PRJNA731285
Chromosome-scale genomes of wild mulberry highlight the evolution of karyotype, sex determination, adaptation and domestication of mulberry
Wild mulberries are valuable genetic resources for studying evolution of karyotype and domestication. Morus. notabilis and Morus. yunnanensis are obviously different from the cultivated mulberry (Morus alba) in karyotype and adaptability. Their underlying mechanisms of adaptation and contributions to the cultivated mulberry remain unknown. By using a combination of the single molecule real-time (SMRT) sequencing technology from Pacific Biosciences (PacBio), next-generation sequencing technology, and high-resolution chromosome conformation capture (Hi-C), the genome of two wild mulberry species M. notabilis and M. yunnanensis were sequenced and assembled, respectively.We generated a total of ~16 Gb (~45-fold coverage, 1.57 million reads) of PacBio long reads, 167-fold coverage high- throughput chromatin conformation capture (Hi-C) data, and 70-fold coverage of Illumina paired-end reads (21.3 Gb) for M. notabilis. A total of ~29 Gb (~81-fold coverage, 1.92 million reads) of PacBio long reads, 165-fold coverage high- throughput chromatin conformation capture (Hi-C) data, and 65-fold coverage of Illumina paired-end reads (20.6 Gb) for M. yunnanensis. After primary assembly using CANU, we acquired a 333 Mb (1,830 contigs with an N50 of 1.50 Mb) of assembled sequence for M. notabilis. Meanwhile, an assembly of 359 Mb (996 contigs with an N50 of 5.40 Mb) of M. yunnanensis assembled sequence was obtained. Then, the contigs were corrected and polished with corrected PacBio reads and Illumina paired-end sequences. Improved contigs were respectively rebuilt with HaploMerger2 into two sub-assemblies (ref and alt).Finally, by using Hi-C data with Juicer and 3D-dna,the size of ref sub-assembly genome of M. notabilis is 301 Mb, consisting of 539 scaffolds with an N50 of 2.7 Mb at 93.6% BUSCO (BUSCO v3.0.2) completeness, and 96.47% of the entire genome sequences were anchored on 6 chromosomes. The size of ref sub-assembly genome of M. yunnanensis is 313 Mb, consisting of 234 scaffolds with an N50 of 6.5 Mb at 94.1% BUSCO completeness, and 95.1% of the entire genome sequences were anchored on 6 chromosomes.