| Abstract Detail
Recent Topics Posters Lee, Bora [1], Roalson, Eric [2], Kim, Sangtae [1]. Long-read NGS sequencing clarified complex structure of a chloroplast genome in Carex lupulina (Cyperaceae). The chloroplast (cp) genome of Carex has extra-ordinary complex structure compared to that of other typical angiosperms. As a first cp genome in Carex, our previous study showed that cp genome of C. siderosticta was extremely large (195 kbps) and has many short internal repeats (>100 bps). In comparison with Typha, one of the basal-group taxa in Poales, there are big structural changes including six large inversions, three translocations, ten gene losses, and one gene duplication (trnfM-CAU). Only a partial assembly was possible in this study with short Illumina reads and the completion of genome sequence has been done with re-sequencing of entire genome region using Sanger method. In this study, we report a cp genome of C. lupulina as another cp genome in Carex based on Nanopore sequencing. Long-reads of Nanopore sequence enables us to reconstruct the complex structure of cp genome of which complete assembly was not possible just using short-read Illumina platform. The size of cp genome of C. lupulina (246 kbp) was the second largest in the reported angiosperm cp genomes. Compared to C. siderosticta, there are two large inverted translocations (ca. 5.2 kbp and 43 kbp) in the large single-copy region. Long-read NGS sequencing in Carex will be a key tool to understand complex cp structural evolution in Carex.
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1 - Sungshin Univ., Dept. of Biology, Seoul, Seoul, 01133, Republic of Korea
2 - Washington State University, School Of Biological Sciences, Abelson Hall 339, Pullman, WA, 99164, United States
Keywords:
Carex
Nanopore
Chloroplast.
Presentation Type:
Session: P, Recent Topics Posters
Location: Arizona Ballroom/Starr Pass
Date: Monday, July 29th, 2019
Time: 5:30 PM
Number: PRT026
Abstract ID:1403
Candidate for Awards:None |
