ArticleG3 (Bethesda, Md.)2022
A chromosome-level reference genome of a Convolvulaceae species Ipomoea cairica.
Article in G3 (Bethesda, Md.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Diploid chromosome-level genome assembly of the Amazonian endemic morning glory Ipomoea cavalcantei D.F. Austin.Scientific data · 2026Article
- Telomere-to-Telomere Genome Assembly of TwoBiomolecules · 2026Article
- Chromosome level assembly and annotation of Cuscuta campestris Yunck. ("field dodder"), a model parasitic plant.G3 (Bethesda, Md.) · 2025Article
- Comparative analysis of the GATA transcription factors in sevenFrontiers in plant science · 2025Article
- Comparative analysis of the LEA gene family in seven Ipomoea species, focuses on sweet potato (Ipomoea batatas L.).BMC plant biology · 2024Article
- First whole-genome sequence and assembly of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species, using Oxford Nanopore Technologies.G3 (Bethesda, Md.) · 2024Article
- Genome-wide comparative analysis of the valine glutamine motif containing genes in four Ipomoea species.BMC plant biology · 2023Article
- Era of gapless plant genomes: innovations in sequencing and mapping technologies revolutionize genomics and breeding.Current opinion in biotechnology · 2023Review
- Comparative analysis of theFrontiers in plant science · 2023Article
- EndHiC: assemble large contigs into chromosome-level scaffolds using the Hi-C links from contig ends.BMC bioinformatics · 2022Article
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12 authors.
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Abstract
Ipomoea cairica is a perennial creeper that has been widely introduced as a garden ornamental across tropical, subtropical, and temperate regions. Because it grows extremely fast and spreads easily, it has been listed as an invasive species in many countries. Here, we constructed the chromosome-level reference genome of Ipomoea cairica by Pacific Biosciences HiFi and Hi-C sequencing, with the assembly size of 733.0 Mb, the contig N50 of 43.8 Mb, the scaffold N50 of 45.7 Mb, and the Benchmarking Universal Single-Copy Orthologs complete rate of 98.0%. Hi-C scaffolding assigned 97.9% of the contigs to 15 pseudo-chromosomes. Telomeric repeat analysis reveals that 7 of the 15 pseudo-chromosomes are gapless and telomere to telomere. The transposable element content of Ipomoea cairica is 73.4%, obviously higher than that of other Ipomoea species. A total of 38,115 protein-coding genes were predicted, with the Benchmarking Universal Single-Copy Orthologs complete rate of 98.5%, comparable to that of the genome assembly, and 92.6% of genes were functional annotated. In addition, we identified 3,039 tRNA genes and 2,403 rRNA genes in the assembled genome. Phylogenetic analysis showed that Ipomoea cairica formed a clade with Ipomoea aquatica, and they diverged from each other 8.1 million years ago. Through comparative genome analysis, we reconfirmed that a whole genome triplication event occurred specific to Convolvulaceae family and in the ancestor of the genus Ipomoea and Cuscuta. This high-quality reference genome of Ipomoea cairica will greatly facilitate the studies on the molecular mechanisms of its rapid growth and invasiveness.
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