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

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

doi:10.1038/ncomms14953

Abstract

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.

Highlights

Lettuce (Lactuca sativa) is a major crop and a member of the large, highly successful Compositae family of flowering plants
We sequenced and assembled the genome of L. sativa using a variety of approaches that included a wide range of mate-pair libraries and in vitro proximity ligation to generate large superscaffolds based on long-range contact frequencies detected between scaffolds[13]
The genome size of L. sativa is typical of many Compositae species[46], despite the family having rapid-cycling weedy species

Summary

Introduction

Lettuce (Lactuca sativa) is a major crop and a member of the large, highly successful Compositae family of flowering plants. They are recognizable by their characteristic compound inflorescences that comprise many true flowers This cosmopolitan family is present in diverse habitats; Compositae species are successful colonizers of disturbed habitats and thrive in a range of extreme environments including deserts, tundra and salt flats[1,4]. We sequenced and assembled the genome of L. sativa using a variety of approaches that included a wide range of mate-pair libraries and in vitro proximity ligation to generate large superscaffolds based on long-range contact frequencies detected between scaffolds[13]. The resulting assembly is one of the more complete for any plant species reported so far, for a genome larger than 2 Gb with a high repeat content, and provides the first high-quality, comprehensive reference genome for analysis of the Compositae family

Methods

Results

Conclusion