Whole Genome Sequencing of Chinese and African Water Yam Accessions

According to our field observation and previous phenotype- and SSR-based studies [12 (link),16 (link)], a total of 44 accessions (Table 1) representing the major cultivars of D. alata in China were selected for whole genome sequencing. These accessions, with high phenotypic diversity, covered the main distribution area of this species in China, from west (Lijiang, Yunnan Province, geographic coordinates (gc): 26°43′ N, 100°15′ E) to east (Taizhou, Zhejiang Province, gc: 28°38′ N, 121°27′ E), and from south (Sanya, Hainan Province, gc: 18°24′ N, 109°45′ E) to north (Xuzhou, Jiangsu Province, gc: 34°39′ N, 116°35′ E). In addition, we also specifically selected accessions that have greatly contributed to the breeding and research of this species and accessions highly resistant to abiotic and biotic stress. Genomic DNA from each accession was extracted from fresh or silica gel-dried leaves using a DNAsecure Plant Kit (Tiangen Biotech, Beijing, China), according to the manufacturer’s protocol. The DNA concentration and integrity were measured on an Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA, USA), together with agarose gel electrophoresis. Paired-end libraries with an insert size of 350 bp were constructed and then sequenced on the BGISEQ-500 platform to generate raw sequences with a 150 bp read length. The library construction and sequencing were conducted at Wuhan Benagen Tech Solutions Company Limited, Wuhan, China.
Additionally, whole-genome sequencing datasets encompassing eight African accessions of D. alata (Table 1) were downloaded from the National Centre of Biotechnology Information (NCBI) Sequence Read Archive (SRA) database and were converted to the FASTQ format using the fastq-dump utility from the SRA Toolkit v.2.9.6 [43 (link)].