Construction, characterization, and preliminary BAC-end sequence analysis of a bacterial artificial chromosome library of the tea plant (Camellia sinensis).

Jinke Lin,Rod A Wing,Dave Kudrna

doi:10.1155/2011/476723

Abstract

We describe the construction and characterization of a publicly available BAC library for the tea plant, Camellia sinensis. Using modified methods, the library was constructed with the aim of developing public molecular resources to advance tea plant genomics research. The library consists of a total of 401,280 clones with an average insert size of 135 kb, providing an approximate coverage of 13.5 haploid genome equivalents. No empty vector clones were observed in a random sampling of 576 BAC clones. Further analysis of 182 BAC-end sequences from randomly selected clones revealed a GC content of 40.35% and low chloroplast and mitochondrial contamination. Repetitive sequence analyses indicated that LTR retrotransposons were the most predominant sequence class (86.93%–87.24%), followed by DNA retrotransposons (11.16%–11.69%). Additionally, we found 25 simple sequence repeats (SSRs) that could potentially be used as genetic markers.

Highlights

Since 1994, bacterial artificial chromosome (BAC) libraries have become an invaluable resource tool to initiate genomics research in the areas of genome sequencing, physical mapping, positional cloning, complex analysis of targeted genomic regions, and analysis of gene structure and function [1,2,3,4,5,6,7,8]
To avoid contamination with small, trapped DNA fragments and improve the size and uniformity of the inserts, the high molecular weight (HMW) genomic DNA was partially digested with HindIII and three separate size fractionations were collected
We found that Long terminal repeats (LTRs) retrotransposons are the predominant class of repeat elements in C. sinensis followed by DNA retroelements

Summary

Introduction

Since 1994, bacterial artificial chromosome (BAC) libraries have become an invaluable resource tool to initiate genomics research in the areas of genome sequencing, physical mapping, positional cloning, complex analysis of targeted genomic regions, and analysis of gene structure and function [1,2,3,4,5,6,7,8]. BAC-end sequencing (BES) is a powerful tool that enhances the value of BAC libraries as a genomic resource by providing partial sequence information that can be used to understand genome content and architecture and develop genetic markers [10, 11]. Tea (Camellia sinensis) is an important world beverage [15]. Tea polyphenols (catechins) and antioxidants, saponin, polysaccharides, L-theanine, pigments, and tea water extracts are the most important components that contribute to tea’s medicinal qualities [16,17,18,19]

Methods

Results

Discussion

Conclusion