ArticleBMC plant biology2022
Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica).
Article in BMC plant biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 11 citations in OpenAlex.
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- Spatiotemporal dynamics of age-related genes and the regulatory network of LaAGL2-3 in Larix kaempferi (Lamb.) Carr. based on the latest genome annotation.BMC plant biology · 2025Article
- Integrated transcriptomic and WGCNA identify drought-responsive TFs in Larix olgensis.BMC plant biology · 2025Article
- Antibiotic stress-induced hormesis in phytoplankton and bacteria through their mutual cooperation.Science advances · 2025Article
- Screening and Functional Evaluation of FourPlants (Basel, Switzerland) · 2024Article
- UAV Photogrammetry for Estimating Stand Parameters of an Old Japanese Larch Plantation Using Different Filtering Methods at Two Flight Altitudes.Sensors (Basel, Switzerland) · 2023Article
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7 authors at 2 institutions in 1 country.
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Abstract
backgroundJapanese larch (Larix kaempferi) is an economically important deciduous conifer species that grows in cool-temperate forests and is endemic to Japan. Kuril larch (L. gmelinii var. japonica) is a variety of Dahurian larch that is naturally distributed in the Kuril Islands and Sakhalin. The hybrid larch (L. gmelinii var. japonica × L. kaempferi) exhibits heterosis, which manifests as rapid juvenile growth and high resistance to vole grazing. Since these superior characteristics have been valued by forestry managers, the hybrid larch is one of the most important plantation species in Hokkaido. To accelerate molecular breeding in these species, we collected and compared full-length cDNA isoforms (Iso-Seq) and RNA-Seq short-read, and merged them to construct candidate gene as reference for both Larix species. To validate the results, candidate protein-coding genes (ORFs) related to some flowering signal-related genes were screened from the reference sequences, and the phylogenetic relationship with closely related species was elucidated.
resultsUsing the isoform sequencing of PacBio RS ll and the de novo assembly of RNA-Seq short-read sequences, we identified 50,690 and 38,684 ORFs in Japanese larch and Kuril larch, respectively. BUSCO completeness values were 90.5% and 92.1% in the Japanese and Kuril larches, respectively. After comparing the collected ORFs from the two larch species, a total of 19,813 clusters, comprising 22,571 Japanese larch ORFs and 22,667 Kuril larch ORFs, were contained in the intersection of the Venn diagram. In addition, we screened several ORFs related to flowering signals (SUPPRESSER OF OVEREXPRESSION OF CO1: SOC1, LEAFY: LFY, FLOWERING Locus T: FT, CONSTANCE: CO) from both reference sequences, and very similar found in other species.
conclusionsThe collected ORFs will be useful as reference sequences for molecular breeding of Japanese and Kuril larches, and also for clarifying the evolution of the conifer genome and investigating functional genomics.
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