Characterization of expressed sequence tags from a full-length enriched cDNA library of Cryptomeria japonica male strobili

Futamura, Norihiro; Totoki, Yasushi; Toyoda, Atsushi; Igasaki, Tomohiro; Nanjo, Tokihiko; Seki, Motoaki; Sakaki, Yoshiyuki; Mari, Adriano; Shinozaki, Kazuo; Shinohara, Kenji

doi:10.1186/1471-2164-9-383

Cited by 71 publications

(46 citation statements)

References 67 publications

(73 reference statements)

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“…These observations showed that there were very few tissue-specific transcripts. Although Futamura et al (2008) reported the construction of a full-length cDNA library of the male strobilus of C. japonica and globally characterized expressed genes, many of the genes they isolated may not show male strobilus-specific expression. Moreover, the gene profiling associated with each developmental stage of the male strobilus of C. japonica has not been reported.…”

Section: Discussionmentioning

confidence: 99%

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Spatiotemporal gene expression profiles associated with male strobilus development in Cryptomeria japonica by suppression subtractive hybridization

et al. 2011

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To identify the genes associated with the formation and development of the male strobilus of Cryptomeria japonica D. Don (Sugi), male strobilus-specific suppression subtractive hybridization (SSH) libraries were constructed from three different stages of male strobilus development. From these SSH libraries, 1,012 unigene sets including 314 contigs were assembled from 2,448 sequences. The profiles of the genes isolated from the SSH libraries differed strongly according to developmental stage: 49%, 13% and 29% of genes were unique to the early stage (stage E), tetrad stage (stage T), and mature stage (stage M) SSH libraries, respectively. To evaluate the reliability of the SSH libraries, we focused on the eight genes strongly concentrated in the three SSH libraries and performed RT-PCR analysis. All genes tested were expressed more strongly in the male strobilus than in the shoot. Our findings suggest that the gene profiles associated with male strobilus development differ in both number and kind of dominantly expressed genes.

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Section: Discussionmentioning

confidence: 99%

“…Global analyses of the expressed genes in mature pollen and the male strobilus of C. japonica have been reported by Futamura et al (2006Futamura et al ( , 2008. However, no profiling data are available of gene expression that is associated with different developmental stages of the male strobilus or pollen.…”

Section: Introductionmentioning

confidence: 99%

Spatiotemporal gene expression profiles associated with male strobilus development in Cryptomeria japonica by suppression subtractive hybridization

et al. 2011

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“…Protein-coding sequences for T. distichum, C. japonica and Chamaecyparis obtusa We used 3,976 contig sequences from T. distichum and 32,167 complete cDNA sequences from C. japonica obtained from a Sugi genome database (Futamura et al, 2008). We used Chamaecyparis obtusa (Siebold & Zucc.)…”

Section: Methodsmentioning

confidence: 99%

“…Taxodium and Cryptomeria belong to the same subfamily, Taxodioideae, and these genera diverged roughly 90 million years ago (MYA) (Aulenback and LePage, 1998;Leslie et al, 2012). Recently, partial sequences of more than thirty thousand complete cDNAs of C. japonica have been released (Futamura et al, 2008). To analyze the rate and pattern of nucleotide substitutions between the Taxodium and Cryptomeria lineages, we determined cDNA sequences from T. distichum using next-generation sequencing (NGS) technology.…”

Section: Introductionmentioning

confidence: 99%

Evolutionary rate variation in two conifer species, Taxodium distichum (L.) Rich. var. distichum (baldcypress) and Cryptomeria japonica (Thunb. ex L.f.) D. Don (Sugi, Japanese cedar)

2015

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With the advance of sequencing technologies, large-scale data of expressed sequence tags and full-length cDNA sequences have been reported for several conifer species. Comparative analyses of evolutionary rates among diverse taxa provide insights into taxon-specific molecular evolutionary features and into the origin of variation in evolutionary rates within genomes and between species. Here, we estimated evolutionary rates in two conifer species, Taxodium distichum and Cryptomeria japonica, to illuminate the molecular evolutionary features of these species, using hundreds of genes and employing Chamaecyparis obtusa as an outgroup. Our results show that the mutation rates based on synonymous substitution rates (dS) of T. distichum and C. japonica are approximately 0.67 × 10 -9 and 0.59 × 10 -9 /site/year, respectively, which are 15-25 times lower than those of annual angiosperms. We found a significant positive correlation between dS and GC3. This implies that a local mutation bias, such as context dependency of the mutation bias, exists within the genomes of T. distichum and C. japonica, and/or that selection acts on synonymous sites in these species. In addition, the means of the ratios of synonymous to nonsynonymous substitution rate in the two species are almost the same, suggesting that the average intensity of functional constraint is constant between the lineages. Finally, we tested the possibility of positive selection based on the site model, and detected one candidate gene for positive selection.

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“…In Japan, approximately 20 % of adults suffer from C. japonica and Chamaecyparis obtusa pollinosis (Okuda 2003), which has become a serious health problem. Many studies have been performed on the flowering of C. japonica, such as histological analysis (Hashizume 1962), estimation of clonal variation of flower production (Saito and Kawasaki 1984), and recently, genetic analysis including establishment of cDNA or expressed sequence tag libraries (Futamura et al 2008;Kurita et al 2011) from male reproductive organs.…”

Section: Introductionmentioning

confidence: 99%

Inheritance of male flower production in Cryptomeria japonica (sugi) estimated from analysis of a diallel mating test

Tsubomura

Fukatsu

Nakada

et al. 2012

Annals of Forest Science

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Context Clonal variation of flower production has been investigated thoroughly in coniferous tree species because of the importance of flowering in seed production from seed orchards. However, the inheritance of flower production by progeny test has not been previously studied well, so the heritability of male flower production of Cryptomeria japonica, the most important species for forestry and the main cause of pollinosis in Japan, was estimated to provide fundamental data for pollen control in seed orchards and plantation forests. Methods Male flower production in C. japonica was investigated for three years using 20 full-sib families created by a diallel mating design with six parents using gibberellin treatment to promote flowering. Results The narrow-sense individual tree heritability of male flower production in each year was estimated as ranging from 0.777 ± 0.339 to 1.050 ± 0.346 by sib analyses. The contribution of general combining ability to the total variance varied from 24.1 to 35.6 %. The highest contribution of specific combining ability was 1.42 %. By selecting the top 50 % of parental clones for reduced male flower production, the genetic gain in lowering male flower productivity was predicted as 46.1–53.0 %. Conclusion Our results suggest that male flower production in C. japonica is under strong genetic control and that control of male flowering by breeding is possible with a well-designed program.

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Characterization of expressed sequence tags from a full-length enriched cDNA library of Cryptomeria japonica male strobili

Cited by 71 publications

References 67 publications

Spatiotemporal gene expression profiles associated with male strobilus development in Cryptomeria japonica by suppression subtractive hybridization

Spatiotemporal gene expression profiles associated with male strobilus development in Cryptomeria japonica by suppression subtractive hybridization

Evolutionary rate variation in two conifer species, <i>Taxodium</i> <i>distichum</i> (L.) Rich. var. <i>distichum</i> (baldcypress) and <i>Cryptomeria japonica</i> (Thunb. ex L.f.) D. Don (Sugi, Japanese cedar)

Inheritance of male flower production in Cryptomeria japonica (sugi) estimated from analysis of a diallel mating test

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