ArticleApplications in plant sciences2016
Low-coverage, whole-genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery.
Article in Applications in plant sciences, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 43 citations in OpenAlex.
- Article
- Divergence and reticulation in the Mexican white oaks: ecological and phylogenomic evidence on species limits and phylogenetic networks in the Quercus laeta complex (Fagaceae).Annals of botany · 2024Article
- Article
- Echoes of ancient introgression punctuate stable genomic lineages in the evolution of figs.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Article
- Whole-genome sequencing of a year-round fruiting jackfruit (Frontiers in plant science · 2022Article
- Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae).Systematic biology · 2021Article
- Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics.Applications in plant sciences · 2021Article
- Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Systematic biology · 2020Article
- Strategies for reducing per-sample costs in target capture sequencing for phylogenomics and population genomics in plants.Applications in plant sciences · 2020Review
- Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis).Genes · 2019Article
- An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae.Applications in plant sciences · 2019Article
- A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-Medoids Clustering.Systematic biology · 2019Article
- Genome sequences of horticultural plants: past, present, and future.Horticulture research · 2019Review
- Practical considerations for plant phylogenomics.Applications in plant sciences · 2018Review
- Low-coverage, whole-genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery.Applications in plant sciences · 2016Article
- HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment.Applications in plant sciences · 2016Article
- Fun-sized library prep: Miniaturization is a valid method for per-sample cost reduction in targeted sequencing of angiosperm DNA.Applications in plant sciencesArticle
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
premise of the studyWe used moderately low-coverage (17×) whole-genome sequencing of Artocarpus camansi (Moraceae) to develop genomic resources for Artocarpus and Moraceae. METHODS AND
resultsA de novo assembly of Illumina short reads (251,378,536 pairs, 2 × 100 bp) accounted for 93% of the predicted genome size. Predicted coding regions were used in a three-way orthology search with published genomes of Morus notabilis and Cannabis sativa. Phylogenetic markers for Moraceae were developed from 333 inferred single-copy exons. Ninety-eight putative MADS-box genes were identified. Analysis of all predicted coding regions resulted in preliminary annotation of 49,089 genes. An analysis of synonymous substitutions for pairs of orthologs (Ks analysis) in M. notabilis and A. camansi strongly suggested a lineage-specific whole-genome duplication in Artocarpus.
conclusionsThis study substantially increases the genomic resources available for Artocarpus and Moraceae and demonstrates the value of low-coverage de novo assemblies for nonmodel organisms with moderately large genomes.
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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.