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Highlights • First PAH tolerance comparative analyses in Spartina. • Increased tolerance in the allopolyploid S. anglica compared to its parents. • Expression analysis of candidate GST genes (Tau family) in Spartina. • Allopolyploidization reprogrammed GST genes expression patterns under phenanthrene-induced stress. • The neo-allopolyploid S. anglica is a suitable candidate for phytoremediation. Abstract Genome doubling or polyploidy is a widespread phenomenon in plants where it has important evolutionary consequences affecting the species distribution and ecology. PAHs are ubiquitous organic pollutants, which represent a major environmental concern. Recent data showed that tolerance to organic xenobiotics involve specific signaling pathways, and detoxifying gene sets referred as 'the xenome'. However, no data are available about how polyploidy impacts tolerance to organic xenobiotics. In the present paper, we investigated PAH tolerance following allopolyploidization in Spartina alterniflora , S. maritima and their derived allopolyploid species S. anglica. We performed comparative analyses of cellular compartmentalization, photosynthetic indices, and oxidative stress markers under phenanthrene-induced stress, and found that S. anglica exhibit increased tolerance compared to its parents. Based on 52 genes potentially involved in phenanthrene detoxification previously identified in A. thaliana, we investigated the Spartina xenome using genomic and transcriptomic available resources. Subsequently, we focused on GSTs, a ubiquitous enzymes class involved in organic xenobiotic detoxification. We examined expression profiles of selected genes by RT-qPCR, and revealed various patterns of parental expression alteration in the allopolyploid. The impacts of allopolyploidization on phenanthrene-induced stress and their potential ecological implications are discussed. The neo-allopolyploid S. anglica appears as a potential candidate for phytoremediation in PAH-polluted marshes. [ABSTRACT FROM AUTHOR]

Whole genome duplications (WGDs), also known as polyploid events, have played a crucial role in the evolutionary success of angiosperms across recent and ancient timescales. A recurrent observation from the analysis of allopolyploids is that one of the parental subgenomes is generally more dominant, referred to as ‘subgenome dominance’, based on higher gene content and expression patterns. Subgenome dominance has far reaching implications to research areas ranging from crop improvement efforts to evolutionary and ecological studies. However, the analysis of subgenome dominance in more ancient polyploids is complicated by a long history of homoeologous exchanges among subgenomes. Here, we will discuss how resulting homoeolog rearrangements and replacements have been ignored in previous studies and urge future studies to integrate phylogenetic approaches to assign homoeologs to parental subgenomes. [ABSTRACT FROM AUTHOR]

A morphologically different, perennial and highly pungent Capsicum cultivar ‘Dalle Khursani’ is available in the Darjeeling district of West Bengal over many decades. Its counterpart in Sikkim was identified as polyploid Capsicum cultivar with 2n = 4x = 48 chromosomes. However, cytogenetical status of the cultivar growing in West Bengal was lacking. The present study has carried out extensive morphological, chromosomal and molecular analysis on seven ‘Dalle Khursani’ populations of West Bengal. Our results on flower morphology explicitly delimit ‘Dalle Khursani’ populations from the members of ‘ C. annuum complex’. Somatic and gametic chromosome analysis has clearly established their polyploid chromosome number 4x = 48 and allopolyploid nature of the cultivar (2n = 4x = 48). Fluorescent banding analysis with CMA revealed CMA + ve/DAPI-ve heterochromatin blocks in four ‘Dalle Khursani’ populations for the first time indicating the prevalence of GC rich heterochromatin in the studied taxon. RAPD based genomic DNA analysis has exhibited similar banding profile within the populations and their complete difference from the diploid members of ‘ C. annuum complex’. Our present studies in conformity with our earlier report have firmly established that allopolyploidy in Capsicum is not a rarity. It is available in Indian states and will help the Capsicum researchers and breeders in their future crop improvement programmes. [ABSTRACT FROM AUTHOR]

The formation of an allopolyploid species involves the merger of genomes with separate evolutionary histories and thereby different genomic legacies. Contrary to expectations from theory, genes from one are often lost preferentially in allopolyploids — there is biased fractionation. Here, we provide an overview of two ways in which the genomic legacies of the progenitors may impact the fate of duplicated genes in allopolyploids. Specifically, we discuss the role of homeolog expression biases in setting the stage for biased fractionation, and the evidence for transposable element silencing as a possible mechanism for homeolog expression biases. Finally, we highlight how differences between the progenitors with respect to accumulation of deleterious variation may affect trajectories of duplicate gene evolution in allopolyploids. [ABSTRACT FROM AUTHOR]

The chrysanthemums ( Chrysanthemum × morifolium Ramat.) are a well-known group of traditional ornamental flowers in China and have been cultivated all over the world. Yet the origin of chrysanthemum cultivars has been highly debated. In this study we employ the nuclear low-copy LFY gene to study the evolutionary history of chrysanthemum cultivars. The structure of the LFY gene in all Chrysanthemum species examined is highly conserved with three exons and two introns. The length of the LFY gene in Chrysanthemum varied from 2, 887 to 3, 348 bp. The two introns exhibited high levels of variation in length and sequence composition at the intraspecific and interspecific levels. Phylogenetic analysis of the whole LFY sequences of Chrysanthemum resulted in topologies that contained three major clades. The LFY sequences from the same cultivars are present in two or three clades, supporting that hybridization and allopolyploidy were important mechanisms in the origins of different chrysanthemums. Our results suggest that different cultivars had different ancestors. Chrysanthemum indicum , C. zawadskii and C. nankingense were likely the direct ancestors of most chrysanthemum cultivars examined. Chrysanthemum vestitum is a putative ancestor for some cultivars, and may have indirectly involved in the development of the chrysanthemum cultivars. Sequences of the LFY gene are informative to shed insights into the origin of chrysanthemum cultivars and show great potential as a phylogenetic marker to decipher the phylogeny of Chrysanthemum and its close relatives. [ABSTRACT FROM AUTHOR]

High-throughput molecular analysis is challenging in a non-model species. Proteomics has a great potential to characterize non-model species. We went beyond the level of simply ‘identifying’ the proteins of interest during osmotic stress experiments in an allopolyploid crop ( in casu banana) and focus on an important stress family: the cytoplasmic HSP70s. HSP70s were already identified earlier in proteomics studies as an important player during stress but an insight into the different family members and their polymorphisms was lacking. One particular spot within a whole spot trail drew our attention: its abundance was significantly higher after osmotic stress. What distinguishes this spot from its brother and sister spots? To understand what was special about that particular spot, we characterized the whole spot family in roots and meristem cultures. Using an 2D-DIGE LC–MS/MS approach we were able to measure a proteotypic peptide for each paralog. From our data it is clear that the different paralogs have evolved over time and do not necessarily behave the same when subjected to a stress treatment. The presumable paralog that particularly reacted to the osmotic stress in roots and meristems is located on chromosome 2 and the promoter region contains a unique ABRE element. Biological significance To our knowledge, this is the first time that a proteomics approach has led to the exploration of a protein family at the paralog and allelic variant level in a crop. Moreover we identified a specific osmotic responsive cytoplasmic HSP70 isoform, the HSP70 paralog 2, at the protein level. We have shown that the availability of genomic resources as well as the technique used for proteomics analysis are crucial in being able to go beyond the ‘usual suspects’. [ABSTRACT FROM AUTHOR]

Allotriploid lilies can produce aneuploid or euploid functional female gametes and can be used as the maternal parents in lily introgression breeding. In this study, the genome composition of 14 allopolyploid progenies, including 5 progenies which were derived from LLO × TTTT, 5 progenies which were derived from LLO × OTOT, and 4 BC 2 progenies which were derived from MAD × AA/AAAA, were analyzed using genomic in situ hybridization (GISH) technique. The GISH results indicated that all of the 10 progenies which were derived from LLO × TTTT/OTOT were aneuploids, 4 BC 2 progenies were euploids. Moreover, LLO always produced aneuploid functional female gametes, giving rise to aneuploid progenies, and MAD produced euploid functional female gametes including n or 2 n gametes. Most interestingly, T/O recombinant chromosomes, which were caused by abnormal meiosis, were observed in 2 progenies of LLO × OTOT. Based on the analysis, we proposed that aneuploids might provide a promising approach for lily breeding. [ABSTRACT FROM AUTHOR]