Exploring the Cunninghamia lanceolata(Lamb.) Hook Genome by BAC Sequencing

Abstract

Cunninghamia lanceolata (Lamb.)Hook is an important economic timber tree in China. However, its genome characteristics have not been extensively assessed. To better understand its genome information, the bacterial artificial chromosome (BAC) library of chinese fir was constructed. A total of 422 BAC clones were selected and divided into 10 pools and sequenced, and with an average insert size of 121 kb, ranging from 97 to 145 kb. A total of 61,902,523 bp of reference sequences were sequenced and assembled, and based on an estimated genome size of 11.6 Gb for Chinese fir, the BAC library was estimated to have a total coverage of 0.53% genome equivalents. Bioinformatics analyses were also performed for repeated sequences, tRNAs, coding gene prediction, and functional annotation. The results of this study provide insights into the brief structure of the Chinese fir genome and has generated gene data that will facilitate molecular investigations on the mechanisms underlying tree growth.

Keywords: BAC; China; Chinese fir; Cunninghamia lanceolata (lamb.); genome.

FIGURE 1

Pulsed-field gel electrophoresis of randomly selected. clones from Chinese fir BAC library.

FIGURE 2

Distribution of the insert fragments from the Chinese fir BAC library.

FIGURE 3

Venn diagram of the number of proteins annotated against public protein databases. A total of 445 proteins were differentially expressed, of which 336, 257, and 387 genes were functionally annotated using GO, KOG, and KEGG, respectively. Around 169 tags were shared by the three groups.

FIGURE 4

GO classification.

FIGURE 5

KOG classification.

FIGURE 6

KEGG classification.

FIGURE 7

Percentagedot plot analysis of SSR locus statistics using BAC data.

FIGURE 8

The fragment matching rate insix pools.