Abstract:
Paris polyphylla
Smith var.
yunnanensi
s (Liliaceae) is an important traditional
medicinal plant of the Yunnan Province in China. Ho
wever, the genomic information
regarding this plant is limited. To further underst
and its molecular background, we
conducted Illumina HiSeq 2000 second-generation seq
uencing of this plant species.
Approximately 30,198,679 reads with an average leng
th of 202 bases were obtained from
its root cells. These reads were assembled into 56,
095 unique sequences and
approximately 49.7% of the unique sequences were an
notated by Basic Local Alignment
Search Tool (BLAST) similarity searches against pub
lic sequence databases. Most of
these unigenes were mapped to carbohydrate metaboli
sm, energy metabolism, and
secondary metabolite biosynthetic pathways. Additio
nally, 3,853 EST-SSRs were
identified as potential molecular markers in our un
igenes. Of these, 9 nuclear SSR
markers were employed to assess genetic diversity a
nd structure of 11 geographically
disjunct populations. The present study revealed a
moderate genetic diversity (He= 0.527)
and low genetic differentiation (Fst= 0.103), which
may be ascribed to an earlier period of
more pronounced gene flow when the species had a mo
re continuous distribution. The 11
studied populations were divided into two clusters
based on the UPGMA dendrogram,
which were not congruent with their geographical di
stributions. Overall, the root
transcriptome sequences generated in this study rev
eal novel gene expression profiles and
offer important clues for further study of the mole
cular mechanism of
Paris
’ root
secondary metabolite synthesis and population genet
ics. The EST-SSR markers identified
will also facilitate marker-assisted selection in
Paris
breeding.
Keywords:
HiSeq second-generation sequence, Saponin, Simple s
equence repeat.
