title: Carotenoid biosynthetic genes in Brassica rapa: comparative genomic analysis, phylogenetic analysis, and expression profiling.
abstract: BACKGROUND
  Carotenoids are isoprenoid compounds synthesized by all photosynthetic organisms. Despite much research on carotenoid biosynthesis in the model plant Arabidopsis thaliana, there is a lack of information on the carotenoid pathway in Brassica rapa. To better understand its carotenoid biosynthetic pathway, we performed a systematic analysis of carotenoid biosynthetic genes at the genome level in B. rapa.
  
  
  RESULTS
  We identified 67 carotenoid biosynthetic genes in B. rapa, which were orthologs of the 47 carotenoid genes in A. thaliana. A high level of synteny was observed for carotenoid biosynthetic genes between A. thaliana and B. rapa. Out of 47 carotenoid biosynthetic genes in A. thaliana, 46 were successfully mapped to the 10 B. rapa chromosomes, and most of the genes retained more than one copy in B. rapa. The gene expansion was caused by the whole-genome triplication (WGT) event experienced by Brassica species. An expression analysis of the carotenoid biosynthetic genes suggested that their expression levels differed in root, stem, leaf, flower, callus, and silique tissues. Additionally, the paralogs of each carotenoid biosynthetic gene, which were generated from the WGT in B. rapa, showed significantly different expression levels among tissues, suggesting differentiated functions for these multi-copy genes in the carotenoid pathway.
  
  
  CONCLUSIONS
  This first systematic study of carotenoid biosynthetic genes in B. rapa provides insights into the carotenoid metabolic mechanisms of Brassica crops. In addition, a better understanding of carotenoid biosynthetic genes in B. rapa will contribute to the development of conventional and transgenic B. rapa cultivars with enriched carotenoid levels in the future.
authors.affiliation: Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No. 12, Beijing, 100081, P. R. China. lprdream@126.com.
authors.forename: Peirong
authors.initials: P
authors.lastname: Li
authors.affiliation: Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No. 12, Beijing, 100081, P. R. China. zhangshujiang@caas.cn.
authors.forename: Shujiang
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No. 12, Beijing, 100081, P. R. China. zhangshifan@caas.cn.
authors.forename: Shifan
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No. 12, Beijing, 100081, P. R. China. lifei@mail.caas.net.cn.
authors.forename: Fei
authors.initials: F
authors.lastname: Li
authors.affiliation: Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No. 12, Beijing, 100081, P. R. China. zhanghui05@caas.cn.
authors.forename: Hui
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No. 12, Beijing, 100081, P. R. China.
authors.forename: Feng
authors.initials: F
authors.lastname: Cheng
authors.affiliation: Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No. 12, Beijing, 100081, P. R. China. wujian@caas.cn.
authors.forename: Jian
authors.initials: J
authors.lastname: Wu
authors.affiliation: Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No. 12, Beijing, 100081, P. R. China. wangxiaowu@caas.cn.
authors.forename: Xiaowu
authors.initials: X
authors.lastname: Wang
authors.affiliation: Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No. 12, Beijing, 100081, P. R. China. sunrifei@caas.cn.
authors.forename: Rifei
authors.initials: R
authors.lastname: Sun
mesh_terms: D053898:Biosynthetic Pathways; D029741:Brassica rapa / Q000737:chemistry / Q000235:genetics*; D002338:Carotenoids / Q000096:biosynthesis* / Q000235:genetics; D032461:Chromosomes, Plant; D018506:Gene Expression Regulation, Plant; D005810:Multigene Family; D009928:Organ Specificity; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D026801:Synteny
chemical_list: D010940:Plant Proteins; D002338:Carotenoids