Journal Article

Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce

Xu, Chunyan, Wang, Zhiwen, Song, Chi, Xu, Xun, Kozik, Alexander, Lavelle, Dean O., Truco, María-José, Michelmore, Richard W., Yang, Xinhua, Arikit, Siwaret, Xu, Huaqin, Froenicke, Lutz, Xia, Liangfeng, Meyers, Blake C., Zhu, Shilin, Cox, Kyle, Xia, Rui, Korf, Ian, Reyes-Chin-Wo, Sebastian

2017

Overview

Lettuce ( Lactuca sativa ) is a major crop and a member of the large, highly successful Compositae family of flowering plants. Here we present a reference assembly for the species and family. This was generated using whole-genome shotgun Illumina reads plus in vitro proximity ligation data to create large superscaffolds; it was validated genetically and superscaffolds were oriented in genetic bins ordered along nine chromosomal pseudomolecules. We identify several genomic features that may have contributed to the success of the family, including genes encoding Cycloidea -like transcription factors, kinases, enzymes involved in rubber biosynthesis and disease resistance proteins that are expanded in the genome. We characterize 21 novel microRNAs, one of which may trigger phasiRNAs from numerous kinase transcripts. We provide evidence for a whole-genome triplication event specific but basal to the Compositae. We detect 26% of the genome in triplicated regions containing 30% of all genes that are enriched for regulatory sequences and depleted for genes involved in defence. Genome assembly for many plant species can be challenging due to large size and high repeat content. Here, the authors use in vitro proximity ligation to assemble the genome of lettuce, revealing a family-specific triplication event and providing a comprehensive reference genome for a member of the Compositae.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 45/22 / 45/23 / 45/47 / 45/77 / 631/114/2785/2302 / 631/208/514/2254 / 631/208/742/3933 / 631/449/2491/2174 / Asteraceae - classification / Asteraceae - genetics / Biosynthesis / Chromosome Mapping / Chromosomes / Chromosomes, Plant - genetics / Disease resistance / Flowering plants / Gene Expression Profiling / Gene Expression Regulation, Plant / Genes, Plant - genetics / Genome, Plant - genetics / Genome-Wide Association Study / Genomes / Genomics - methods / Humanities and Social Sciences / Kinases / Lactuca - genetics / Lettuce / Molecular Sequence Annotation / multidisciplinary / Phylogeny / Science / Science (multidisciplinary) / Triploidy / Whole Genome Sequencing