A host plant genome (Zizania latifolia) after a century‐long endophyte infection

Abstract

These authors contributed equally to this work. SUMMARYDespite the importance of host-microbe interactions in natural ecosystems, agriculture and medicine, the impact of long-term (especially decades or longer) microbial colonization on the dynamics of host genomes is not well understood. The vegetable crop 'Jiaobai' with enlarged edible stems was domesticated from wild Zizania latifolia (Oryzeae) approximately 2000 years ago as a result of persistent infection by a fungal endophyte, Ustilago esculenta. Asexual propagation via infected rhizomes is the only means of Jiaobai production, and the Z. latifolia-endophyte complex has been maintained continuously for two centuries. Here, genomic analysis revealed that cultivated Z. latifolia has a significantly smaller repertoire of immune receptors compared with wild Z. latifolia. There are widespread gene losses/mutations and expression changes in the plant-pathogen interaction pathway in Jiaobai. These results show that continuous long-standing endophyte association can have a major effect on the evolution of the structural and transcriptomic components of the host genome.

De-novoassembly of zucchini genome reveals a whole genome duplication associated with the origin of theCucurbitagenus

“…Thus, both the 4DTv and gene family phylogenies are consistent with a duplication that happened in the ancestral species that gave rise to the Cucurbita genus short after its split from the ancestor of C. melo , C. sativus and C. lanatus about 30 ± 4 My 70 . The evolutionary rate derived from this time estimation is consistent with that found in other plants with a recent WGD like Nelumbo nucifera (4DTv = 0.17, 18 Mya) 71 , Glycine max (0.057, 13 Mya) 72 , Zizania latifolia (0.07, 13 Mya) 73 , and Setaria italica (0.38, 70 Mya) 74 . Populus trichocarpa would be an exception with a much lower evolution rate (0.1, 60-65 Mya) 75 , but this discrepancy could be due to the longer generation time of this plant 76 .…”

De novo assembly of the zucchini genome reveals a whole‐genome duplication associated with the origin of the Cucurbita genus

“…Therefore, both the 4DTv and gene family phylogenies are consistent with a duplication that occurred in the ancestral species that gave rise to the Cucurbita genus shortly after its split from the ancestor of C. melo , C. sativus and C. lanatus approximately 30 ± 4 Mya (Schaefer et al ., ). The evolutionary rate derived from this time estimation is consistent with that found in other plants with a recent WGD like Nelumbo nucifera (4DTv = 0.17, 18 Mya) (Wang et al ., ), Glycine max (0.057, 13 Mya) (Schmutz et al ., ), Zizania latifolia (0.07, 13 Mya) (Guo et al ., ) and Setaria italica (0.38, 70 Mya) (Zhang et al ., ). Populus trichocarpa would be an exception with a much lower evolution rate (0.1, 60–65 Mya) (Tuskan et al ., ), but this discrepancy could be due to the longer generation time of this plant (Smith and Donoghue, ).…”

Landscape-Scale Genetic Structure of Wild Rice Zizania latifolia: The Roles of Rivers, Mountains and Fragmentation

“…Moreover, some eminent traits in Z. latifolia are used for rice breeding owing to its close relationship to rice (Oryza sativa L.) (Chen Y. et al, 2006). And the release of genome sequences of Z. latifolia would greatly accelerate the progress of molecular breeding related to the species (Guo et al, 2015). Therefore, wild Z. latifolia populations not only have important ecological functions in aquatic ecosystems, but also are important genetic resources.…”