Transcriptome Characteristics and Six Alternative Expressed Genes Positively Correlated with the Phase Transition of Annual Cambial Activities in Chinese Fir (Cunninghamia lanceolata (Lamb.) Hook)

Abstract

BackgroundThe molecular mechanisms that govern cambial activity in angiosperms are well established, but little is known about these molecular mechanisms in gymnosperms. Chinese fir (Cunninghamia lanceolata (Lamb.) Hook), a diploid (2n = 2x = 22) gymnosperm, is one of the most important industrial and commercial timber species in China. Here, we performed transcriptome sequencing to identify the repertoire of genes expressed in cambium tissue of Chinese fir.Methodology/Principal FindingsBased on previous studies, the four stage-specific cambial tissues of Chinese fir were defined using transmission electron microscopy (TEM). In total, 20 million sequencing reads (3.6 Gb) were obtained using Illumina sequencing from Chinese fir cambium tissue collected at active growth stage, with a mean length of 131 bp and a N50 of 90 bp. SOAPdenovo software was used to assemble 62,895 unigenes. These unigenes were further functionally annotated by comparing their sequences to public protein databases. Expression analysis revealed that the altered expression of six homologous genes (ClWOX1, ClWOX4, ClCLV1-like, ClCLV-like, ClCLE12, and ClPIN1-like) correlated positively with changes in cambial activities; moreover, these six genes might be directly involved in cambial function in Chinese fir. Further, the full-length cDNAs and DNAs for ClWOX1 and ClWOX4 were cloned and analyzed.ConclusionsIn this study, a large number of tissue/stage-specific unigene sequences were generated from the active growth stage of Chinese fir cambium. Transcriptome sequencing of Chinese fir not only provides extensive genetic resources for understanding the molecular mechanisms underlying cambial activities in Chinese fir, but also is expected to be an important foundation for future genetic studies of Chinese fir. This study indicates that ClWOX1 and ClWOX4 could be possible reverse genetic target genes for revealing the molecular mechanisms of cambial activities in Chinese fir.

Transcriptome Characterization of the Chinese Fir (Cunninghamia lanceolata (Lamb.) Hook.) and Expression Analysis of Candidate Phosphate Transporter Genes

“…The unigenes which were not annotated in the existing databases might lack a characterized protein domain to match in the database, but some of those unigenes could also be potential specific genes for Chinese fir. In total, 203,404 unigenes were annotated in our study, which was far more than the previous study of the number of unigenes in the Chinese fir [23,25]. The species similarity analysis revealed possible incompletely defined genetic backgrounds for Chinese fir [48].…”

“…However, the quality of the data may be affected by several factors, including the contamination of adapter sequences, poor quality reads, and assembly errors [23]. In this study, a total of 236,529,278 clean reads and 35.47 Gbs of databases were obtained from Chinese fir transcriptomes, which is much more than any previously published transcriptome research on Chinese fir [23][24][25]43]. Due to a lack of homologous unigenes, the average length of unigenes for non-model plants is usually less than 500 bp [26,44,45].…”

“…As a non-model plant species with a very large genome size that is typical of conifers (20 to 30 Gb), the limited molecular research of Chinese fir has focused primarily on transcript profile investigations and patterns of gene expression [24,25]. However, the development of next-generation DNA sequencing technologies provides a revolutionary tool for transcriptomics to detect information about a given sample's RNA content [23].…”

“…Huang et al used transcriptome sequencing to characterize the candidate genes related to cellulose and lignin biosynthesis in Chinese fir; in total, they found 49 unigenes [23]. Wang et al characterized the cambial tissues transcriptome of Chinese fir and identified six alternatively expressed genes correlated with cambial activities [25]. These recently acquired transcriptome data for Chinese fir have been highly informative, but until now, have been limited and only focused on vascular cambium activity or dark-grown cotyledons, and no root or leaf transcriptome data has been released in NCBI (National Center for Biotechnology Information) to date (as of August 2017).…”

Effects of different mixed planting patterns on nutrient contents in Cunninghamia lanceolata

“…It is one of the most important timber tree species in South China and the number and area of C. lanceolata plantations is still increasing [1]. With the continuous development of society, the demand for C. lanceolata is increasing and becoming more and more important in social economy [2]. However, yield decline in C. lanceolata plantations has become a big problem in recently years because of the bad forest management of C. lanceolata plantation, such as successive short rotations and slash burning, which caused primarily the depletion of soil nutrient [3][4][5].…”