Transcriptome analysis of immature xylem in the Chinese fir at different developmental phases

Abstract

Background.Chinese fir [Cunninghamia lanceolata (Lamb.) Hook.] is one of the most important native tree species for timber production in southern China. An understanding of overall fast growing stage, stem growth stage and senescence stage cambium transcriptome variation is lacking. We used transcriptome sequencing to identify the repertoire of genes expressed during development of xylem tissue in Chinese fir, aiming to delineate the molecular mechanisms of wood formation. Results. We carried out transcriptome sequencing at three different cultivation ages (7Y, 15Y and 21Y) generating 68.71 million reads (13.88 Gbp). A total of 140,486 unigenes with a mean size of 568.64 base pairs (bp) were obtained via de novo assembly. Of these, 27,427 unigenes (19.52%) were further annotated by comparison to public protein databases. A total of 5,331 (3.79%) unigenes were mapped into 118 pathways by searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Differentially expressed genes (DEG) analysis identified 3, 16 and 5,899 DEGs from the comparison of 7Y vs. 15Y, 7Y vs. 21Y and 15Y vs. 21Y, respectively, in the immature xylem tissues, including 2,638 significantly up-regulated and 3,280 significantly down-regulated genes. Besides, five NAC transcription factors, 190 MYB transcription factors, and 34 WRKY transcription factors were identified respectively from Chinese fir transcriptome.Conclusion. Our results revealed the active transcriptional pathways and identified the DEGs at different cultivation phases of Chinese fir wood formation. This transcriptome dataset will aid in understanding and carrying out future studies on the molecular basis of Chinese fir wood formation and contribute to future artificial production and applications.

Transcriptome analysis provides insights into wood formation during larch tree aging

“…The molecular aspects of the effects of age on wood formation in trees have been studied, and different classes of genes controlling wood formation have been revealed (Li et al 2010Xu et al 2016;Zhang et al 2016). Especially, using cryosectioning and RNA-Seq methods, Xu et al (2016) compared the transcriptome of vascular cambium tissue in Cunninghamia lanceolata at juvenile, transitional, and mature stages to study the effects of age on cambium activity.…”

“…In studies of the molecular mechanisms of tree aging, many age-related genes have been identified (Busov et al 2004;Carlsbecker et al 2004;Diego et al 2004;Fernández-Ocaña et al 2010;García-López et al 2014;Hutchison et al 1990;Li et al 2010Xu et al 2016;Zhang et al 2016), such as miR156 (Wang et al 2011b) and Flowering Locus T (Böhlenius et al 2006;Hsu et al 2006Hsu et al , 2011, and some have been used to change the agronomic traits of plants (Flachowsky et al 2012;Kotoda et al 2006;Li et al 2013a;Yamagishi et al 2014). Larix kaempferi is a forest tree of important ecological and economic value, widely grown in the Northern Hemisphere, but its genome has not been sequenced.…”

Chinese Fir Breeding in the High-Throughput Sequencing Era: Insights from SNPs

“…This feature makes it more attractive for conifer tree breeders to adopt the high-throughput sequencing (HTS) platform as a straightforward tool in their molecular breeding program.Chinese fir (Cunninghamia lanceolata) is one of the major commercial conifer species in China. It covers~21.4% of man-made plantations and supplies up to 20%-30% of the total commercial timber production of China [19,20]. Highly valued for timber and essential ecosystem services this conifer has been used as a major breeding subject of the tree improvement programs of China for over 50 years [21].…”

Peer Review #1 of "Genome-wide identification and expression analysis of the MYB transcription factor in moso bamboo (Phyllostachys edulis) (v0.2)"

“…In the present study, 85 PeMYBs were identified in moso bamboo, and the number of PeMYB members was slightly less than that found in other monocotyledonous and dicotyledonous plants (Dubos et al, 2010;Li et al, 2016c;Zhang et al, 2016). It is likely that the bamboo genome is a draft, which does not cover the entire genome (Peng et al, 2013).…”

“…Diametrically, the amino acid sequence outside of the DNAbinding domain, the C-terminus, is an activated structure that is highly divergent in length and sequence, which gives rise to the functional diversity of the MYB proteins (Kranz, Scholz & Weisshaar, 2000;Jin & Martin, 1999). Based on the number of repeats, the MYB family is classified into four subfamilies, namely, 1R-MYB (MYB-related), 2R-MYB (R2R3-MYB), 3R-MYB (R1R2R3-MYB) and 4R-MYB (Dubos et al, 2010;He et al 2016). In plants, R2R3-MYB are the largest and most common MYB TFs (Dubos et al, 2010;Du et al, 2013;Niu, Jiang & Xu, PeerJ reviewing PDF | (2018:08:30682:2:1:NEW 7 Dec 2018)…”