Search

Background: Ginkgo biloba L. (Ginkgoaceae) is one of the most distinctive plants. It possesses a suite of fascinating characteristics including a large genome, outstanding resistance/tolerance to abiotic and biotic stresses, and dioecious reproduction, making it an ideal model species for biological studies. However, the lack of a high-quality genome sequence has been an impediment to our understanding of its biology and evolution. Findings: The 10.61 Gb genome sequence containing 41,840 annotated genes was assembled in the present study. Repetitive sequences account for 76.58% of the assembled sequence, and long terminal repeat retrotransposons (LTR-RTs) are particularly prevalent. The diversity and abundance of LTR-RTs is due to their gradual accumulation and a remarkable amplification between 16 and 24 million years ago, and they contribute to the long introns and large genome. Whole genome duplication (WGD) may have occurred twice, with an ancient WGD consistent with that shown to occur in other seed plants, and a more recent event specific to ginkgo. Abundant gene clusters from tandem duplication were also evident, and enrichment of expanded gene families indicates a remarkable array of chemical and antibacterial defense pathways. Conclusions: The ginkgo genome consists mainly of LTR-RTs resulting from ancient gradual accumulation and two WGD events. The multiple defense mechanisms underlying the characteristic resilience of ginkgo are fostered by a remarkable enrichment in ancient duplicated and ginkgo-specific gene clusters. The present study sheds light on sequencing large genomes, and opens an avenue for further genetic and evolutionary research. [ABSTRACT FROM AUTHOR]

Cardamine occulta, recently reported also as 'Asian C. flexuosa', is originally a native East Asian weed of paddy fields and other open habitats. It has been recorded throughout the world and is now also spreading widely in Europe. However, how this species differs morphologically from European C. flexuosa and its closest relatives in Asia (C. kokaiensis and C. scutata) is not fully known, particularly because it became widely recognized as a new taxon only recently. We used chromosome counting and flow cytometry to determine ploidies and genome size variation in these four species and morphometric analyses to ascertain their morphological differentiation. A uniformly octoploid level (2n = 64) is confirmed here for C. occulta and a tetraploid level for C. flexuosa and C. scutata (2n = 32). Here we formally describe C. kokaiensis, which is restricted to East Asia (Japan, Honshu; eastern China, Zhejiang Province; perhaps also the Russian Far East) and determine it to be a tetraploid. Considerable differences in monoploid genome size were revealed between these taxa, suggesting their mostly allopolyploid origins. Morphological differences between the species are demonstrated, and detailed morphological descriptions and an identification key are provided. [ABSTRACT FROM AUTHOR]