Xiaogang Dai

The willow genome and divergent evolution from poplar after the common genome duplication

Willows (Salix) and poplars (Populus) are known worldwide as woody species with diverse uses. Although these two genera diverged from each other around the early Eocene, they share numerous traits, including the same chromosome number of 2n = 38 and the common ‘Salicoid’ genome duplication with a high macrosynteny. However, most willow species flower early in their lives with short, small and sometimes indistinct stems, and thus differ from poplars in their life histories and habits. In addition, multiple inter- and intrachromosomal rearrangements have been detected involving chromosomal regions present in both lineages, suggestive of the likely genomic divergence after the common genome duplication.

Different autosomes evolved into sex chromosomes in the sister genera of Salix and Populus

Willows (Salix) and poplars (Populus) are dioecious plants in Salicaceae family. Sex chromosome in poplar genome was consistently reported to be associated with chromosome XIX. In contrast to poplar, this study revealed that chromosome XV was sex chromosome in willow. Previous studies revealed that both ZZ/ZW and XX/XY sex-determining systems could be present in some species of Populus. In this study, sex of S. suchowensis was found to be determined by the ZW system in which the female was the heterogametic gender. Gene syntenic and collinear comparisons revealed macrosynteny between sex chromosomes and the corresponding autosomes between these two lineages. By contrast, no syntenic segments were found to be shared between poplars and willows sex chromosomes. Syntenic analysis also revealed substantial chromosome rearrangements between willows alternate sex chromatids. Since willow and poplar originate from a common ancestor, we proposed that evolution of autosomes into sex chromosomes in these two lineages occurred after their divergence. Results of this study indicate that sex chromosomes in Salicaceae are still at the early stage of evolutionary divergence. Additionally, this study provided valuable information for better understanding the genetics and evolution of sex chromosome in dioecious plants.

DNA fingerprinting of oil camellia cultivars with SSR markers

Oil camellia (Camellia oleifera Abel.) is a widely cultivated economically important plant. In China, more than 100 elite cultivars have been authorized for commercial plantations, representing the developmental base for the oil camellia industry. Since oil camellia seedlings are frequently traded and introduced to new places, there is an active demand to develop a rapid and reliable identification toolkit to protect and ensure the effective use of these resources. In this study, ten highly polymorphic simple sequence repeat (SSR) primer pairs were screened from the SSR primer database of oil camellia, and DNA fingerprints of 128 elite oil camellia cultivars were constructed with these primer pairs. By analyzing the fingerprinting profiles, all of these cultivars were found to have unique DNA fingerprints, except ‘Changlin 40’ and ‘Fuyang 40’, which shared a complete similarity across all of the fingerprints generated by these ten SSR primer pairs, indicating that they were either synonyms or vegetative mutants. Synonyms are a major source of confusion in protecting and managing new varieties of plants. Although the synonymy of these two cultivars needs to be further confirmed, our data indicated a high possibility of synonyms among the authorized oil camellia cultivars. This study provides a desirable genetic toolkit for the identification and management of the elite oil camellia cultivars, and also for the intellectual property right protection of breeders.

Differential retention and expansion of the ancestral genes associated with the paleopolyploidies in modern rosid plants, as revealed by analysis of the extensins super-gene family.

BackgroundAll modern rosids originated from a common hexapolyploid ancestor, and the genomes of some rosids have undergone one or more cycles of paleopolyploidy. After the duplication of the ancient genome, wholesale gene loss and gene subfunctionalization has occurred. Using the extensin super-gene family as an example, we tracked the differential retention and expansion of ancestral extensin genes in four modern rosids, Arabidopsis, Populus, Vitis and Carica, using several analytical methods.ResultsThe majority of extensin genes in each of the modern rosids were found to originate from different ancestral genes. In Arabidopsis and Populus, almost half of the extensins were paralogous duplicates within the genome of each species. By contrast, no paralogous extensins were detected in Vitis and Carica, which have only undergone the common γ-triplication event. It was noteworthy that a group of extensins containing the IPR006706 domain had actively duplicated in Arabidopsis, giving rise to a neo-extensin around every 3 million years. However, such extensins were absent from, or rare in, the other three rosids. A detailed examination revealed that this group of extensins had proliferated significantly in the genomes of a number of species in the Brassicaceae. We propose that this group of extensins might play important roles in the biology and in the evolution of the Brassicaceae. Our analyses also revealed that nearly all of the paralogous and orthologous extensin-pairs have been under strong purifying selection, leading to the strong conservation of the function of extensins duplicated from the same ancestral gene.ConclusionsOur analyses show that extensins originating from a common ancestor have been differentially retained and expanded among four modern rosids. Our findings suggest that, if Arabidopsis is used as the model plant, we can only learn a limited amount about the functions of a particular gene family. These results also provide an example of how it is essential to learn the origination of a gene when analyzing its function across different plant species.

VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity

Background. In order to understand the colocalization of genetic loci amongst species, synteny and collinearity analysis is a frequent task in comparative genomics research. However many analysis software packages are not effective in visualizing results. Problems include lack of graphic visualization, simple representation, or inextensible format of outputs. Moreover, higher throughput sequencing technology requires higher resolution image output. Implementation. To fill this gap, this paper publishes VGSC, the Vector Graph toolkit of genome Synteny and Collinearity, and its online service, to visualize the synteny and collinearity in the common graphical format, including both raster (JPEG, Bitmap, and PNG) and vector graphic (SVG, EPS, and PDF). Result. Users can upload sequence alignments from blast and collinearity relationship from the synteny analysis tools. The website can generate the vector or raster graphical results automatically. We also provide a java-based bytecode binary to enable the command-line execution.

Corrigendum to “VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity”

[This corrects the article DOI: 10.1155/2016/7823429.].

GESearch: An Interactive GUI Tool for Identifying Gene Expression Signature

The huge amount of gene expression data generated by microarray and next-generation sequencing technologies present challenges to exploit their biological meanings. When searching for the coexpression genes, the data mining process is largely affected by selection of algorithms. Thus, it is highly desirable to provide multiple options of algorithms in the user-friendly analytical toolkit to explore the gene expression signatures. For this purpose, we developed GESearch, an interactive graphical user interface (GUI) toolkit, which is written in MATLAB and supports a variety of gene expression data files. This analytical toolkit provides four models, including the mean, the regression, the delegate, and the ensemble models, to identify the coexpression genes, and enables the users to filter data and to select gene expression patterns by browsing the display window or by importing knowledge-based genes. Subsequently, the utility of this analytical toolkit is demonstrated by analyzing two sets of real-life microarray datasets from cell-cycle experiments. Overall, we have developed an interactive GUI toolkit that allows for choosing multiple algorithms for analyzing the gene expression signatures.

Molecular discrimination and ploidy level determination for elite willow cultivars

Willow (Salix spp.), a woody plant in forms of tree, sub-tree, or shrub, has long been cultivated as an important fiber resource and for environmental protection. To manage commercial willow plantations, there is an increasing demand for the genetic discrimination of willow cultivars based on molecular markers. In this study, based on the genomic sequences of Salix suchowensis, a core set of 16 highly polymorphic simple sequence repeat (SSR) primer pairs were selected for the molecular discrimination of different willow cultivars. Using these primer pairs, DNA fingerprints of a collection of 25 elite willow cultivars were generated and their genetic identities were analyzed based on the SSR genotyping profiles and the UPGMA clustering. Subsequently, we examined the ploidy levels of these cultivars by combining SSR marker genotyping with flow cytometry measurements. It was found that, in this collection, the shrub cultivars were mainly presented as diploids, while cultivars in tree form mainly existed as polyploids. This study established a reference DNA fingerprinting database for managing the commercial willow cultivars, and the determination of their ploidy levels provided critical information for aiding the polyploid breeding programs in willows.