The pomegranate (Punica granatum L.) draft genome dissects genetic divergence between soft‐ and hard‐seeded cultivars

Abstract

Summary Complete and highly accurate reference genomes and gene annotations are indispensable for basic biological research and trait improvement of woody tree species. In this study, we integrated single‐molecule sequencing and high‐throughput chromosome conformation capture techniques to produce a high‐quality and long‐range contiguity chromosome‐scale genome assembly of the soft‐seeded pomegranate cultivar ‘Tunisia’. The genome covers 320.31 Mb (scaffold N50 = 39.96 Mb; contig N50 = 4.49 Mb) and includes 33 594 protein‐coding genes. We also resequenced 26 pomegranate varieties that varied regarding seed hardness. Comparative genomic analyses revealed many genetic differences between soft‐ and hard‐seeded pomegranate varieties. A set of selective loci containing SUC8‐like, SUC6, FoxO and MAPK were identified by the selective sweep analysis between hard‐ and soft‐seeded populations. An exceptionally large selective region (26.2 Mb) was identified on chromosome 1. Our assembled pomegranate genome is more complete than other currently available genome assemblies. Our results indicate that genomic variations and selective genes may have contributed to the genetic divergence between soft‐ and hard‐seeded pomegranate varieties.

Identification of the SUT Gene Family in Pomegranate (Punica granatum L.) and Functional Analysis of PgL0145810.1

“…The rapid development of high-throughput sequencing and bioinformatics analysis technology has made transcriptome analysis easy for researchers to detect the genes associated with complex quantitative traits [55,56]. Through transcriptomic analysis, NAC1, WRKY, MYB and MYC transcription factors were proved to be responsible for the formation of seed hardness in pomegranate [13,14]. Our study first reveals that the expression of SUC genes (PgL0099690.1, PgL0145810.1, PgL0145770.1 and PgL0328370.1) is involved in the development of seeds in pomegranate.…”

“…The lignin content in the seed coat has a positive correlation with the characteristics of seed hardness, and amount [11,12]. Based on the transcriptomic analysis, WRKY, AP2 like, MYC, MYB and NAC transcription factors (TFs) are expressed differently in soft-and hard-seed pomegranate varieties [13,14]. The miRNA-mRNA influence seed hardness in pomegranate by acting on the cell wall.…”

Small RNA and mRNA Sequencing Reveal the Roles of microRNAs Involved in Pomegranate Female Sterility

“…Through sequencing of 18 samples, a total of 409.8 Gb clean reads were generated, and the number of reads yielded from the 18 small RNA sequencing libraries ranged from 22.3 to 23.1 million. After aligning against the pomegranate reference genome, 84.8% to 89.6% of the reads in 18 libraries were mapped to the pomegranate reference genome [31] (Table S1), with CG content that varied from 47.1% to 50.1% (Table S1). The number of unique sRNAs for 18 accessions ranged from 8.4 to 10.2 million, and 77% to 82.2% were mapped to the pomegranate reference genome [31] (Table S1).…”

“…After aligning against the pomegranate reference genome, 84.8% to 89.6% of the reads in 18 libraries were mapped to the pomegranate reference genome [31] (Table S1), with CG content that varied from 47.1% to 50.1% (Table S1). The number of unique sRNAs for 18 accessions ranged from 8.4 to 10.2 million, and 77% to 82.2% were mapped to the pomegranate reference genome [31] (Table S1). Small RNAs of 20 to 24 nucleotides (nt) in length were dominant in all 18 sequencing libraries ( Figure 1b), of which the 24 nt length small RNAs showed a large percentage in the small RNA libraries (Figure 1b) and the 21 nt length small RNAs also showed a large percentage in the small RNA libraries (Figure 1b), suggesting the existence of post-transcription during pomegranate ovule development.…”

“…Moreover, small RNAs which were only detected in one of the 18 libraries were also removed before subsequent analysis. The filtered reads for each sample were aligned against the pomegranate "Tunisia" genome [31] using the Bowtie2 program (Version 2.3.4.1) without mismatch [49]. Only mapped reads were used for further analyses.…”