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 Resources>>Comparative Genomics>>Intra-species Comparison:
I. Introduction for 5 genome-sequenced Sesamum indicum varities

Until now, the researchers from all over the world have released genome sequences of 5 S. indicum varities, including Zhongzhi13, Yuzhi11, Swetha, Baizhima and Mishuozhima.  The genome sequences of S. indicum var. Zhongzhi13 was released by Oil Crops Research Institute, Chinese Academy of Agricultrual Sciences, P.R.China. Its genome size was 269Mb, which was assembled 13 chromosomes and 4,436 unanchored scaffold sequences [1]. The genome sequences of S. indicum var. Yuzhi11 was released by Henan Sesame Research Center, Henan Academy of Agricultural Sciences, P.R.China. Its genome size was 209Mb, which was assembled 5,868 unanchored scaffold sequences [2]. The genome sequences of S. indicum var. Swetha was released by Division of Genomic Resources, National Bureau of Plant Genetic Resources, Indian Council of Agricultural Research, Ministry of Agriculture, India. Its genome size was 344Mb, which was assembled 76,023 unanchored scaffold sequences [3]. The genome sequences of S. indicum var. Baizhima and Mishuozhima were released by Oil Crops Research Institute, Chinese Academy of Agricultrual Sciences, P.R.China. Their genome size were 263Mb and 248Mb, which were assembled 73,395 and 49,167 unanchored contig sequences [4].

II. The collinear analysis among  5 genome-sequenced Sesamum indicum varities or cultivars

The collinear analysis among 5 genome-sequenced Sesamum indicum varities were employed a new algorithm, Burrows-Wheeler Aligner's Smith-Waterman Alignment (BWA-SW), which was used to align long sequences up to 1 Mb against a large sequences. The algorithm is as accurate as SSAHA2, more accurate than BLAT, and is several to tens of times faster than both. [5].

Species Total Scaffolds or Contigs Anchored Scaffolds or Contigs Unanchored Scaffolds or Contigs
Sesamum indicum var. Zhongzhi13 vs. var. Yuzhi11 5,868 2,788 3,080
Sesamum indicum var. Zhongzhi13 vs. var. Swetha 76,023 18,390 57,633
Sesamum indicum var. Zhongzhi13 vs. cv. Baizhima 73,395 18,825 54,570
Sesamum indicum var. Zhongzhi13 vs. cv. Mishuozhima 49,167 21,373 27,794

 
Reference:

1. Linhai Wang, Qiuju Xia, Yanxin Zhang, Xiaodong Zhu, Xiaofeng Zhu, Donghua Li, Xuemei Ni, Yuan Gao, Haitao Xiang, Xin Wei, Jingyin Yu, Zhiwu Quan and Xiurong Zhang. Updated sesame genome assembly and fine mapping of plant height and seed coat color QTLs using a new high-density genetic map. BMC Genomics 2016, 17:31, doi: 10.1186/s12864-015-2316-4.

2. Haiyang Zhang, Hongmei Miao, Lei Wang, Lingbo Qu, Hongyan Liu, Qiang Wang and Meiwang Yue.Genome sequencing of the important oilseed crop Sesamum indicum L. Genome Biology 2013, 14:401, http://genomebiology.com/2013/14/1/401.

3. Downloaded from https://www.ncbi.nlm.nih.gov/Traces/wgs/?val=JPLX01.

4. Xin Wei, Kunyan Liu, Yanxin Zhang, Qi Feng, Linhai Wang, Yan Zhao, Donghua Li, Qiang Zhao, Xiaodong Zhu, Xiaofeng Zhu, Wenjun Li, Danlin Fan, Yuan Gao, Yiqi Lu, Xianmei Zhang, Xiumei Tang, Congcong Zhou, Chuanrang Zhu, Lifeng Liu, Ruichun Zhong, Qilin Tian, Ziruo Wen, Qijun Weng, Bin Han, Xuehui Huang & Xiurong Zhang. Genetic discovery for oil production and quality in sesame. Nature Communications, 2016, 33:8609, doi: 10.1038/ncomms9609.

5. Heng Li, Richard Durbin. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010, Vol. 26 no. 5, pages 589–595, doi:10.1093/bioinformatics/btp698.
 

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