ArticlePlant biotechnology journal2017
An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance.
Article in Plant biotechnology journal, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
20 citing papers in PubMed, 42 citations in OpenAlex.
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- Flow Sorting-Assisted Optical Mapping.Methods in molecular biology (Clifton, N.J.) · 2023Article
- An improved reference genome forFrontiers in plant science · 2023Article
- Genes Associated with Biological Nitrogen Fixation Efficiency Identified Using RNA Sequencing in Red Clover (Life (Basel, Switzerland) · 2022Article
- Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security.The New phytologist · 2022Review
- Progress of Genomics-Driven Approaches for Sustaining Underutilized Legume Crops in the Post-Genomic Era.Frontiers in genetics · 2022Review
- Variation in Ribosomal DNA in the GenusPlants (Basel, Switzerland) · 2021Article
- An Improved Protocol forInternational journal of molecular sciences · 2021Article
- Transcriptome analysis reveals major transcriptional changes during regrowth after mowing of red clover (Trifolium pratense).BMC plant biology · 2021Article
- Prospects forFrontiers in plant science · 2021Review
- Pedigree analysis of pre-breeding efforts in Trifolium spp. germplasm in New Zealand.BMC genetics · 2020Article
- Gene Expression Maps in Plants: Current State and Prospects.Plants (Basel, Switzerland) · 2019Review
- LPCAT1 promotes brain metastasis of lung adenocarcinoma by up-regulating PI3K/AKT/MYC pathway.Journal of experimental & clinical cancer research : CR · 2019Article
- Adapting legume crops to climate change using genomic approaches.Plant, cell & environment · 2019Review
- Genetic Diversity Linked to Haplotype Variation in the World Core Collection ofFrontiers in plant science · 2019Article
- Large-Scale Structural Variation Detection in Subterranean Clover Subtypes Using Optical Mapping.Frontiers in plant science · 2018Article
- Intact DNA purified from flow-sorted nuclei unlocks the potential of next-generation genome mapping and assembly inMethodsX · 2018Article
- Climate Clever Clovers: New Paradigm to Reduce the Environmental Footprint of Ruminants by Breeding Low Methanogenic Forages Utilizing Haplotype Variation.Frontiers in plant science · 2017Article
Corrections and comments
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Authors and funding
11 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Subterranean clover is an important annual forage legume, whose diploidy and inbreeding nature make it an ideal model for genomic analysis in Trifolium. We reported a draft genome assembly of the subterranean clover TSUd_r1.1. Here we evaluate genome mapping on nanochannel arrays and generation of a transcriptome atlas across tissues to advance the assembly and gene annotation. Using a BioNano-based assembly spanning 512 Mb (93% genome coverage), we validated the draft assembly, anchored unplaced contigs and resolved misassemblies. Multiple contigs (264) from the draft assembly coalesced into 97 super-scaffolds (43% of genome). Sequences longer than >1 Mb increased from 40 to 189 Mb giving 1.4-fold increase in N50 with total genome in pseudomolecules improved from 73 to 80%. The advanced assembly was re-annotated using transcriptome atlas data to contain 31 272 protein-coding genes capturing >96% of the gene content. Functional characterization and GO enrichment confirmed gene expression for response to water deprivation, flavonoid biosynthesis and embryo development ending in seed dormancy, reflecting adaptation to the harsh Mediterranean environment. Comparative analyses across Papilionoideae identified 24 893 Trifolium-specific and 6325 subterranean-clover-specific genes that could be mined further for traits such as geocarpy and grazing tolerance. Eight key traits, including persistence, improved livestock health by isoflavonoid production in addition to important agro-morphological traits, were fine-mapped on the high-density SNP linkage map anchored to the assembly. This new genomic information is crucial to identify loci governing traits allowing marker-assisted breeding, comparative mapping and identification of tissue-specific gene promoters for biotechnological improvement of forage legumes.
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