2020
DOI: 10.1101/2020.04.21.054320
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Inspecting abundantly expressed genes in male strobili in sugi (Cryptomeria japonica D. Don) via a highly accurate cDNA assembly

Abstract: 21Sugi (Cryptomeria japonica D. Don) is an important conifer used for afforestation in Japan. 22 two tissue-specific libraries were compared, principal component analysis (PCA) showed that 34 there were significant differences between male strobili and leaf and bark sets. The highest three 35 upregulated transcription factors stood out as orthologs to angiosperms. The identified signature-36 like domain of the transcription factors demonstrated the accuracy of the assembly. Based on the 37 evaluation of differ… Show more

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Cited by 4 publications
(8 citation statements)
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“…To identify causative single nucleotide variations (SNVs) and/or insertions or deletions (indels) in expressed genes, we analysed RNA-sequencing (RNA-Seq) data from six libraries (Table S1) from the mapping family of MS1. These data have been reported in Ueno et al 25 and Wei et al 26 . In this study, we focused on the levels of gene expression and selected candidate genes using the following criteria: 1) expression levels (in transcripts per million [tpm]) in leaf or bark tissue < 10; 2) expression levels (tpm) in fertile strobili was more than twice compared to those in sterile strobili.…”
Section: Rna-sequencing and Ms1 Annotationsupporting
confidence: 86%
“…To identify causative single nucleotide variations (SNVs) and/or insertions or deletions (indels) in expressed genes, we analysed RNA-sequencing (RNA-Seq) data from six libraries (Table S1) from the mapping family of MS1. These data have been reported in Ueno et al 25 and Wei et al 26 . In this study, we focused on the levels of gene expression and selected candidate genes using the following criteria: 1) expression levels (in transcripts per million [tpm]) in leaf or bark tissue < 10; 2) expression levels (tpm) in fertile strobili was more than twice compared to those in sterile strobili.…”
Section: Rna-sequencing and Ms1 Annotationsupporting
confidence: 86%
“…RNA-sequencing (RNA-Seq) data were analysed to identify the genetic variation specific to individuals with the recessive allele (ms1) of MS1 among the cDNA sequences expressed in male strobili of C. japonica. RNA-Seq data from six libraries (Table S1) were used 26 . The genotype of MS1 for these samples was determined based on phenotype and/or artificial crossing.…”
Section: Resultsmentioning
confidence: 99%
“…2 Graduate School of Science and Technology, Niigata University, Niigata, Japan. 3 Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan. 4 National Institute for Basic Biology, Okazaki, Aichi, Japan.…”
Section: Supplementary Informationmentioning
confidence: 99%
“…Therefore, breeding efforts are currently focused on producing a sterile pollen cultivar [2]. A candidate gene for male sterility, MALE STERILITY 1 (MS1), has been identified by transcriptome analysis and linkage mapping [3][4][5]. Sequencing analysis of the gene (CJt020762: 2,479 bp) from 83 samples identified 49 haplotypes with observed (H O ) and expected (H E ) heterozygosity of 0.892 and 0.920, respectively (Additional file 1), along with the two deletion mutations, both of which were expected to result in the mutant alleles which cause sterility (ms1-1 and ms1-2 of the haplotype 38 and 4, respectively) [4].…”
Section: Introductionmentioning
confidence: 99%