Status of Sweetpotato Genome Sequencing Under TRAS Collaboration

Sweetpotato (Ipomoea batatas(L.) Lam) is widely cultivated and consumed as a crop around the world, especially in Eastern Asia. The sweetpotato genome sequencing consortium consist with six organizations, Institute of Sweetpotato Research, Chinese Academy of Agricultural Sciences (China), China Agricultural University (China), Rural Development Administration (Korea), Korea Research Institute of Bioscience and Biotechnology (Korea), National Agriculture and Food Research Organization (Japan) and Kazusa DNA Research Institute (Japan).

Because of the complex genome structure of sweetpotato (2N = 6x = 90, genome size = 2.5Gb) we have tried de novo genome assembly of a wild relative diploid species, I. trifida, prior to sweetpotato. First, de novo whole-genome sequencing was performed with two lines of I. trifida, namely the selfed line Mx23Hm and the highly heterozygous line 0431-1, using the Illumina HiSeq platform. The total lengths of the assembled sequences of Mx23Hm (ITR_r1.0) was 513 Mb, while that of 0431-1 (ITRk_r1.0) was 712 Mb. Then, Pacbio and Illumina assembly scaffolds was constructed for Mx23Hm (ITR_r2.1). Pseudomolecules were developed based on ITR_r2.1 and a SNP linkage map.

Meanwhile sweetpotato genome sequencing of a Chinese variety ‘Xushu 18’ was performed by Illumina and PacBio platforms. The denovo aseembly by FALCON with 155.5 Gb PacBio reads constructed 86,498 scaffolds of which total length was 3.0Gb. Linkage map construction using the S₁ population of Xushu 18 and transcriptome analysis are also performed for alignment of scaffolds and precise gene annotation, respectively.