Search

Diospyros sutchuensis is a national protected wild plant species with narrow distribution and extremely small population in southwestern China. At present, the genomic information of this species is lacking and its phylogenetic relationships among Diospyros remain unclear. In this study, the chloroplast genome of D. sutchuensis was sequenced by Illumina platform, assembled and annotated by Getorganelle v1.7.3.4 and PGA, and analyzed by DnaSP 6.12.03 for sequence comparison, REPuter, Tandem Reapeats Finder, MISA for repetitive sequences, CodonW1.4 for codon usage bias, and EasyCodemL for selection pressure. Meanwhile, based on four different chloroplast genome sequence datasets, the phylogenetic relationships between D. sutchuensis and 11 Diospyros species were analyzed using IQtree. The results were as follows: (1) The chloroplast genome of D. sutchuensis was 157 917 bp in length, including two inverted repeats (IRs) of 26 111 bp, which was separated by large single copy (LSC) and short single copy (SSC) of 87 303 bp and 18 392 bp, respectively. The GC content was 37.4%. (2) The genome contained 113 genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. A total of 49 long repeats, 27 tandem repeats, and 34 simple sequence repeats were identified. There were 31 high-frequency codons in protein-coding genes, most of them ended in A or U, and the most used codons were the ones encoding leucine. The coding regions were more conserved than the non-coding ones, and 10 regions were identified as most divergent hotspots for potential molecular markers. There had been positive selection on ndhB, ndhG, ndhI, rbcL, rpoB, petB, petD and rps12 among protein-coding genes. (3) Phylogenetic analyses showed that D. sutchuensis was closely related to D. rhombifolia and D. cathayensis. Together with D. hainanensis, these four species formed a monophyletic group. The phylogenetic tree constructed from the chloroplast genomes had the highest support values, indicating that the chloroplast genomes with most variable and informative sites are more suitable for phylogenetic studies of Diospyros. The results provide useful chloroplast genomic resources for germplasm identification, genetic diversity conservation, repopulation, and phylogenetic analysis of D. sutchuensis as well as Diospyros.

Cotinus is an oligo‐specific ornamentally valuable genus with a disjunct distribution in the Northern Hemisphere. Traditionally, the taxonomy of Cotinus was mainly based on leaf morphological characteristics. However, the limited availability of genomic information greatly hindered the study of molecular evolution and phylogeny of this genus. This study sequenced the chloroplast (cp) genomes of all currently recognized taxa of Cotinus, including three species and four varieties. A comparative analysis was performed to investigate their cp genome characteristics and evolution. Furthermore, we inferred the phylogenetic relationships of Cotinus based on whole cp genomes, protein‐coding genes, and nuclear ITS data. All cp genomes exhibited a typical quadripartite structure with genome sizes ranging from 158,865 to 160,155 bp. A total of 113–114 genes were identified in the genomes. Seven non‐coding and four coding regions were identified as the most divergent hotspots for potential molecular barcodes and phylogenetic markers. Selection pressure analysis showed that there had been positive selection on genes matK and rps8 in the Cotinus cp genomes. Phylogenetic results confirmed that Cotinus is a monophyletic group but the widely distributed species Cotinus coggygria is not monophyletic. The divergence‐time analysis suggested that Cotinus underwent an evolutionary divergence from the middle Eocene and rapid adaptive radiation from the middle Miocene. This study revealed new insights into the cp genome evolution and phylogeny of Cotinus and related taxa. [ABSTRACT FROM AUTHOR]

Allium ovalifolium var. leuconeurum is an endemic plant in Southwest China. The complete chloroplast genome sequence of A. ovalifolium var. leuconeurum was generated by de novo assembly using high-throughput sequencing. The length of chloroplast genome was 153,635 bp in length, containing a large-single copy region (LSC) of 82,693 bp, a small-single copy region (SSC) of 17,932 bp, and a pair of inverted repeats (IRa and IRb) regions of 26,505 bp. The genome contains 132 genes, including 86 protein-coding genes, 8 rRNA genes, and 38 tRNA genes. Phylogenetic analysis with the reported chloroplast sequences shows that A. ovalifolium var. leuconeurum is more closely related to Allium prattii, both of which belong to the Sect. Anguinum. [ABSTRACT FROM AUTHOR]

Background: Elaiosomes are specialized fleshy and edible seed appendages dispersed by ants. Lipids are the primary components of elaiosomes. Chelidonium majus is a well-known plant, the seeds of which are dispersed by ants. Previous studies have identified the presence of primary fatty acids in its elaiosomes and seeds. However, the molecular mechanisms underlying fatty acid biosynthesis in elaiosomes remain unknown., Methods: In order to gain a comprehensive transcriptional profile of the elaiosomes and seeds of C. majus , and understand the expression patterns of genes associated with fatty acid biosynthesis, four different developmental stages, including the flower-bud (Ch01), flowering (Ch02), young seed (Ch03), and mature seed (Ch04) stages, were chosen to perform whole-transcriptome profiling through the RNA-seq technology (Illumina NGS sequencing)., Results: A total of 63,064 unigenes were generated from 12 libraries. Of these, 7,323, 258, and 11,540 unigenes were annotated with 25 Cluster of Orthologous Groups, 43 Gene Ontology terms, and 373 Kyoto Encyclopedia of Genes and Genomes pathways, respectively. In addition, 322 genes were involved in lipid transport and metabolism, and 508 genes were involved in the lipid metabolism pathways. A total of 41 significantly differentially expressed genes (DEGs) involved in the lipid metabolism pathways were identified, most of which were upregulated in Ch03 compared to Ch02, indicating that fatty acid biosynthesis primarily occurs during the flowering to the young seed stages. Of the DEGs, acyl-ACP thioesterases, acyl carrier protein desaturase ( DESA1 ), and malonyl CoA-ACP transacylase were involved in palmitic acid synthesis; stearoyl-CoA desaturase and DESA1 were involved in oleic acid synthesis, and acyl-lipid omega-6 desaturase was involved in linoleic acid synthesis., Competing Interests: The authors declare that they have no competing interests.