Construction and characterization of a bacterial artificial chromosome library for Camellia sinensis
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Tea is a popular and natural non-alcoholic beverage, and is produced from fresh leaves of Camellia sinensis. Tea leaves contain many bioactive compounds that have significant health benefits. We constructed a high quality bacterial artificial chromosome (BAC) library by using the fresh petals of C. sinensis “Shuchazao” for genome sequencing and improvement of genomic assembly. BAC library is still a significant tool for studies of functional genomes and preservation of precious genetic resources. The BAC library contains 161,280 clones with an average insert size of 113 kb, which represents approximately 6.2-fold coverage of haploid genome equivalents of C. sinensis. We characterized 20 complete BAC clones and 738 BAC end sequences (BESs) ranging from 105 to 917 bp. In addition, we predicted cis-regulatory elements of LAR (leucoanthocyanidin reductase), TCS (caffeine synthase), and TS (theanine synthetase) involved in tea characteristic metabolite synthesis and identified a larger number of light-responsive cis-acting elements in these three genes. Meanwhile, we analyzed alternative splicing of these three genes. Furthermore, 12 pairs of SSR primers were successfully amplified in tea plant DNA. The tea BAC library was a critical resource to accomplish de novo whole-genome sequencing, accelerate gene discovery and enhance molecular breeding of C. sinensis.
KeywordsTea plant BAC library BAC end sequencing SSR Alternative splicing
This work received financial support from the Science and Technology Project of AnHui Province, China (Project 13Z03012), Tea Genome Project of AnHui Province, China, the Special Innovative Province Construction in Anhui province in 2015 (15czs08032), the Central Guiding the Science and Technology Development of the Local (2016080503B024), the Major Project of Chinese National Programs for Fundamental Research and Development (2012CB722903), the Natural Science Foundation of Anhui Province (No.1608085QC60), and the Youth Foundation of Anhui Agricultural University (2016ZR012). We appreciate Chun Liu (Beijing Genome Institute at Shenzhen, China) for technical support and analysis. We are grateful to the unknown editor at the elixigen editing service (ID151023-6181) for the English polishing.
Conceived and designed the experiment: WC and SJ; analyzing data: WL, WH, TL, JY, LZ, YH, and DW; experiment: SL, DZ, SY, HB, WQ, and LM. TL and WH contributed to writing the text.
Compliance with ethical standards
The authors declare that they have no competing interests.
- Ammiraju JS, Meizhong L, Goicoechea JL, Wenming W, Dave K, Christopher M et al (2006) The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza. Genome Res 16:140–147CrossRefPubMedPubMedCentralGoogle Scholar
- Chen, P. (2010). Shading effects and influences on photosynthesis and quality component of tea in tea plantation. Hunan Agricultural UniversityGoogle Scholar
- Feng C, Bluhm BH, Correll JC (2015) Construction of a spinach bacterial artificial chromosome (BAC) library as a resource for gene identification and marker development. Plant Molecular. Biology Reporter:1–10Google Scholar
- Gordon D (2003) Viewing and editing assembled sequences using Consed. Current protocols in bioinformatics 11.12(11-11.12):43Google Scholar
- Jin Q, Chen Z, Sun W, Lin F, Xue Z, Huang Y, Tang X (2016) Cloning and Bioinformatical analysis of anthocyanin synthase gene and its promoter in Camellia sinensis. J Tea Sci 36:219–228Google Scholar
- Kuehnbaum NL, Kormendi A, Britz-McKibbin P (2013) Multisegment injection-capillary electrophoresis-mass spectrometry: a high-throughput platform for metabolomics with high data fidelity. Anal Chem 85:10664–10669Google Scholar
- Li P (2005) International Rice Genome Sequencing Project. 2005. The map-based sequence of the rice genome. Nature 436:793–800Google Scholar
- Lin J, Kudrna D, Wing RA (2011) Construction, characterization, and preliminary BAC-end sequence analysis of a bacterial artificial chromosome library of the tea plant (Camellia sinensis) J Biomed Biotechnol 2011:476723Google Scholar
- Liu J, Yuan D, Si H, Pang X, Tang X, Yang J (2013a) Effects of shading on ingredients of tea shoots in different seasons. Southwest China J Agric Sci 26:115–118Google Scholar
- Liu C, Guo Y, Lu T, Wu H, Na R, Li X, Guan W, Ma Y (2013b) Construction and preliminary characterization analysis of Wuzhishan miniature pig bacterial artificial chromosome library with approximately 8-fold genome equivalent coverage. Biomed Res Int Google Scholar
- Luo M, Wing RA (2003) An improved method for plant BAC library construction. In: Plant functional genomics. Springer, pp 3–19Google Scholar
- Matsuura T, Kakuda T (1990) Effects of precursor, temperature, and illumination on Theanine accumulation in tea callus. Agric Biol Chem 37:2033–2051Google Scholar
- Pan Y, Deng Y, Lin H, Kudrna DA, Wing RA, Li L, Zhang Q, Luo M (2014) Comparative BAC-based physical mapping of Oryza sativa ssp. indica var. 93–11 and evaluation of the two rice reference sequence assemblies. Plant J 77:795-805Google Scholar
- Rozen S, Skaletsky H (1999) Primer3 on the WWW for general users and for biologist programmers. Bioinforma Methods Protocol:365–386Google Scholar
- Sasazuki S, Tamakoshi A, Matsuo K, Ito H, Wakai K, Nagata C, Mizoue T, Tanaka K, Tsuji I, Inoue M, Tsugane S (2012) Green tea consumption and gastric cancer risk: an evaluation based on a systematic review of epidemiologic evidence among the Japanese population. Jpn J Clin Oncol 42:335–346CrossRefPubMedGoogle Scholar
- Taniguchi F, Hirai, N. and Yamaguchi, S, (2006) Estimation of the genome size of tea (Camellia sinensis), camellia (C. japonica), and their interspecific hybrids by flow cytometry. Journal of the Remote Sensing Society of Japan (Japan):1-7Google Scholar
- Wu C, Nimmakayala P, Santos F, Springman R, Scheuring C, Meksem K, Lightfoot D, Zhang H (2004) Construction and characterization of a soybean bacterial artificial chromosome library and use of multiple complementary libraries for genome physical mapping. Theor Appl Genet 109:1041–1050CrossRefPubMedGoogle Scholar
- Xia E, Zhang H, Sheng J, Li K, Zhang Q, Kim C, et al (2017) The tea tree genome provides insights into tea flavor and independent evolution of caffeine biosynthesis. Molecular PlantGoogle Scholar
- Yim Y, Davis G, Duru N, Musket T, Linton E, Messing J, McMullen M, Soderlund C, Polacco M, Gardiner J, Coe E (2002) Characterization of three maize bacterial artificial chromosome libraries toward anchoring of the physical map to the genetic map using high-density bacterial artificial chromosome filter hybridization. Plant Physiol 130:1686–1696CrossRefPubMedPubMedCentralGoogle Scholar
- Zhang H, Xia E, Huang H, Jiang J, Liu B, Gao L (2015) De novo transcriptome assembly of the wild relative of tea tree (Camellia taliensis) and comparative analysis with tea transcriptome identified putative genes associated with tea quality and stress response. BMC Genomics 16:298CrossRefPubMedPubMedCentralGoogle Scholar