Understanding the processes that regulate plant sink formation and development at the molecular level will contribute to the areas of crop breeding, food production and plant evolutionary studies. We report the annotation and analysis of the draft genome sequence of the radish Raphanus sativus var. hortensis (long and thick root radish) and transcriptome analysis during root development. Based on the hybrid assembly approach of next-generation sequencing, a total of 383 Mb (N50 scaffold: 138.17 kb) of sequences of the radish genome was constructed containing 54,357 genes. Syntenic and phylogenetic analyses indicated that divergence between Raphanus and Brassica coincide with the time of whole genome triplication (WGT), suggesting that WGT triggered diversification of Brassiceae crop plants. Further transcriptome analysis showed that the gene functions and pathways related to carbohydrate metabolism were prominently activated in thickening roots, particularly in cell proliferating tissues. Notably, the expression levels of sucrose synthase 1 (SUS1) were correlated with root thickening rates. We also identified the genes involved in pungency synthesis and their transcription factors.

The results suggest that Ainsliaea species evolved allopatrically and that the descendants were isolated in the eastern (between SE China and Japan, through Taiwan and the Ryukyu Islands) and western (Yunnan Province and its surrounding areas, including the Himalayas, the temperate region of Southeast Asia, and Sichuan Province) sides of the Sino-Japanese region. The results suggest that two distinct lineages of Ainsliaea have independently evolved in environmentally heterogeneous regions within the Sino-Japanese region. These regions have maintained rich and original floras due to their diverse climates and topographies.

Understanding the role of habitat-associated adaptation in reducing gene flow resulting in population differentiation and speciation is a major issue in evolutionary biology. We demonstrate a significant role for habitat divergence in species isolation between two naturally hybridizing riparian and nonriparian plants, Ainsliaea faurieana and A. apiculata (Asteraceae), on Yakushima Island, Japan. By analyzing the fine-scale population structure at six sympatric sites, we found that variations in leaf shape, geography,

Habitat and geographical features of river systems strongly influence gene flow and spatial genetic patterning in riparian plant populations. We investigated the patterns of genetic diversity within and among populations of Ainsliaea faurieana relative to different spatial conditions (along a river, among rivers, and among regions on an island), based on nuclear and chloroplast microsatellite DNA variations. Within an individual river system, we found higher haplotype diversities in downstream populations, and in a Bayesian analysis of recent migration, we detected unidirectional gene movements from upstream to downstream, indicating water-mediated dispersal along the river. Mantel tests detected no isolation-by-distance in genetic variation, suggesting the maintenance of a metapopulation with wide-range seed dispersal by water. Moreover, the observed high level of genetic differentiation, especially in the cpDNA (F(ST) = 0.539), indicated a metapopulation structure with frequent extinction and colonization. On a larger scale, we found high population differentiation and clear genetic structuring among regions, suggesting that gene flow was restricted by geographical features (mountains separating river systems) for relatively long periods. Our findings of genetic structures based on different spatial conditions elucidated patterns and ranges of historical and contemporary gene movement in a plant species that is persistent in extremely disturbed riparian environments.

BackgroundThe respective role and relative importance of natural selection and gene flow in the process of population divergence has been a central theme in the speciation literature. A previous study presented conclusive evidence that wild radish on Japanese islands comprises two genetically isolated lineages: the southern and northern groups. However, a general understanding of the lineage isolation with frequent seed flow of the coastal plant species is still unclear. We surveyed nucleotide polymorphisms over 14 nuclear loci in 72 individuals across the Japan–Ryukyu Islands Arc to address the demographic history of wild radish utilising the isolation-with-migration (IM) model. In addition, we investigated the flowering times of individuals in different wild radish lineages, with and without cold exposure, to assess their respective vernalisation responses.ResultsCoalescent simulations suggested that divergence between the southern and northern lineages of wild radish began ~18,000 years ago, initially during the Last Glacial Maximum (LGM) period. The gene flow from the southern to northern groups was considerably higher than that in the opposite direction, indicating effective dispersal of viable seeds via the northward Kuroshio Current. Our greenhouse experiments indicated that cold exposure was not required for flowering in the southern group, but could advance the date of flowering, suggesting that vernalisation would be facultative in the southern group. In contrast, the northern group was either unable to flower or flowered later without prior cold exposure, and thus had an obligate requirement for cold treatment.ConclusionsThe south–north lineage divergence in wild radish could be triggered by a directional change in the sea current during the ice age, despite gene flow due to the high dispersability and longevity of seeds. We also found that temperature profoundly affected the vernalisation responses of wild radish, which may repress reproductive success and ultimately drive and reinforce intra-specific differentiation between the two lineages of wild radish. This study provides new insights into the maintenance of lineage differentiation with on-going gene flow in coastal plants.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0655-7) contains supplementary material, which is available to authorized users.