Draft genomes of two artocarpus plants, jackfruit (A. heterophyllus) and breadfruit (A. altilis)

Abstract

Supplementary material : Figure S1. K-mer (K = 17) analysis of the two genomes, Figure S2. Distribution of sequencing depth of the assembly data, Figure S3. Distribution of the length and number of the sca old in two species, Figure S4. The distribution of GC content, Figure S5. Comparison of GC content across closely related species, Figure S6. Statistics of gene models in A. altilis, A. heterophyllus, F. vesca, M. domestica, M. notabilis, Prunus persica, and Ziziphus jujube, Figure S7. The collinearity between two species, Table S1. Statistics of the raw and clean data of DNA sequencing, Table S2. Summary statistics of the transcriptome data, Table S3. Estimation of the genome size based on K-mer statistics, Table S4. BUSCO evaluation of the annotated protein-coding genes in A. altilis and A. heterophyllus, Table S5. Analysis of gene families of di erent species, Table S6. Enriched GO terms (level 3) of genes in families with expansion, Table S7. Enriched pathways of genes in families with expansion.Two of the most economically important plants in the Artocarpus genus are jackfruit (A. heterophyllus Lam.) and breadfruit (A. altilis (Parkinson) Fosberg). Both species are long-lived trees that have been cultivated for thousands of years in their native regions. Today they are grown throughout tropical to subtropical areas as an important source of starch and other valuable nutrients. There are hundreds of breadfruit varieties that are native to Oceania, of which the most commonly distributed types are seedless triploids. Jackfruit is likely native to theWestern Ghats of India and produces one of the largest tree-borne fruit structures (reaching up to 45 kg). To-date, there is limited genomic information for these two economically important species. Here, we generated 273 Gb and 227 Gb of raw data from jackfruit and breadfruit, respectively. The high-quality reads from jackfruit were assembled into 162,440 sca olds totaling 982 Mb with 35,858 genes. Similarly, the breadfruit reads were assembled into 180,971 sca olds totaling 833 Mb with 34,010 genes. A total of 2822 and 2034 expanded gene families were found in jackfruit and breadfruit, respectively, enriched in pathways including starch and sucrose metabolism, photosynthesis, and others. The copy number of several starch synthesis-related genes were found to be increased in jackfruit and breadfruit compared to closely-related species, and the tissue-specific expression might imply their sugar-rich and starch-rich characteristics. Overall, the publication of high-quality genomes for jackfruit and breadfruit provides information about their specific composition and the underlying genes involved in sugar and starch metabolism.National Key Research and Development Program of China (No. 2016YFE0122000), the Shenzhen Municipal Government of China, (no. JCYJ20150831201123287 and No. JCYJ20160510141910129), the Guangdong Provincial Key Laboratory of Genome Read and Write (no. 2017B030301011), Illumina Greater Good Initiative and the NMPA Key Laboratory for Rapid Testing Technology of Drugs.http://www.mdpi.com/journal/genesam2020BiochemistryGeneticsMicrobiology and Plant Patholog