Transcriptome and proteomic analysis of mango (Mangifera indica Linn) fruits.
Here we used Illumina RNA-seq technology for transcriptome sequencing of a mixed fruit sample from 'Zill' mango (Mangifera indica Linn) fruit pericarp and pulp during the development and ripening stages. RNA-seq generated 68,419,722 sequence reads that were assembled into 54,207 transcripts with a mean length of 858bp, including 26,413 clusters and 27,794 singletons. A total of 42,515(78.43%) transcripts were annotated using public protein databases, with a cut-off E-value above 10(-5), of which 35,198 and 14,619 transcripts were assigned to gene ontology terms and clusters of orthologous groups respectively. Functional annotation against the Kyoto Encyclopedia of Genes and Genomes database identified 23,741(43.79%) transcripts which were mapped to 128 pathways. These pathways revealed many previously unknown transcripts. We also applied mass spectrometry-based transcriptome data to characterize the proteome of ripe fruit. LC-MS/MS analysis of the mango fruit proteome was using tandem mass spectrometry (MS/MS) in an LTQ Orbitrap Velos (Thermo) coupled online to the HPLC. This approach enabled the identification of 7536 peptides that matched 2754 proteins. Our study provides a comprehensive sequence for a systemic view of transcriptome during mango fruit development and the most comprehensive fruit proteome to date, which are useful for further genomics research and proteomic studies.


CONCLUSIONS
Our study provides a comprehensive sequence for a systemic view of both the transcriptome and proteome of mango fruit, and a valuable reference for further research on gene expression and protein identification. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
Department of Horticulture, State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou 310058, China; Ministry of Agriculture Key Laboratory of Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, Guangdong, China.
Hong-xia
HX
Wu
Department of Horticulture, State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou 310058, China.
Hui-min
HM
Jia
Ministry of Agriculture Key Laboratory of Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, Guangdong, China.
Xiao-wei
XW
Ma
Ministry of Agriculture Key Laboratory of Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, Guangdong, China.
Song-biao
SB
Wang
Ministry of Agriculture Key Laboratory of Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, Guangdong, China.
Quan-sheng
QS
Yao
Ministry of Agriculture Key Laboratory of Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, Guangdong, China.
Wen-tian
WT
Xu
Ministry of Agriculture Key Laboratory of Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, Guangdong, China.
Yi-gang
YG
Zhou
Department of Horticulture, State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou 310058, China. Electronic address: gaozhongshan@zju.edu.cn.
Zhong-shan
ZS
Gao
Ministry of Agriculture Key Laboratory of Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, Guangdong, China.
Ru-lin
RL
Zhan
D005638:Fruit / Q000235:genetics / Q000378:metabolism; D031022:Mangifera / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000096:biosynthesis / Q000235:genetics; D020543:Proteome / Q000096:biosynthesis / Q000235:genetics; D040901:Proteomics / Q000379:methods; D018749:RNA, Plant / Q000096:biosynthesis / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods; D059467:Transcriptome / Q000502:physiology*
D010940:Plant Proteins; D020543:Proteome; D018749:RNA, Plant
Mango (Mangifera indica Linn.); Mass spectrometry; Proteomics; RNA-Seq; Transcriptome