Abstract
Moso bamboo is an important forest species with a variety of ecological, economic, and cultural values. However, the gene annotation information of moso bamboo is only based on the transcriptome sequencing, lacking the evidence of proteome. The lignification and fiber in moso bamboo leads to a difficulty in the extraction of protein using conventional methods, which seriously hinders research on the proteomics of moso bamboo. The purpose of this study is to establish efficient methods for extracting the total proteins from moso bamboo for following mass spectrometry-based quantitative proteome identification. Here, we have successfully established a set of efficient methods for extracting total proteins of moso bamboo followed by mass spectrometry-based label-free quantitative proteome identification, which further improved the protein annotation of moso bamboo genes. In this study, 10,376 predicted coding genes were confirmed by quantitative proteomics, accounting for 35.8% of all annotated protein-coding genes. Proteome analysis also revealed the protein-coding potential of 1015 predicted long noncoding RNA (lncRNA), accounting for 51.03% of annotated lncRNAs. Thus, mass spectrometry-based proteomics provides a reliable method for gene annotation. Especially, quantitative proteomics revealed the translation patterns of proteins in moso bamboo. In addition, the 3284 transcript isoforms from 2663 genes identified by Pacific BioSciences (PacBio) single-molecule real-time long-read isoform sequencing (Iso-Seq) was confirmed on the protein level by mass spectrometry. Furthermore, domain analysis of mass spectrometry-identified proteins encoded in the same genomic locus revealed variations in domain composition pointing towards a functional diversification of protein isoform. Finally, we found that part transcripts targeted by nonsense-mediated mRNA decay (NMD) could also be translated into proteins. In summary, proteomic analysis in this study improves the proteomics-assisted genome annotation of moso bamboo and is valuable to the large-scale research of functional genomics in moso bamboo. In summary, this study provided a theoretical basis and technical support for directional gene function analysis at the proteomics level in moso bamboo.
Highlights
Bamboo belongs to gramineous plants with about 90 genera and 1200 species [1]
Phenol extraction combined with acetonitrile precipitation method could extract 7192 and 9336 proteins from seedlings and leaves of moso bamboo, respectively
Proteome analysis based on high-resolution mass spectrometry can accurately help to establish and modify genome coding gene annotation information of species, which has been reported in many model plants
Summary
Bamboo belongs to gramineous plants with about 90 genera and 1200 species [1]. It is a major non-wood forest species and widely distributed in tropical, subtropical and temperate zones [2]. Moso bamboo has been cultivated for a long time and is one of the main bamboo species in China, and is rich in lignocellulose [3]. Moso bamboo has many important economic, cultural and ecological values, such as edible bamboo shoot, timber, ornamental, and greening values [5,6,7]. Because of its important economic value and ecological perspectives, it has attracted the attention of community forestry, and has been regarded as the main model plant in the study of plant biology of bambusoideae
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