Genome and transcriptome of Lettuce

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(Contributed by Li Bo)

       Lettuce (Lactuca sativa L.) is animportant vegetable crop species. L. sativa is diploid with 2n=2x= 18chromosomes and an estimated genome size of 2.5 Gb[1,2]. Generationof a comprehensive reference genome was challenging due to its size and highrepeat content.

       Reyes-Chin-Wo etal.[3] sequenced andassembled the genome of L. sativa using a variety of approaches thatincluded a wide range of mate-pair libraries and in vitro proximityligation to generate large superscaffolds based on long-range contactfrequencies detected between scaffolds[4]. In vitro proximityligation is an application of the chromosome conformation capture technologiesto aid genome assembly[5]; this approach has been reported foranimal but not for plant genomes[6,7]. The assembly was validatedgenetically and superscaffolds were arranged in genetic bins ordered along thenine chromosomal linkage groups. They identified several genomic features that may have contributed to thesuccess of the family, including genes encoding Cycloidea-liketranscription factors, kinases, enzymes involved in rubber biosynthesisand disease resistance proteins that are expanded in the genome. Thisstudy also characterized 21 novel microRNAs, one of which may trigger phasiRNAsfrom numerous kinase transcripts. Thwy provide evidence for awhole-genome triplication event specific but basal to the Compositae,detect 26% of the genome in triplicated regions containing 30% of allgenes that are enriched for regulatory sequences and depleted for genesinvolved in defence. The resulting assembly is one of the more completespecies reported, particularly for a genome larger than 2 Gb with a high repeatcontent, and provides the first high-quality, comprehensive reference genomefor analysis of the Compositae family.

       Wei Zhang et al.[8] sequenced a total of 445 Lactucaaccessions, including major lettuce crop types and wild relative species, andgenerated a comprehensive map of lettuce genome variations. In-depth analysesof population structure and demography revealed that lettuce was firstdomesticated near the Caucasus, which was marked by loss of seed shattering. Thisstudy also identified the genetic architecture of other domestication traitsand wild introgressions in major resistance clusters in the lettuce genome.Such as they detected a strong signal around 164.5Mb on chromosome 7, where a PHYTOCHROMEC (PHYC) gene resides. Two major haplotypes of PHYC were discoveredin cultivated lettuce, and the accessions carrying the reference G alleledisplayed a significant delay in flowering date accompanied by reduced PHYCexpression. They also identified two associated regions on chromosomes 5 and 9,consistent with two previous studies. These two regions contained RedLettuce Leaves 2 (RLL2), which encodes an MYB transcriptionregulator, and Anthocyanin Synthase (ANS), which encodes a key enzyme inanthocyanin biosynthesis.

       Zhang et al.[9] reported the RNAsequencing of 240 lettuce accessions sampled from the major horticultural typesand wild relatives, generating 1.1 million single nucleotide polymorphisms(SNPs). Demographic modeling indicates that there was a single domesticationevent for lettuce. They identified a list of regions as putative selectivesweeps that occurred during domestication and divergence, respectively. Genome-wideassociation studies (GWAS) identify 5311 expression quantitative trait loci(eQTL) regulating the expression of 4105 genes, including nine eQTLs regulatinggenes associated with flavonoid biosynthesis. GWAS for leaf color detects sixcandidate loci responsible for the variation of anthocyanins in lettuce leaves.Thisstudy provides a comprehensive understanding of the domestication and theaccumulation of anthocyanins in lettuce.

Reference:

[1] Michaelson, M. J., Price, H. J., Ellison, J. R. &Johnston, J. S. Comparison of plant DNA contents determined by Feulgenmicrospectrophotometry and laser flow cytometry. Am. J. Bot. 78, 183–188(1991).

[2] Koopman, W. J. M. & De Jong, J. H. A numericalanalysis of karyotypes and DNA amounts in lettuce cultivars and species(Lactuca subsect. Lactuca, Compositae). Acta Bot. Neerl. 45, 211–222 (1996).

[3] Reyes-Chin-WoS, Wang Z, Yang X, Kozik A, Arikit S, Song C, Xia L, Froenicke L, Lavelle DO,Truco MJ, Xia R, Zhu S, Xu C, Xu H, Xu X, Cox K, Korf I, Meyers BC, MichelmoreRW. Genome assemblywith in vitro proximity ligation data and whole-genome triplication in lettuce.Nat Commun. 8:14953 (2017).

[4] Putnam, N. H. et al. Chromosome-scale shotgunassembly using an in vitro method for long-range linkage. Genome Res. 26,342–350 (2016).

[5] Flot, J.-F., Marie-Nelly, H. & Koszul, R. Contactgenomics: scaffolding and phasing (meta)genomes using chromosome 3D physicalsignatures. FEBS Lett. 589, 2966–2974 (2015).

[6] Rice, E. S. et al. Improved genome assembly of American alligatorgenome reveals conserved architecture of estrogen signaling. Genome Res.27(5):686-696 (2017).

[7] Session, A. M. et al. Genome evolution in theallotetraploid frog Xenopus laevis. Nature. 538, 336–343 (2016).

[8] Wei T, vanTreuren R, Liu X, Zhang Z, Chen J, Liu Y, Dong S, Sun P, Yang T, Lan T, Wang X,Xiong Z, Liu Y, Wei J, Lu H, Han S, Chen JC, Ni X, Wang J, Yang H, Xu X, KuangH, van Hintum T, Liu X, Liu H. Whole-genome resequencing of 445 Lactucaaccessions reveals the domestication history of cultivated lettuce. Nat Genet.53(5):752-760 (2021).[9] Zhang L, Su W, Tao R, Zhang W, Chen J, Wu P, Yan C, Jia Y, Larkin RM,Lavelle D, Truco MJ, Chin-Wo SR, Michelmore RW, KuangH.RNA sequencing provides insights into the evolutionof lettuce and the regulation of flavonoid biosynthesis. Nat Commun. 8(1):2264(2017).