p, 8q, and 20q, whereas losses most often occurred at 18q, 4q, and 8p. Gains of 13q, 8q, and 20q, and loss of 18q occurred more often in carcinomas than in adenomas (p = 0.005, p = 0.05, p = 0.05, and p = 0.02, respectively). Aneuploid tumours showed more gains than losses (mean 9.3 v 4.9, p = 0.02), in contrast to diploid tumours where gains and losses were nearly balanced (mean 3.1 v 4.1, p = 0.5).

CONCLUSIONS

The most striking difference between chromosomal aberrations in colorectal adenomas and carcinomas, as detected by CGH, is an increased number of chromosomal gains that show a nonrandom distribution. Gains of 13q and also of 20q and 8q seem especially to be involved in the progression of adenomas to carcinomas, possibly owing to low level overexpression of oncogenes at these loci.

Assessment of chromosomal gains and losses in oral squamous cell carcinoma by comparative genomic hybridisation

Cytogenetic studies have demonstrated that oral squamous cell carcinomas (OSCCs) are usually characterised by complex karyotypes with many marker chromosomes. We analysed the genetic changes of six OSCC cell cultures by comparative genomic hybridisation (CGH). The CGH technique provides information on chromosomal gains and losses of the whole tumour genome in a single experiment and can therefore identify regions that harbour putative tumour suppressor genes (in the case of loss of chromosomal material) or oncogenes (in the case of gain or amplification of chromosomal material). Recurrent losses were detected at chromosome arms Xp and 3p (four cases). Gains consistently occurred at chromosome arms 8q and 9q (four cases) and at 1q, 3q, 5p, 7p, and 9p (three cases). The same six tumour cultures have previously been analysed by classical karyotyping. An important discrepancy between the two techniques was the number of losses detected: 55 with karyotyping versus 26 with CGH. On the basis of the cytogenetic complexity of these tumours and on FISH experiments that confirmed the CGH results, we conclude that genetic changes, particularly losses, can be more reliably detected by CGH analysis.