Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome

Verwaaijen, Bart; Wibberg, Daniel; Nelkner, Johanna; Gordin, Miriam; Rupp, Oliver; Winkler, Anderson M.; Bremges, Andreas; Blom, Jochen; Grosch, Rita; Pühler, Alfred; Schlüter, Andreas

doi:10.1016/j.jbiotec.2017.12.021

Cited by 12 publications

(11 citation statements)

References 33 publications

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“…In a previous publication reporting on the lettuce cv. Tizian genome, a subset of 291 pathogen receptor gene candidates (PRG) associated with various pathogens was found within the genome 17 . Of these, 157 PRG candidates were significantly differentially expressed in response to interaction with R. solani .…”

Section: Resultsmentioning

confidence: 99%

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A comprehensive analysis of the Lactuca sativa, L. transcriptome during different stages of the compatible interaction with Rhizoctonia solani

Verwaaijen

Wibberg

Winkler

et al. 2019

Sci Rep

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The leafy green vegetable Lactuca sativa , L. is susceptible to the soil-born fungus Rhizoctonia solani AG1-IB. In a previous study, we reported on the transcriptional response of R. solani AG1-IB (isolate 7/3/14) during the interspecies interaction with L. sativa cv. Tizian by means of RNA sequencing. Here we present the L. sativa transcriptome and metabolome from the same experimental approach. Three distinct interaction zones were sampled and compared to a blank (non-inoculated) sample: symptomless zone 1, zone 2 showing light brown discoloration, and a dark brown zone 3 characterized by necrotic lesions. Throughout the interaction, we observed a massive reprogramming of the L. sativa transcriptome, with 9231 unique genes matching the threshold criteria for differential expression. The lettuce transcriptome of the light brown zone 2 presents the most dissimilar profile compared to the uninoculated zone 4, marking the main stage of interaction. Transcripts putatively encoding several essential proteins that are involved in maintaining jasmonic acid and auxin homeostasis were found to be negatively regulated. These and other indicator transcripts mark a potentially inadequate defence response, leading to a compatible interaction. KEGG pathway mapping and GC-MS metabolome data revealed large changes in amino acid, lignin and hemicellulose related pathways and related metabolites.

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Section: Resultsmentioning

confidence: 99%

“…Concerning the lettuce cv. Tizian genome, we previously identified a high number of genes associated with plant defences 17 . Moreover, substantial research efforts have been conducted for the lettuce cv.…”

Section: Introductionmentioning

confidence: 99%

A comprehensive analysis of the Lactuca sativa, L. transcriptome during different stages of the compatible interaction with Rhizoctonia solani

Verwaaijen

Wibberg

Winkler

et al. 2019

Sci Rep

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“…We identified orthologous and paralogous groups using the annotated genes and the other eight species, A. thaliana (Cheng et al, 2017), Camptotheca acuminata (Zhao et al, 2017), Catharanthus roseus (Kellner et al, 2015), Coffea canephora (Denoeud et al, 2014), Daucus carota (Cai et al, 2015), Lactuca sativa (Verwaaijen et al, 2018), Rhododendron delavayi (Zhang et al, 2017) and Vitis vinifera (Jaillon et al, 2007) by orthomcl (version 2.0.9) (Li, Stoeckert, & Roos, 2003) and mmseqs (Hauser, Steinegger, & Söding, 2016) with an e-value threshold of 1e-5. Subsequently, we selected 1,971 single-copy orthogroups and constructed phylogenetic relationships between these species.…”

Section: Phylogenetic Analysis and Estimation Of Divergence Timementioning

confidence: 99%

Genomic analyses of a “living fossil”: The endangered dove‐tree

Yang

Zhang

et al. 2020

Molecular Ecology Resources

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Davidia involucrata Baill, also known as the dove‐tree, is a living fossil and an endangered species currently restricted to the mountains of southwestern and central China. It has a beautiful and innovative trait of high horticultural value: two white bracts covering the flower caputila. Here, we report on the chromosome‐scale genome of this species using single‐molecule real‐time long reads and chromosome conformation capture (Hi‐C) techniques. This species has a larger genome size of 1,169 Mb and contains relatively more genes (42,554) than the closely related species Camptotheca acuminata (397 Mb and 31,825 genes). Both species shared one recent whole genome duplication before their divergence. The expansion of the repetitive elements after their divergence contributed greatly to the increase in the genome size of the dove‐tree. Photosynthesis‐related genes were almost absent or showed reduced expression in the bracts of the dove‐tree, while defence‐ and chemical‐related genes increased greatly, highlighting the important roles of the bracts in protecting flowers and attracting pollinators. The effective population size of the dove‐tree continuously decreased during the climate changes of the Quaternary. Such climate sensitivity should be fully considered in conservation efforts for this relict endangered species in the context of continuous climate warming in the future.

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“…Moreover, six of them carried nonsynonymous SNVs (3508, 3614, 414, 4087, 857, and 1310, Figure 3). This finding is extremely meaningful if we consider that nearly half (24/50) of the discriminating SNPs fall in a genomic window (49.6 Mb) that represents less than 2.1% of the entire lettuce genome (2.22 Gb, [55]).…”

Section: Discussionmentioning

confidence: 99%

Genotyping by RAD Sequencing Analysis Assessed the Genetic Distinctiveness of Experimental Lines and Narrowed down the Genomic Region Responsible for Leaf Shape in Endive (Cichorium endivia L.)

Patella

Palumbo

Ravi

et al. 2020

Genes

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The characterization of genetic diversity in elite breeding stocks is crucial for the registration and protection of new varieties. Moreover, experimental population structure analysis and information about the genetic distinctiveness of commercial materials are essential for crop breeding programs. The purpose of our research was to assess the genetic relationships of 32 endive (Cichorium endivia L.) breeding lines, 18 from var. latifolium (escarole) and 14 from var. crispum (curly), using heterologous Cichorium intybus-derived simple sequence repeats (SSR) markers and single-nucleotide polymorphisms (SNP) markers. We found that 14 out of 29 SSR markers were successfully amplified, but only 8 of them were related to polymorphic loci. To overcome the limitation of the low number of informative SSR marker loci, an alternative SNP-based approach was employed. The 4621 SNPs produced by a restriction site-associated DNA marker sequencing approach were able to fully discriminate the 32 endive accessions; most importantly, as many as 50 marker loci were found to distinguish the curly group from the escarole group. Interestingly, 24 of the marker loci mapped within a peripheral segment of chromosome 8 of lettuce (Lactuca sativa L.), spanning a chromosomal region of 49.6 Mb. Following Sanger sequencing-based validation, three genes were determined to carry nonsynonymous SNPs, and one of them matched a putative ortholog of AtELP1, subunit 1 of the Elongator complex. Considering that several previously characterized Elongator complex subunit mutants exhibited elongated and/or curly leaf phenotypes, this gene should be taken into consideration for a better understanding of the underlying mechanism controlling leaf shape in endive.

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Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome

Cited by 12 publications

References 33 publications

A comprehensive analysis of the Lactuca sativa, L. transcriptome during different stages of the compatible interaction with Rhizoctonia solani

A comprehensive analysis of the Lactuca sativa, L. transcriptome during different stages of the compatible interaction with Rhizoctonia solani

Genomic analyses of a “living fossil”: The endangered dove‐tree

Genotyping by RAD Sequencing Analysis Assessed the Genetic Distinctiveness of Experimental Lines and Narrowed down the Genomic Region Responsible for Leaf Shape in Endive (Cichorium endivia L.)

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