ArticleBMC genomics2015
Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
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- Genome-wide characterization and development of SSR markers for genetic diversity analysis in northwestern Himalayas Walnut (3 Biotech · 2023Article
- Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes.Nature communications · 2023Article
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- Genomic insights into lineage-specific evolution of the oleosin family in Euphorbiaceae.BMC genomics · 2022Article
- Chromosome-scale assembly reveals asymmetric paleo-subgenome evolution and targets for the acceleration of fungal resistance breeding in the nut crop, pecan.Plant communications · 2021Article
- Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding.Nature communications · 2021Article
- Co-located quantitative trait loci mediate resistance to Agrobacterium tumefaciens, Phytophthora cinnamomi, and P. pini in Juglans microcarpa × J. regia hybrids.Horticulture research · 2021Article
- Genetic Analysis of Walnut (G3 (Bethesda, Md.) · 2020Article
- Computational Identification and Comparative Analysis of Conserved miRNAs and Their Putative Target Genes in thePlants (Basel, Switzerland) · 2020Article
- A high-quality walnut genome assembly reveals extensive gene expression divergences after whole-genome duplication.Plant biotechnology journal · 2020Article
- High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome.GigaScience · 2020Article
- Distinguishing Sichuan Walnut Cultivars and Examining Their Relationships withFrontiers in plant science · 2020Article
- Genomics: cracking the mysteries of walnuts.Journal of genetics · 2019Review
- A new genomic tool for walnut (Juglans regia L.): development and validation of the high-density Axiom™ J. regia 700K SNP genotyping array.Plant biotechnology journal · 2019Article
- Genome-wide comparison reveals divergence of cassava and rubber aquaporin family genes after the recent whole-genome duplication.BMC genomics · 2019Article
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMutations often accompany DNA replication. Since there may be fewer cell cycles per year in the germlines of long-lived than short-lived angiosperms, the genomes of long-lived angiosperms may be diverging more slowly than those of short-lived angiosperms. Here we test this hypothesis.
resultsWe first constructed a genetic map for walnut, a woody perennial. All linkage groups were short, and recombination rates were greatly reduced in the centromeric regions. We then used the genetic map to construct a walnut bacterial artificial chromosome (BAC) clone-based physical map, which contained 15,203 exonic BAC-end sequences, and quantified with it synteny between the walnut genome and genomes of three long-lived woody perennials, Vitis vinifera, Populus trichocarpa, and Malus domestica, and three short-lived herbs, Cucumis sativus, Medicago truncatula, and Fragaria vesca. Each measure of synteny we used showed that the genomes of woody perennials were less diverged from the walnut genome than those of herbs. We also estimated the nucleotide substitution rate at silent codon positions in the walnut lineage. It was one-fifth and one-sixth of published nucleotide substitution rates in the Medicago and Arabidopsis lineages, respectively. We uncovered a whole-genome duplication in the walnut lineage, dated it to the neighborhood of the Cretaceous-Tertiary boundary, and allocated the 16 walnut chromosomes into eight homoeologous pairs. We pointed out that during polyploidy-dysploidy cycles, the dominant tendency is to reduce the chromosome number.
conclusionSlow rates of nucleotide substitution are accompanied by slow rates of synteny erosion during genome divergence in woody perennials.
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