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Additional file 9. Alignment of known CONSTANS genes and a set of other angiosperm and gymnosperm sequences. Japanese larch open reading frames are shown in green. Kuril larch open reading frames are shown in blue.

Additional file 8. Alignment of known FT/FT-like and MFT genes and a set of other angiosperm and gymnosperm sequences. Japanese larch open reading frames are shown in green. Kuril larch open reading frames are shown in blue.

Additional file 5. Number of open reading frames (ORFs) similar to NCBI sequeces and other species according to BLASTp E-value cutoff values. a) ORFs obtained from Japanese larch, b) ORFs obtained from ORF Kuril larch.

Additional file 11. Summary of assembly and characterization.

Additional file 2. Gene ontology (GO) categories in biological process (BP) that encoded proteins with sequence similarity (E-value ≤ 1e-10) in the NCBI database. a) Japanese larch, b) Kuril larch. Gene ontology (GO) categories in cellular component (CC) that encoded proteins with sequence similarity (E-value ≤ 1e-10) in the NCBI database. a) Japanese larch, b) Kuril larch. Gene ontology (GO) categories in molecular function (MF) that encoded proteins with sequence similarity (E-value ≤ 1e-10) in the NCBI database. a) Japanese larch, b) Kuril larch.

Additional file 1. Stacked percent of the ORFs with top hits against NCBI nr database in each region on the Venn diagram. Blue shows the plant and fungal species (gbpln) in the GenBank nucleotide divisions. Orange shows ratio of “no hit”. Gray showed ratio of other divisions. LK and LG shows Japanese and Kuril larch, respectively.

Additional file 6. Alignment of known MADS-box genes and a set of other angiosperm and gymnosperm sequences. Japanese larch open reading frames are shown in green. Kuril larch open reading frames are shown in blue.

Additional file 7. Alignment of known LEAFY and NEEDLY genes and a set of other angiosperm and gymnosperm sequences. Japanese larch open reading frames are shown in green. Kuril larch open reading frames are shown in blue.

Additional file 1: Figure S1. The phenotypes in an F1 population before inoculation and from 14â days post-inoculation (dpi) of PWN until 56 dpi. Full view of individual numbers 1 to 96.The phenotypes in an F1 population before inoculation and from 14â days post-inoculation (dpi) of PWN until 56 dpi. Full view of individual numbers 97 to 198.

Figure S1. Validation of microarray data by qRT-PCR at the base. Bars represent the means Âą standard errors of the means (SE) for three biological replicates. (DOCX 142 kb)

Figure S2. Validation of microarray data by qRT-PCR in the middle. Bars represent the means Âą standard errors of the means (SE) for three biological replicates. (DOCX 143 kb)

The size distribution of our reference sequences in some model plant species. (PPTX 147Â kb)

Figure S3. Validation of microarray data by qRT-PCR in needles. Bars represent the means Âą standard errors of the means (SE) for three biological replicates. (DOCX 141 kb)

Summary of collected ESTs, assembly and SNP discovery in this study. (PPTX 56Â kb)

Clonal plantations of Thujopsis dolabrata var. hondae have been established in Ishikawa Prefecture, Japan, since at least the 1800s. Historical planting of the species has led to the development of vegetatively propagated local cultivars, which originated from ‘donor’ trees that have often been conserved in sacred groves or avenues at shrines and temples. These donor trees must have been selected from natural populations. In this study, we estimated the origin and genetic variability of clones identified among old planted trees and clonal plantations of T. dolabrata var. hondae, using 19 microsatellite markers. We discovered 12 clones among old planted trees, including 5 identical to members of a set of 14 we previously identified in plantations (giving 21 clones in total). Based on analyses combining assignment and exclusion tests, we inferred origins of 8 of those 21 clones: 6 may have originated from a natural population distributed in Ishikawa, 1 from Hokkaido and Aomori, and the other from Iwate and Yamagata, suggesting the clones constituting cultivars have multiple origins. The clones identified in plantations have significantly lower genetic variability and higher relatedness, indicating that clones of cultivars have a much narrower genetic base than those of natural populations. We suggest new clones selected from natural populations elsewhere, as well as Ishikawa, are needed for future breeding of T. dolabrata var. hondae to develop clonal forestry for this species., ファイル公開：2020/12/01

• Premise of the study: Expressed sequence tag–simple sequence repeat (EST-SSR) markers were developed from Thujopsis dolabrata var. hondae (Cupressaceae) using Illumina sequencing to investigate the genetic diversity and population structure of the genus Thujopsis. • Methods and Results: Twenty-two primer pairs were developed from ESTs of T. dolabrata var. hondae. The primers amplified di- and trinucleotide repeat-containing sequences. Polymorphisms were assessed in 81 individuals from two T. dolabrata var. hondae populations and one T. dolabrata population. The number of alleles ranged from one to 17 per locus. The observed and expected heterozygosities ranged from 0.000 to 1.000 and from 0.000 to 0.926, respectively. • Conclusions: These new EST-SSR markers will be useful in analyses of the genetic diversity and population structure of the genus Thujopsis.