Abstract Detail

Phylogenomics

Jung, Jongduk [1], Kim, Kyung Hee [2], Yang, Tae-Jin [2], Park, Jongsun [3], Kim, Sangtae [4].

A complete chloroplast sequences from Carex siderosticta Hance (Cyperaceae): one of the largest chloroplast genome in angiosperms.

  Determination of the complete chloroplast (cp) genome for a taxon included in a certain clade of angiosperms is crucial to understand the evolution and diversification of that clade. To date, complete cp genome sequences have been determined from about 450 taxa in angiosperms. Although Poales is one of the largest orders in angiosperms, cp genomes from only two families (Typhaceae and Poaceae) in 18 families of Poales have been reported. Cyperaceae is one of the largest families in Poales. In this study, we successfully determined the entire cp genome of Carex siderosticta, a representative of Cyperaceae, based on the Next Generation Sequencing (NGS) technique using the Illumina/Solexa platform. In the raw reads of the 45 G base pairs, the cp genome sequences are filtered using the reference cp genomes (Typha latifolia and Oryza sativa) and are successfully assembled with multiple assemblers. Four borders of two inverted repeat regions and other ambiguous parts in the assembled sequences were confirmed by the Sanger method. Chloroplast genome of C. siderosticta was extremely large (195,251 bp) compare to the previously reported cp genomes in angiosperms. To detect structural variations, cp genome of C. siderosticta was directly compared with two previously reported cp genomes in Poales (T. latifolia and O. sativa). We confirmed that the large size of cp genome is due to the expansion of two inverted repeat regions (IR), having 41,905 bps per an IR: the size of an IR in T. latifolia and O. sativa is only 25 Kbps and 21 Kbps, respectively. Hypothetical structural symplesiomorphic features were reconstructed with the phylogenetic tree of Poales.

1 - Sungshin Women's University, Department of Biology, Seoul , 136-742, Rep. of Korea
2 - Seoul National University, Department of Plant Science, College of Agriculture and Life Science, Seoul, 151-742, Rep. of Korea
3 - Stronghold Innovation Center, Seoul, Republic of Korea
4 - Sungshin Women's University, Department of Biology, Seoul 136-742, Rep. of Korea

Keywords:
Carex siderosticta
Cyperaceae
Chloroplast genome
Illumina
IR.

Presentation Type: Poster:Posters for Topics
Session: P
Location: Eyrie/Boise Centre
Date: Monday, July 28th, 2014
Time: 5:30 PM
Number: PPL004
Abstract ID:736
Candidate for Awards:None