ArticleGenetics2008
Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae.
Article in Genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- Image-Based Quantitative Analysis of Epidermal Morphology in Wild Potato Leaves.Plants (Basel, Switzerland) · 2024Article
- Metabolic and transcriptomic analyses of nectaries reveal differences in the mechanism of nectar production between monocots (Ananas comosus) and dicots (Nicotiana tabacum).BMC plant biology · 2024Article
- Genetic analysis of heat tolerance in hot pepper: insights from comprehensive phenotyping and QTL mapping.Frontiers in plant science · 2023Article
- The nature and organization of satellite DNAs inFrontiers in plant science · 2023Article
- Keeping time in the dark: Potato diel and circadian rhythmic gene expression reveals tissue-specific circadian clocks.Plant direct · 2022Article
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- Allelic variation for alpha-Glucan Water Dikinase is associated with starch phosphate content in tetraploid potato.Plant molecular biology · 2022Article
- Evolution of a guarded decoy protease and its receptor in solanaceous plants.Nature communications · 2020Article
- A universal chromosome identification system for maize and wild Zea species.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2020Article
- Evolutionary Rate Heterogeneity and Functional Divergence of Orthologous Genes inBiomolecules · 2019Article
- Environmental and epigenetic regulation of Rider retrotransposons in tomato.PLoS genetics · 2019Article
- Nucleotide sequence polymorphism in theJournal of genetics · 2019Article
- Comparative Transcriptome Analysis in Eggplant Reveals Selection Trends during Eggplant Domestication.International journal of genomics · 2019Article
- Comparative Oligo-FISH Mapping: An Efficient and Powerful Methodology To Reveal Karyotypic and Chromosomal Evolution.Genetics · 2018Article
- Association Study Reveals Novel Genes Related to Yield and Quality of Fruit in Cape Gooseberry (Frontiers in plant science · 2018Article
- Parallel evolution of the POQR prolyl oligo peptidase gene conferring plant quantitative disease resistance.PLoS genetics · 2017Article
- Article
- Distinct Patterns of Gene Gain and Loss: Diverse Evolutionary Modes of NBS-Encoding Genes in Three Solanaceae Crop Species.G3 (Bethesda, Md.) · 2017Article
- Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data.Nature genetics · 2017Article
- Conservation and Dispersion of Genes Conferring Resistance to Tomato Begomoviruses between Tomato and Pepper Genomes.Frontiers in plant science · 2017Article
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7 authors.
Funding
Abstract
Comparative genomics is a powerful tool for gaining insight into genomic function and evolution. However, in plants, sequence data that would enable detailed comparisons of both coding and noncoding regions have been limited in availability. Here we report the generation and analysis of sequences for an unduplicated conserved syntenic segment (CSS) in the genomes of five members of the agriculturally important plant family Solanaceae. This CSS includes a 105-kb region of tomato chromosome 2 and orthologous regions of the potato, eggplant, pepper, and petunia genomes. With a total neutral divergence of 0.73-0.78 substitutions/site, these sequences are similar enough that most noncoding regions can be aligned, yet divergent enough to be informative about evolutionary dynamics and selective pressures. The CSS contains 17 distinct genes with generally conserved order and orientation, but with numerous small-scale differences between species. Our analysis indicates that the last common ancestor of these species lived approximately 27-36 million years ago, that more than one-third of short genomic segments (5-15 bp) are under selection, and that more than two-thirds of selected bases fall in noncoding regions. In addition, we identify genes under positive selection and analyze hundreds of conserved noncoding elements. This analysis provides a window into 30 million years of plant evolution in the absence of polyploidization.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.