SummaryPolyploidy is a major driving force in plant evolution and speciation. Phenotypic changes often arise with the formation, natural selection and domestication of polyploid plants. However, little is known about the consequence of hybridization and polyploidization on root hair development.Here, we report that root hair length of synthetic and natural allopolyploid wheats is significantly longer than those of their diploid progenitors, whereas no difference is observed between allohexaploid and allotetraploid wheats.The expression of wheat gene TaRSL4, an orthologue of AtRSL4 controlling the root hair development in Arabidopsis, was positively correlated with the root hair length in diploid and allotetraploid wheats. Moreover, transcript abundance of TaRSL4 homoeologue from A genome (TaRSL4-A) was much higher than those of other genomes in natural allopolyploid wheat. Notably, increased root hair length by overexpression of the TaRSL4-A in wheat led to enhanced shoot fresh biomass under nutrient-poor conditions.Our observations indicate that increased root hair length in allohexaploid wheat originated in the allotetraploid progenitors and altered expression of TaRSL4 gene by genome interplay shapes root hair length in allopolyploid wheat.

Ginger (Zingiber officinale), the type species of Zingiberaceae, is one of the most widespread medicinal plants and spices. Here, we report a high-quality, chromosome-scale reference genome of ginger ‘Zhugen’, a traditionally cultivated ginger in Southwest China used as a fresh vegetable, assembled from PacBio long reads, Illumina short reads, and high-throughput chromosome conformation capture (Hi-C) reads. The ginger genome was phased into two haplotypes, haplotype 1 (1.53 Gb with a contig N50 of 4.68 M) and haplotype 0 (1.51 Gb with a contig N50 of 5.28 M). Homologous ginger chromosomes maintained excellent gene pair collinearity. In 17,226 pairs of allelic genes, 11.9% exhibited differential expression between alleles. Based on the results of ginger genome sequencing, transcriptome analysis, and metabolomic analysis, we proposed a backbone biosynthetic pathway of gingerol analogs, which consists of 12 enzymatic gene families, PAL, C4H, 4CL, CST, C3’H, C3OMT, CCOMT, CSE, PKS, AOR, DHN, and DHT. These analyses also identified the likely transcription factor networks that regulate the synthesis of gingerol analogs. Overall, this study serves as an excellent resource for further research on ginger biology and breeding, lays a foundation for a better understanding of ginger evolution, and presents an intact biosynthetic pathway for species-specific gingerol biosynthesis.

Common wheat is an allohexaploid (BBAADD) that originated from the hybridization and polyploidization of the diploid Aegilops tauschii (DD) with the allotetraploid Triticum turgidum (BBAA). Phenotypic changes often arise with the formation and evolution of allopolyploid wheat, but little is known about the evolution of root traits in different wheat species with varying ploidy levels. Here, we reported that the lateral root number on the primary root (LRNPR) of synthetic and natural allohexaploid wheats (BBAADD) is significantly higher than that of their allotetraploid (BBAA) and diploid (AA and SS) progenitors, but is much lower than that of their diploid (DD) progenitors. The expression of the wheat gene TaLBD16, an ortholog of the Arabidopsis LATERAL ORGAN BOUNDARIES-DOMAIN16/ASYMMETRIC LEAVES2-LIKE18 (LBD16), which is involved in lateral root development in Arabidopsis, was positively correlated with the LRNPR in diploid and allopolyploid wheats. In natural and synthetic allohexaploid wheats, the transcript of the TaLBD16 from the D genome (TaLBD16-D) was relatively more abundant compared with TaLBD16-A and TaLBD16-B. Consistent with the observed variation in LRNPR, the divergence in the expression of TaLBD16 homoeologous genes occurred before the formation of polyploidy wheat. Collectively, our observations indicate that the D genome played a crucial role in the increased lateral root number of allohexaploid wheats compared with their allotetraploid progenitors, and that TaLBD16-D was one of the key genes involved in the formation of lateral root number during wheat evolution.

BackgroundHorizontal transfer (HT) of transposable elements (TEs) into a new genome is considered as an important force to drive genome variation and biological innovation. However, most of the HT of DNA transposons previously described occurred between closely related species or insects.ResultsIn this study, we carried out a detailed analysis of four DNA transposons, which were found in the first sequenced twisted-wing parasite, Mengenilla moldrzyki. Through the homology-based strategy, these transposons were also identified in other insects, freshwater planarian, hydrozoans, and bats. The phylogenetic distribution of these transposons was discontinuous, and they showed extremely high sequence identities (>87%) over their entire length in spite of their hosts diverging more than 300 million years ago (Mya). Additionally, phylogenies and comparisons of transposons versus orthologous gene identities demonstrated that these transposons have transferred into their hosts by independent HTs.ConclusionsHere, we provided the first documented example of HT of CACTA transposons, which have been so far extensively studied in plants. Our results demonstrated that bats had continuously acquired new DNA elements via HT. This implies that predation on a large quantity of insects might increase bat exposure to HT. In addition, parasite-host interaction might facilitate exchanging of their genetic materials.Electronic supplementary materialThe online version of this article (doi:10.1186/s13100-014-0033-1) contains supplementary material, which is available to authorized users.

Key messageThe developmental stage of anther development is generally more sensitive to abiotic stress than other stages of growth. Specific ROS levels, plant hormones and carbohydrate metabolism are disturbed in anthers subjected to abiotic stresses. Abstract As sessile organisms, plants are often challenged to multiple extreme abiotic stresses, such as drought, heat, cold, salinity and metal stresses in the field, which reduce plant growth, productivity and yield. The development of reproductive stage is more susceptible to abiotic stresses than the vegetative stage. Anther, the male reproductive organ that generate pollen grains, is more sensitive to abiotic stresses than female organs. Abiotic stresses affect all the processes of anther development, including tapetum development and degradation, microsporogenesis and pollen development, anther dehiscence, and filament elongation. In addition, abiotic stresses significantly interrupt phytohormone, lipid and carbohydrate metabolism, alter reactive oxygen species (ROS) homeostasis in anthers, which are strongly responsible for the loss of pollen fertility. At present, the precise molecular mechanisms of anther development under adverse abiotic stresses are still not fully understood. Therefore, more emphasis should be given to understand molecular control of anther development during abiotic stresses to engineer crops with better crop yield.