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MADS-box is a critical transcription factor regulating the development of floral organs and plays essential roles in the growth and development of floral transformation, flower meristem determination, the development of male and female gametophytes, and fruit development. In this study, 36 MIKC-type MADS-box genes were identified in the &lsquo, Taishanhong&rsquo, pomegranate genome. By utilizing phylogenetic analysis, 36 genes were divided into 14 subfamilies. Bioinformatics methods were used to analyze the gene structure, conserved motifs, cis-acting elements, and the protein interaction networks of the MIKC-type MADS-box family members in pomegranate, and their expressions pattern in different tissues of pomegranate were analyzed. Tissue-specific expression analysis revealed that the E-class genes (PgMADS03, PgMADS21, and PgMADS27) were highly expressed in floral tissues, while PgMADS29 was not expressed in all tissues, indicating that the functions of the E-class genes were differentiated. PgMADS15 of the C/D-class was the key gene in the development network of pomegranate flower organs, suggesting that PgMADS15 might play an essential role in the peel and inner seed coat development of pomegranate. The results in this study will provide a reference for the classification, cloning, and functional research of pomegranate MADS-box genes.

The cultivated apple (Malus domestica Borkh.) is one of the most important crop fruits with high-economic values in the world. In the present study, we characterized the complete chloroplast (cp) g...

Apple is one of the most important fruit crops in international trade. In this study, we presented the complete mitochondrial genome sequence of apple cultivar ‘Yantai Fuji 8’. The complete mitocho...

Pomegranates (Punica granatum L.) are one of the most popular fruit trees cultivated in arid and semi-arid tropics and subtropics. In this study, we determined and characterized three complete chloroplast (cp) genomes of P. granatum cultivars with different phenotypes using the genome skimming approach. The complete cp genomes of three pomegranate cultivars displayed the typical quadripartite structure of angiosperms, and their length ranged from 156,638 to 156,639 bp. They encoded 113 unique genes and 17 are duplicated in the inverted regions. We analyzed the sequence diversity of pomegranate cp genomes coupled with two previous reports. The results showed that the sequence diversity is extremely low and no informative sites were detected, which suggests that cp genome sequences may be not be suitable for investigating the genetic diversity of pomegranate genotypes. Further, we analyzed the codon usage pattern and identified the potential RNA editing sites. A comparative cp genome analysis with other species within Lythraceae revealed that the gene content and organization are highly conserved. Based on a site-specific model, 11 genes with positively selected sites were detected, and most of them were photosynthesis-related genes and genetic system-related genes. Together with previously released cp genomes of the order Myrtales, we determined the taxonomic position of P. granatum based on the complete chloroplast genomes. Phylogenetic analysis suggested that P. granatum form a single clade with other species from Lythraceae with a high support value. The complete cp genomes provides valuable information for understanding the phylogenetic position of P. gramatum in the order Myrtales.

Spiraea blumei G. Don is an ornamental shrub widely distributed in Eastern Asia. Here, we reported and characterized the complete chloroplast (cp) genome sequence of S. blumei (GenBank accession number: MN418904) to provide genomic resources for promoting its conservation. The total chloroplast genome is 155,957 bp in length and contains the typical chloroplast structure, including two inverted repeat (IR) regions of 26,343 bp, a large single-copy (LSC) region of 84,384 bp, and a small single-copy (SSC) region of 18,887 bp. The overall guanine-cytosine (GC) content of the S. blumei chloroplast genome is 36.8%. The cp genome encodes 133 unique genes, including 85 protein-coding genes (PCGs), 40 tRNA genes, and 8 rRNA genes. We used the cp genome of S. blumei and 26 other cp genomes to perform a phylogenetic analysis, which indicated that S. blumei was closely related to S. martini in Rosaceae.

Malus baccata var. xiaojinensis belonging to Rosaceae is not only an ornamental tree but also an apple genotype that is highly tolerant to Fe deficiency. In this study, we reported the complete chloroplast (cp) genome of M. baccata var. xiaojinensis using ILLUMINA sequencing. The whole cp genome is 160,067 bp in length, containing a pair of inverted repeats (IRs) of 26,358 bp, a large single copy (LSC) region of 88,157 bp and a small single copy (SSC) region of 19,194 bp. And, the overall GC content of the cp genome was 36.56%. A total of 110 unique genes were found in the cp genome. 17 genes were duplicated in the IRs, including six protein-coding genes, seven tRNA genes, and four rRNA genes. Fourteen genes contained one intron, whereas three genes (rps12, clpP, and ycf3) contained two introns. The phylogenetic analysis demonstrated a close relationship between M. baccata var. xiaojinensis and Malus hupehensis.

The dwarf M9 (Malus domestica ‘M9’) rootstock is the most widely available Malus rootstock, here we report the complete chloroplast (cp) genome of ‘M9’ rootstock. The size of the complete cp genome was 159,926 bp, with the large-copy (LSC, 88,065 bp) regions, small single-copy (SSC, 19,157 bp) regions, and two inverted repeat regions (IRs, 26,352 bp each). It contained 110 genes, including 78 protein-coding genes, 28 transfer RNA genes (tRNA), and 4 ribosomal RNA genes (rRNA). A phylogenetic tree demonstrated that ‘M9’ rootstock was closely related to M. hupehensis, M. baccata, M. prunifolia, M. micromalus, and M. tschonoskii.

The European wild apple (Malus sylvestris L.) is an important economical fruit crop. In this present study, we characterized the complete chloroplast (cp) genome sequence of Malus sylvestris L. The...

Kerria japonica (L.) DC., a monotypic species endemic to China and Japan, is an important ornamental shrub. In this study, we reported the complete chloroplast genome sequence of K. japonica (L.) DC. ‘pleniflora’ (GenBank accession number: MN418902) to provide genomic resources for its conservation. The total chloroplast (cp) genome is 160,007 bp in length, including a large single-copy region (LSC) of 87,672 bp and a small single-copy region (SSC) of 19,461 bp, which are separated by two inverted repeat (IR) regions of 26,437 bp. The overall guanine-cytosine (GC) content of the genome sequence is 34.0%. The cp genome encodes 132 unique genes, including 84 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. Phylogenetic analysis of 25 cp genomes showed that K. japonica ‘pleniflora’ was most closely related to K. japonica and then had a close genetic relationship with Neviusia cliftonii in Rosaceae.

Prunus cerasifera Ehrh. ‘Pissardii’, is a widespread ornamental and fruit tree. Here, we reported the complete chloroplast (cp) genome of P. cerasifera ‘Pissardii’ (GenBank accession number: MN418903). The total cp genome is 157,952 bp in length, displayed a typical quadripartite structure, including a large single copy region (LSC) of 86,286 bp and a small single copy region (SSC) of 18,926 bp, which are separated by a pair of inverted repeat (IR) regions of 26,370 bp. The overall guanine-cytosine (GC) content of the genome sequence is 36.7%. The cp genome encodes 134 unique genes, including 84 protein-coding genes, 42 tRNA genes, and 8 rRNA genes. Phylogenetic analysis of 27 chloroplast genomes showed that P. cerasifera ‘Pissardii’ was closely related to P. humilis in Rosaceae.

Pomegranate (Punica granatum), as one of the most important fruit trees, is widely cultivated in the tropical and subtropical of the world. In our present study, we assembled a complete chloroplast...

Sweet cherry (Prunus avium L.) is one of the two major species of cherries in world trade. In this study, we determined the complete mitochondrial genome of sweet cherry cultivar ‘summit’ using who...

Background Sweet cherry (Prunus avium) is one of the most popular of the temperate fruits. Previous studies have demonstrated that there were several haplotypes in the chloroplast genome of sweet cherry cultivars. However, none of chloroplast genome of a sweet cherry cultivar were yet released, and the phylogenetic relationships among Prunus based on chloroplast genome data were unclear. Methods In this study, we assembled and annotated the complete chloroplast genome of a sweet cherry cultivar P. avium ‘Summit’ from high-throughput sequencing data. Gene Ontology (GO) terms were assigned to classify the function of the annotated genes. Maximum likelihood (ML) trees were constructed to reveal the phylogenetic relationships within Prunus species, using LSC (large single-copy) regions, SSC (small single-copy) regions, IR (inverted repeats) regions, CDS (coding sequences), intergenic regions, and whole cp genome datasets, respectively. Results The complete plastid genome was 157, 886 bp in length with a typical quadripartite structure of LSC (85,990 bp) and SSC (19,080 bp) regions, separated by a pair of IR regions (26,408 bp). It contained 131 genes, including 86 protein-coding genes, 37 transfer RNA genes and 8 ribosomal RNA genes. A total of 77 genes were assigned to three major GO categories, including molecular function, cellular component and biological process categories. Comparison with other Prunus species showed that P. avium ‘Summit’ was quite conserved in gene content and structure. The non-coding regions, ndhc-trnV, rps12-trnV and rpl32-trnL were the most variable sequences between wild Mazzard cherry and ‘Summit’ cherry. A total of 73 simple sequence repeats (SSRs) were identified in ‘Summit’ cherry and most of them were mononucleotide repeats. ML phylogenetic tree within Prunus species revealed four clades: Amygdalus, Cerasus, Padus, and Prunus. The SSC and IR trees were incongruent with results using other cp data partitions. These data provide valuable genetic resources for future research on sweet cherry and Prunus species.

Our understanding of the bile acid metabolism is limited by the fact that previous analyses have primarily focused on a selected few circulating bile acids; the bile acid profiles of the liver and gastrointestinal tract pools are rarely investigated. Here, we determined how chronic ethanol consumption altered the bile acids in multiple body compartments (liver, gastrointestinal tract, and serum) of rats. Rats were fed a modified Lieber-DeCarli liquid diet with 38% of calories as ethanol (the amount equivalent of 4–5 drinks in humans). While conjugated bile acids predominated in the liver (98.3%), duodenum (97.8%), and ileum (89.7%), unconjugated bile acids comprised the largest proportion of measured bile acids in serum (81.2%), the cecum (97.7%), and the rectum (97.5%). In particular, taurine-conjugated bile acids were significantly decreased in the liver and gastrointestinal tract of ethanol-treated rats, while unconjugated and glycine-conjugated species increased. Ethanol consumption caused increased expression of genes involved in bile acid biosynthesis, efflux transport, and reduced expression of genes regulating bile acid influx transport in the liver. These results provide an improved understanding of the systemic modulations of bile acid metabolism in mammals through the gut-liver axis.—Xie, G., Zhong, W., Li, H., Li, Q., Qiu, Y., Zheng, X., Chen, H., Zhao, X., Zhang, S., Zhou, Z., Zeisel, S. H., Jia, W. Alteration of bile acid metabolism in the rat induced by chronic ethanol consumption.

A child with severe S-adenosylhomocysteine hydrolase (AHCY) deficiency (AHCY c.428A > G, p.Tyr143Cys ; c.982 T > G, p.Tyr328Asp) presented at 8 months of age with growth failure, microcephaly, global developmental delay, myopathy, hepatopathy, and factor VII deficiency. Plasma methionine, S-adenosylmethionine (AdoMet), and S-adenosylhomocysteine (AdoHcy) were markedly elevated and the molar concentration ratio of AdoMet:AdoHcy, believed to regulate a myriad of methyltransferase reactions, was 15% of the control mean. Dietary therapy failed to normalize biochemical markers or alter the AdoMet to AdoHcy molar concentration ratio. At 40 months of age, the proband received a liver segment from a healthy, unrelated living donor. Mean AdoHcy decreased 96% and the AdoMet:AdoHcy concentration ratio improved from 0.52 ± 0.19 to 1.48 ± 0.79 mol:mol (control 4.10 ± 2.11 mol:mol). Blood methionine and AdoMet were normal and stable during 6 months of follow-up on an unrestricted diet. Average calculated tissue methyltransferase activity increased from 43 ± 26% to 60 ± 22%, accompanied by signs of increased transmethylation in vivo. Factor VII activity increased from 12% to 100%. During 6 postoperative months, head growth accelerated 4-fold and the patient made promising gains in gross motor, language, and social skills.

Choline is an essential nutrient critical to brain health. Our objective was to evaluate the association of plasma choline (Cho) and Cho-related compounds with cognition and cerebrovascular patholo...