DataSheet_2_Assembly and analysis of the first complete mitochondrial genome of Punica granatum and the gene transfer from chloroplast genome.pdf

Pomegranate (Punica granatum L.) is one of the oldest fruits with edible, medicinal and ornamental values. However, there is no report on the mitochondrial genome of pomegranate. In this study, the mitochondrial genome of P. granatum was sequenced, assembled and analyzed in detail, while the chloroplast genome was assembled using the same set of data. The results showed that the P. granatum mitogenome had a multi branched structure, using BGI + Nanopore mixed assembly strategy. The total genome length was 404,807 bp, with the GC content of 46.09%, and there were 37 protein coding genes, 20 tRNA genes and three rRNA genes. In the whole genome, 146 SSRs were identified. Besides, 400 pairs of dispersed repeats were detected, including 179 palindromic, 220 forward and one reverse. In the P. granatum mitochondrial genome, 14 homologous fragments of chloroplast genome were found, accounting for 0.54% of the total length. Phylogenetic analysis showed that among the published mitochondrial genomes of related genera, P. granatum had the closest genetic relationship with Lagerstroemia indica of Lythraceae. The 580 and 432 RNA editing sites were predicted on 37 protein coding genes of mitochondrial genome using BEDTools software and online website PREPACT respectively, but all were from C to U, of which ccmB and nad4 gene were most frequently edited, with 47 sites. This study provides a theoretical basis for understanding the evolution of higher plants, species classification and identification, and will also be useful for further utilization of pomegranate germplasm resources.</p

DataSheet_1_Assembly and analysis of the first complete mitochondrial genome of Punica granatum and the gene transfer from chloroplast genome.zip

Pomegranate (Punica granatum L.) is one of the oldest fruits with edible, medicinal and ornamental values. However, there is no report on the mitochondrial genome of pomegranate. In this study, the mitochondrial genome of P. granatum was sequenced, assembled and analyzed in detail, while the chloroplast genome was assembled using the same set of data. The results showed that the P. granatum mitogenome had a multi branched structure, using BGI + Nanopore mixed assembly strategy. The total genome length was 404,807 bp, with the GC content of 46.09%, and there were 37 protein coding genes, 20 tRNA genes and three rRNA genes. In the whole genome, 146 SSRs were identified. Besides, 400 pairs of dispersed repeats were detected, including 179 palindromic, 220 forward and one reverse. In the P. granatum mitochondrial genome, 14 homologous fragments of chloroplast genome were found, accounting for 0.54% of the total length. Phylogenetic analysis showed that among the published mitochondrial genomes of related genera, P. granatum had the closest genetic relationship with Lagerstroemia indica of Lythraceae. The 580 and 432 RNA editing sites were predicted on 37 protein coding genes of mitochondrial genome using BEDTools software and online website PREPACT respectively, but all were from C to U, of which ccmB and nad4 gene were most frequently edited, with 47 sites. This study provides a theoretical basis for understanding the evolution of higher plants, species classification and identification, and will also be useful for further utilization of pomegranate germplasm resources.</p

Additional file 1 of Complete mitogenome assembly of Selenicereus monacanthus revealed its molecular features, genome evolution, and phylogenetic implications

Supplementary Material

Dynamic expression patterns of differentially expressed genes in “ROC”22 after <i>S. scitamineum</i> inoculation.

<p>Notes: 0, 1, 2, 3, <b>−</b>1, <b>−</b>2 and <b>−</b>3 do not refer to the actual expression of the differentially expressed genes, but for the classification mark of gene dynamic changes. Gene numbers represent the actual number of dynamic expression patterns of differentially expressed genes. T1, “ROC”22 sample under sterile water stress after 24 h; T2–T4, “ROC”22 sample under <i>S. scitamineum</i> stress for 24, 48, and 120 h, respectively.</p><p>Dynamic expression patterns of differentially expressed genes in “ROC”22 after <i>S. scitamineum</i> inoculation.</p

Analysis of GO classifications involving differentially co-expressed genes in three models of distinct and notable dynamic expression patterns in both sugarcane genotypes.

<p>Analysis of GO classifications involving differentially co-expressed genes in three models of distinct and notable dynamic expression patterns in both sugarcane genotypes.</p

The optimal number of reference genes required for effective normalization in each of four experimental sets in sugarcane.

<p>The pairwise variation (V_n/V_n+1) was analyzed between normalization factors NF_n and NF_n+1 by geNorm program to determined the optimal number of reference genes for accurate normalization in samples from different sugarcane cultivar samples (1^st set), sugarcane hormone-treated (2^nd set), abiotic-treated (3^rd set) and treatments (hormone-& abiotic-treated, 4^th). <i>ACT</i> stand for “β-actin” and <i>TUB</i> stand for “β-tubulin”.</p

Comparison of the expression stability of 13 reference genes in <i>Saccharum officinarum</i> as calculated by geNorm, Normfinder and deltaCt.

<p>*β-actin,</p><p>**β-tubulin.</p

Assembly results of sugarcane transcriptome using trinity software.

<p>Notes: N50 length is an indicator of measuring assembly effect, which is calculated by the accumulated length of the assembled fragments from long to short. When the sum is greater than or equal to 50% of the total length, the final accumulated fragment length is the N50 value. Mean length = for the average assembly length.</p><p>Assembly results of sugarcane transcriptome using trinity software.</p

Venn diagram showing the number of genes with sustained differential co-expression between both sugarcane cultivars.

<p>DR-up and DR-down denote continuously up-regulated/down-regulated gene sets in “ROC”22 samples at 24, 48 and 120 h after <i>S. scitamineum</i> inoculation compared to control sample 24 h after water inoculation, respectively; DY-up and DY-down denote continuously up-regulated/down-regulated gene sets in Yacheng05-179 samples at 24, 48 and 120 h after <i>S. scitamineum</i> inoculation compared to control sample 24 h after water inoculation, respectively.</p

Dynamic expression patterns of differentially expressed genes in Yacheng05-179 after <i>S. scitamineum</i> inoculation.

<p>Notes: 0, 1, 2, 3, −1, −2 and −3 do not refer to the actual expression of the differentially expressed genes, but for the classification mark of gene dynamic changes. Gene numbers represent the actual number of dynamic expression patterns of differentially expressed genes. T5, Yacheng05-179 sample under sterile water stress after 24 h; T6–T8, Yacheng05-179 samples under <i>S. scitamineum</i> stress for 24, 48, and 120 h, respectively.</p><p>Dynamic expression patterns of differentially expressed genes in Yacheng05-179 after <i>S. scitamineum</i> inoculation.</p