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Shrub willows are widely planted for landscaping, soil remediation, and biomass production, due to their rapid growth rates. Identification of regulatory genes in wood formation would provide clues for genetic engineering of willows for improved growth traits on marginal lands. Here, we conducted an expression quantitative trait locus (eQTL) analysis, using a full sibling F1 population of Salix suchowensis, to explore the genetic mechanisms underlying wood formation. Based on variants identified from simplified genome sequencing and gene expression data from RNA sequencing, 16,487 eQTL blocks controlling 5505 genes were identified, including 2148 cis-eQTLs and 16,480 trans-eQTLs. eQTL hotspots were identified, based on eQTL frequency in genomic windows, revealing one hotspot controlling genes involved in wood formation regulation. Regulatory networks were further constructed, resulting in the identification of key regulatory genes, including three transcription factors (JAZ1, HAT22, MYB36) and CLV1, BAM1, CYCB2;4, CDKB2;1, associated with the proliferation and differentiation activity of cambium cells. The enrichment of genes in plant hormone pathways indicates their critical roles in the regulation of wood formation. Our analyses provide a significant groundwork for a comprehensive understanding of the regulatory network of wood formation in S. suchowensis. [ABSTRACT FROM AUTHOR]

Willows, in the genus Salix, are widespread on the earth with significant ecological and economic values for humans. Although about 500 Salix species have been estimated, the genomic foundation of their adaptations to environments with diverse stresses has been underexplored. Here, we applied a pan-transcriptome approach to investigate the phylogenetic relationships and genetic variations among 16 willow species. A pan-transcriptome of 29,668 gene families was assembled, 69% of which exhibited presence/absence variation across the analyzed species. In comparison to core genes present in all species, shell gene families absent in at least one species were enriched with genes in pathways of signaling transduction and response to stimuli, suggesting their functions in the interaction with diverse environmental factors. A phylogenetic tree of 16 willow species was constructed with high confidence based on 870 single-copy orthologous genes, providing detailed evolutionary relationships of willow sections. The willow species were further assigned into four species clusters using the gene numbers in each family. The diversity of gene family size and gene expression levels among the willow species are closely associated with their geographical distributions. The gene family members involved in DNA repair and cellular response to DNA damage stimuli were expanded in willow species from high-altitude regions in southwestern China, which may contribute to their tolerance to ultraviolet radiation stress. Our study generates a comprehensive pan-transcriptome resource for a large set of Salix species and provides insights into the adaptations of willows to diverse environments, which will be valuable for comparative analysis with other related woody and herbaceous plants. [ABSTRACT FROM AUTHOR]

Many willow species, especially the short-rotation coppice willows, are suitable for development into renewable bioenergy crops. In this study, we conducted high-throughput transcriptome sequencing of a shrub willow, S. suchowensis, to generate expressed sequence tags ( ESTs) for gene discovery and molecular marker development. Totally, 136.1 million clean reads were generated from five different tissues of S. suchowensis using Illumina RNA-seq technology. De novo sequence assembly produced 90 269 unigenes, among which 64 127 unigenes were annotated in one or more of the NR, Swiss-Prot, GO, COG and KEGG databases. A total of 21 052 simple sequence repeats were identified in the expressed sequence assemblies, and a primer database containing 36 912 EST- SSR markers were developed for 12 304 SSR loci. Subsequently, 25 primers were randomly selected for experimental test. Among which, 24 primers succeeded in PCR amplification and 21 produced amplicons in expected sizes, suggesting that the sequence assemblies were of high quality. The established sequence database and marker resource are useful for different aspects of genetic studies on Salix spp., and particularly valuable for marker-assisted breeding of willows. [ABSTRACT FROM AUTHOR]

The complete nucleotide sequences of the mitochondrial (mt) genome of an extremophile species Thellungiella parvula (T. parvula) have been determined with the lengths of 255,773 bp. T. parvula mt genome is a circular sequence and contains 32 protein-coding genes, 19 tRNA genes, and three ribosomal RNA genes with a 11.5% coding sequence. The base composition of 27.5% A, 27.5% T, 22.7% C, and 22.3% G in descending order shows a slight bias of 55% AT. Fifty-three repeats were identified in the mitochondrial genome of T. parvula, including 24 direct repeats, 28 tandem repeats (TRs), and one palindromic repeat. Furthermore, a total of 199 perfect microsatellites have been mined with a high A/T content (83.1%) through simple sequence repeat (SSR) analysis and they were distributed unevenly within this mitochondrial genome. We also analyzed other plant mitochondrial genomes’ evolution in general, providing clues for the understanding of the evolution of organelles genomes in plants. Comparing with other Brassicaceae species, T. parvula is related to Arabidopsis thaliana whose characters of low temperature resistance have been well documented. This study will provide important genetic tools for other Brassicaceae species research and improve yields of economically important plants. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

A letter to the editor is presented on a study conducted on common genome duplication in willow genome and poplar genome.

Gene introgression and hybrid barriers have long been a major focus of studies of geographically overlapping species. Two pine species, Pinus massoniana and P. hwangshanensis, are frequently observed growing adjacent to each other, where they overlap in a narrow hybrid zone. As a consequence, these species constitute an ideal system for studying genetic introgression and reproductive barriers between naturally hybridizing, adjacently distributed species. In this study, we sampled 270 pine trees along an elevation gradient in Anhui Province, China and analyzed these samples using EST-SSR markers. The molecular data revealed that direct gene flow between the two species was fairly low, and that the majority of gene introgression was intermediated by backcrossing. On the basis of empirical observation, the on-site distribution of pines was divided into a P. massoniana zone, a hybrid zone, and a P. hwangshanensis zone. STRUCTURE analysis revealed the existence of a distinct species boundary between the two pine species. The genetic boundary of the hybrid zone, on the other hand, was indistinct owing to intensive backcrossing with parental species. Compared with P. massoniana, P. hwangshanensis was found to backcross with the hybrids more intensively, consistent with the observation that morphological and anatomical characteristics of trees in the contact zone were biased towards P. hwangshanensis. The introgression ability of amplified alleles varied across species, with some being completely blocked from interspecific introgression. Our study has provided a living example to help explain the persistence of adjacently distributed species coexisting with their interfertile hybrids. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome ofMedicago truncatula(M. truncatula) was reported in this study. The mitochondrial genome (mitogenome) was assembled to 271 618 nt. The mitogenome contains 31 protein-coding genes, three rRNA genes and 16 tRNAs. The overall base composition of the mitogenome in descending order is A: 27.21%, C: 22.61%, G: 22.78% and T: 27.40%, and the G + C content is 45.39%. Additionally, 30 exons and 17 introns were identified in eight genes and nine tandem repeats were identified with the period size from 10 nt to 33 nt. Phylogenetic analysis shows that theM. truncatulagenome is evolutionarily closest to that of Lotus japonicas. With the complete mitogenome ofM. truncatula, it is beneficial to the further research of mitogenome of seed plants, and especially helpful for elucidating vital activities of legumes. [ABSTRACT FROM PUBLISHER]

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 poplar's and willow's sex chromosomes. Syntenic analysis also revealed substantial chromosome rearrangements between willow's 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. [ABSTRACT FROM AUTHOR]