Genome size and sequence composition of moso bamboo: a comparative study.
Moso bamboo (Phyllostachys pubescens) is one of the world's most important bamboo species. It has the largest area of all planted bamboo--over two-thirds of the total bamboo forest area--and the highest economic value in China. Moso bamboo is a tetraploid (4x=48) and a special member of the grasses family. Although several genomes have been sequenced or are being sequenced in the grasses family, we know little about the genome of the bambusoids (bamboos). In this study, the moso bamboo genome size was estimated to be about 2034 Mb by flow cytometry (FCM), using maize (cv. B73) and rice (cv. Nipponbare) as internal references. The rice genome has been sequenced and the maize genome is being sequenced. We found that the size of the moso bamboo genome was similar to that of maize but significantly larger than that of rice. To determine whether the bamboo genome had a high proportion of repeat elements, similar to that of the maize genome, approximately 1000 genome survey sequences (GSS) were generated. Sequence analysis showed that the proportion of repeat elements was 23.3% for the bamboo genome, which is significantly lower than that of the maize genome (65.7%). The bamboo repeat elements were mainly Gypsy/DIRS1 and Ty1/Copia LTR retrotransposons (14.7%), with a few DNA transposons. However, more genomic sequences are needed to confirm the above results due to several factors, such as the limitation of our GSS data. This study is the first to investigate sequence composition of the bamboo genome. Our results are valuable for future genome research of moso and other bamboos.
Gui
YiJie
Y
Institute of Crop Science/Institute of Bioinformatics, Zhejiang University, Hangzhou 310029, China.
Wang
Sheng
S
Quan
LiYan
L
Zhou
ChangPing
C
Long
ShiBao
S
Zheng
HuaJun
H
Jin
Liang
L
Zhang
XianYin
X
Ma
NaiXun
N
Fan
LongJiang
L
D004247:DNA / Q000378:metabolism; D004251:DNA Transposable Elements / Q000235:genetics; D030562:Databases, Protein; D019143:Evolution, Molecular; D005434:Flow Cytometry / Q000379:methods; D018745:Genome, Plant; D008957:Models, Genetic; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics; D018626:Retroelements; D031787:Sasa / Q000235:genetics*; D013045:Species Specificity; D020079:Terminal Repeat Sequences; D003313:Zea mays / Q000235:genetics
D004251:DNA Transposable Elements; D018626:Retroelements; D004247:DNA