Plant evolution and environmental adaptation unveiled by long-read whole-genome sequencing ofSpirodela

• DOI: 10.1073/pnas.1910401116
• Publication Date: 2019-09-04T22:55:41Z
• Authors: Dong An; Yong Zhou; Changsheng Li; Qiao Xiao; Tao Wang; Yating Zhang; Yongrui Wu; Yubin Li; Dai-Yin Chao; Joachim Messing; Wenqin Wang
• Keywords: 0301 basic medicine; 2. Zero hunger; Aquatic Organisms; DNA, Plant; Gene Expression Profiling; Sequence Analysis, DNA; 15. Life on land; Adaptation, Physiological; Plant Roots; Evolution, Molecular; 03 medical and health sciences; Tandem Repeat Sequences; Araceae; Genome, Plant; Disease Resistance; Plant Proteins

Aquatic plants have to adapt the environments distinct from where land grow. A critical aspect of adaptation is dynamics sequence repeats, not resolved in older sequencing platforms due incomplete and fragmented genome assemblies short reads. Therefore, we used PacBio long-read Spirodela polyrhiza genome, reaching a 44-fold increase contiguity with an N50 (a median contig lengths) 831 kb filling 95.4% gaps left previous version. Reconstruction repeat regions indicates that sequentially nested long terminal (LTR) retrotranspositions occur early monocot evolution, featured both prokaryote-like gene-rich eukaryotic islands. Protein-coding genes are reduced 18,708 gene models supported by 492,435 high-quality full-length complementary DNA (cDNA) sequences. Different plants, primitive architecture ’s adventitious roots lack lateral root hairs consistent dispensable functions nutrient absorption. Disease-resistant encoding antimicrobial peptides dirigent proteins expanded tandem duplications. Remarkably, disease-resistant only amplified, but also highly expressed, low levels 24-nucleotide (nt) small interfering RNA (siRNA) silence immune system thereby protecting against wide spectrum pathogens pests. The information sheds light on plant evolution environment, facilitates applications bioenergy phytoremediation.