Integrated metabolomic and transcriptomic dynamic profiles of endopleura coloration during fruit maturation in three walnut cultivars.

BACKGROUND: The color of endopleura is a vital factor in determining the economic value and aesthetics appeal of nut. Walnuts (Juglans) are a key source of edible nuts, high in proteins, amino acids, lipids, carbohydrates. Walnut had a variety endopleura color as yellow, red, and purple. However, the regulation of walnut endopleura color remains little known. RESULTS: To understand the process of coloration in endopleura, we performed the integrative analysis of transcriptomes and metabolomes at two developmental stages of walnut endopleura. We obtained total of 4,950 differentially expressed genes (DEGs) and 794 metabolites from walnut endopleura, which are involved in flavonoid and phenolic biosynthesis pathways. The enrichment analysis revealed that the cinnamic acid, coniferyl alcohol, naringenin, and naringenin-7-O-glucoside were important metabolites in the development process of walnut endopleura. Transcriptome and metabolome analyses revealed that the DEGs and differentially regulated metabolites (DRMs) were significantly enriched in flavonoid biosynthesis and phenolic metabolic pathways. Through co-expression analysis, CHS (chalcone synthase), CHI (chalcone isomerase), CCR (cinnamoyl CoA reductase), CAD (cinnamyl alcohol dehydrogenase), COMT (catechol-Omethyl transferase), and 4CL (4-coumaroyl: CoA-ligase) may be the key genes that potentially regulate walnut endopleura color in flavonoid biosynthesis and phenolic metabolic pathways. CONCLUSIONS: This study illuminates the metabolic pathways and candidate genes that underlie the endopleura coloration in walnuts, lay the foundation for further study and provides insights into controlling nut's colour.

Complete chloroplast genome sequence of Pinus tabuliformis var. henryi (Mast.) C.T.Kuan 1983 (Pinaceae).

Pinus tabuliformis var. henryi (Mast.) C.T.Kuan 1983 is an endemic and rare subtropical pine, mainly distributed in central China. In this study, we sequenced the complete chloroplast (cp) genome of P. tabuliformis var. henryi and reported it for the first time. The cp genome was 119,634 base pairs (bp) in total length, including two inverted repeats (IRs, 495 bp), separated by a large single-copy region (LSC, 65,600 bp) and a small single-copy region (SSC, 53,044 bp). There are 114 different genes in the cp genome of P. tabuliformis var. henryi, including 74 protein-coding genes, 36 transfer RNA genes, and four ribosomal RNA genes. The overall GC content of the cp genome was 38.5%. Our phylogenetic analysis of P. tabuliformis var. henryi demonstrated that it was closely related to P. tabuliformis and could be used to identify and analyze its genetic diversity, which was expected to provide new data for taxonomic and phylogenetic studies of Pinus.

Complete chloroplast genome sequence of the carnivorous herb Pinguicula alpina (Lentibulariaceae).

We determined the complete chloroplast genome of Pinguicula alpina, a carnivorous plant using high-throughput sequencing technology. The deduced plastome is a closed circular molecule of 147,479 bp with a quadripartite structure, including a large single-copy region (LSC) of 81,937 bp, a small single-copy region (SSC) of 13,180 bp, and a pair of inverted repeat regions (IRs) of 26,181 bp. It contains 131 genes, comprising 82 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The GC content of the plastome, LSC, SSC, and IR regions are 38.1%, 36.1%, 31.4% and 43.0%, respectively. Phylogenetic analysis revealed that P. alpina was related to P. ehlersiae.

Complete chloroplast genome sequence of Micranthes melanocentra (Saxifragaceae).

The phylogenetic relationships among Micranthes taxa remain unclear due to their diversification. Here, we report the complete chloroplast genome of Micranthes melanocentra obtained using high-throughput sequencing technology to provide genomic information for phylogenetic analyses. The plastome is 155,317 bp, with a large single-copy region (LSC) of 86,784 bp, a small single-copy region (SSC) of 18,007 bp, and a pair of 25,263 bp inverted repeat regions (IRs). The genome contains 132 genes, including 86 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 1 pseudogene. The GC content of the plastome is 37.9%; corresponding values in the LSC, SSC, and IR regions are 36.1%, 31.9%, and 43.3%, respectively. The phylogenetic tree supports the separation of Micranthes from Saxifraga s.l.

Complete chloroplast genome sequence of Solanum erianthum: genome structure and genomic resources.

Solanum erianthum is known for its valuable medicinal properties. In this study, we report its complete chloroplast genome. The chloroplast genome size is 156,343 bp, including a LSC region of 86,855 bp, a SSC region of 18,608 bp and two inverted repeats (IR). The complete chloroplast genome includes a total of 128 unique genes with 83 protein-coding sequences, 37 tRNA and 8 rRNA genes. The results showed that S. erianthum was the most closely related to S. violaceum.

The complete chloroplast genome sequence of Limonium sinense (Plumbaginaceae).

Limonium is a species-rich genus in Plumbaginaceae. In this study, we determined the complete chloroplast genome of Limonium sinense for potential phylogenomic analysis in the future. The plastome is 174,033 bp in length, with a large single-copy region (LSC) of 96,128 bp, a small single-copy region (SSC) of 13,517 bp and a pair of inverted repeat regions (IRs) of 32,194 bp. It contains 132 genes, including 84 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 3 pseudogenes. The overall GC content is 36.7%, while the corresponding values for the LSC, SSC, and IR region are 34.9, 31.1, and 40.6%, respectively. The phylogenetic analysis supported that L. sinense was clustered together with Plumbago auriculata in family Plumbaginaceae.

The complete chloroplast genome sequence of Picea schrenkiana (Pinaceae).

Picea is a phylogenetically complicate genus with great economic and ecological values. Here, we determined the whole complete chloroplast genome of Picea schrenkiana to provide genomic information for phylogenetic analysis of the genus. The plastome of P. schrenkiana is 124,060 bp in size and contains 114 genes, including 74 protein-coding genes, 36 tRNA genes, and four rRNA genes. The overall GC content is 38.7%. Unlike the typical plastome with a conserved quadripartite structure, loss of inverted repeat regions is found in the chloroplast genome. The phylogenetic tree shows that monophyly of P. schrenkiana is well supported.

Transit From Autotrophism to Heterotrophism: Sequence Variation and Evolution of Chloroplast Genomes in Orobanchaceae Species.

The family Orobanchaceae including autotrophic, hemiparasitic, and holoparasitic species, is becoming a key taxa to study the evolution of chloroplast genomes in different lifestyles. But the early evolutionary trajectory in the transit from autotrophism to hemiparasitism still maintains unclear for the inadequate sampling. In this study, we compared 50 complete chloroplast genomes in Orobanchaceae, containing four newly sequenced plastomes from hemiparasitic Pedicularis, to elucidate the sequence variation patterns in the evolution of plastomes. Contrasted to the sequence and structural hypervariabilities in holoparasites, hemiparasitic plastomes exhibited high similarity to those of autotrophs in gene and GC contents. They are generally characterized with functional or physical loss of ndh/tRNA genes and the inverted small-single-copy region. Gene losses in Orobanchaceae were lineage-specific and convergent, possibly related to structural reconfiguration and expansion/contraction of the inverted region. Pseudogenization of ndh genes was unique in hemiparasites. At least in Pedicularis, the ndhF gene might be most sensitive to the environmental factors and easily pseudogenized when autotrophs transit to hemiparasites. And the changes in gene contents and structural variation potentially deeply rely on the feeding type. Selective pressure, together with mutational bias, was the dominant factor of shaping the codon usage patterns. The relaxed selective constraint, potentially with genome-based GC conversion (gBGC) and preferential codon usage, drive the fluctuation of GC contents among taxa with different lifestyles. Phylogenetic analysis in Orobanchaceae supported that parasitic species were single-originated while holoparasites were multiple-originated. Overall, the comparison of plastomes provided a good opportunity to understand the evolution process in Orobanchaceae with different lifestyles.

Characteristics of Organellar Genomes and Nuclear Internal Transcribed Spacers in the Tertiary Relict Genus Dipelta and Their Phylogenomic Implications.

Dipelta (Caprifoliaceae) is a Tertiary relict genus endemic to China, comprising three species with horticultural and medicinal values. For the lack of genomic information, interspecific relationships and divergence times in the genus remain unresolved. In the present study, we assembled and characterized the complete plastomes, the partial mitogenomes, and nuclear internal transcribed spacer (ITS) fragments from genome skimming datasets of 14 Dipelta individuals. The plastomes were conserved in genomic structure, gene order, and gene content, but with highly variable repeat sequences. Three genes (rpl23, ycf1, ycf2) were examined with positive selection, and nine divergent hotpot regions (psbL, accD, rpl23, ycf2, ycf3, rbcL-accD, trnI-CAU-ycf2, ndhH-rps15, and rps18 intron) were potentially valuable for DNA barcodes. Contrasted to the variability in plastome sequences, mitogenomes contained 12 protein-coding genes with limited indels and nucleotide substitutions, and no gene was found under positive selection. Genes in organellar genomes tended to have a similar pattern of codon usage bias, with a preference of A/U ending codons. Phylogenetic trees constructed with plastomes, mitogenomes, and ITS sequences consistently supported that Dipelta was monophyletic, and Dipelta elegans was sister to the other two taxa. Interspecific divergences were estimated at about 33-37 Ma in the Eocene/Oligocene boundary, suggesting the paleo-endemism of the extant species as "living fossils" of the East Asian Flora. Our study well-exhibited that genome skimming could provide valuable genomic information to elucidate the evolutionary history of the complex group in a cost-efficient way.

Framework Phylogeny, Evolution and Complex Diversification of Chinese Oaks.

Oaks (Quercus L.) are ideal models to assess patterns of plant diversity. We integrated the sequence data of five chloroplast and two nuclear loci from 50 Chinese oaks to explore the phylogenetic framework, evolution and diversification patterns of the Chinese oak's lineage. The framework phylogeny strongly supports two subgenera Quercus and Cerris comprising four infrageneric sections Quercus, Cerris, Ilex and Cyclobalanopsis for the Chinese oaks. An evolutionary analysis suggests that the two subgenera probably split during the mid-Eocene, followed by intergroup divergence within the subgenus Cerris around the late Eocene. The initial diversification of sections in the subgenus Cerris was dated between the mid-Oligocene and the Oligocene-Miocene boundary, while a rapid species radiation in section Quercus started in the late Miocene. Diversification simulations indicate a potential evolutionary shift on section Quercus, while several phenotypic shifts likely occur among all sections. We found significant negative correlations between rates of the lineage diversification and phenotypic turnover, suggesting a complex interaction between the species evolution and morphological divergence in Chinese oaks. Our infrageneric phylogeny of Chinese oaks accords with the recently proposed classification of the genus Quercus. The results point to tectonic activity and climatic change during the Tertiary as possible drivers of evolution and diversification in the Chinese oak's lineage.

Complete chloroplast genome of the Meconopsis quintuplinervia (Papaveraceae), a traditional medicine of Tibetan.

As a medicinal herb of Tibetan, Meconopsis quintuplinervia is often utilized for treating pneumonia. In this study, the complete chloroplast genome of M. quintuplinervia was determined by next-generation sequencing technology. The overall genome was 154,997 bp in size, including a large single copy (LSC), a small single copy (SSC) and two inverted repeat (IR) regions, which were 85,153 bp, 17,876 bp, and 25,984 bp in length, respectively. The circular chloroplast genome owned 129 genes, comprising 84 protein-coding genes, 8 ribosomal RNA genes (four rRNA species), and 37 transfer RNA genes. The GC contents of the entire sequence, LSC, SSC, and IR region were 38.5%, 37.1%, 32.8%, and 43%, separately. The maximum likelihood tree revealed that M. quintuplinervia was closely related to M. racemosa with strong support value.

The complete chloroplast genome sequence of Liparis japonica (Orchidaceae).

The Orchidaceae contains numerous species with great ecological and economic values. In this study, the complete chloroplast genome of Liparis japonica was presented by next-generation sequencing technologies. The cpDNA is 152,084 bp in length with a large single copy region (LSC) of 85,398 bp, a small single copy region (SSC) of 14,774 bp, and a pair of inverted repeat regions (IRs) of 25,956 bp. It contains 132 genes, including 79 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and 7 pseudogenes. The overall GC content is 37.0%, while the corresponding values in the LSC, SSC, and IR region are 34.3, 30.0, 43.5%, respectively. The phylogenetic analysis shows that Liparis japonica is sister to Liparis loeselii and the genus Liparis is closely related to Dendrobium.

The complete chloroplast genome sequence of Clintonia udensis (Liliaceae).

The whole chloroplast genome of Clintonia udensis, an import Chinese medicinal herb, was determined by Illumina sequencing data in this study. The cp genome is 153,160 bp in length, with a large single-copy region (LSC) of 83,901 bp, a small single-copy region (SSC) of 17,241 bp and a pair of inverted repeat regions (IRs) of 26,009 bp. It contains 132 genes, including 83 protein-coding genes, 36 tRNA genes, 8 rRNA genes, and 5 pseudogenes. The overall GC content was 37.3%, while the corresponding values in the LSC, SSC and IR region are 35.1, 31.0, and 42.8%, respectively. Phylogenetic analysis indicated that Clintonia udensis was related to Lilioideae species in Liliaceae.

The first complete chloroplast genome sequence from Polemonium chinense (Polemoniaceae).

In this study, the complete chloroplast genome of Polemonium chinense was determined by next-generation sequencing technology. The plastome is 155,578 bp in length, with a large single-copy region (LSC) of 85,864 bp and a small single-copy region (SSC) of 18,246 bp, separated by a pair of inverted repeat regions (IRs) of 25,734 bp. It contains 135 genes, including 89 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 1 pseudogene. The overall GC content is 37.1%, while the corresponding values in the LSC, SSC and IR region are 35.1, 30.3, and 42.9%, respectively. The phylogenetic tree shows that Polemoniaceae is sister to Fouquieriaceae.

The complete chloroplast genomes of Trollius farreri and Anemone taipaiensis (Ranunculaceae).

Ranunculaceae, with high morphological biodiversity and widely ecological amplitude tolerance, has been considered as a new good model for adaptive evolution study. In this study, two high-quality chloroplast genomes of Ranunculaceae were determined by next-generation sequencing technologies. The plastomes of Trollius farreri and Anemone taipaiensis exhibit a conserved quadripartite structure, with 160,612 bp and 160,214 bp in length, presenting similar GC contents (38% and 37.6%). The chloroplast genome of Trollius farreri contains 131 genes, including 87 protein-coding genes, 8 rRNA, and 36 tRNA genes, while the plastome of Anemone taipaiensis harbours 137 genes, including 93 protein-coding genes, 8 rRNA, and 36 tRNA genes. Phylogenetic tree constructed with 21 plastomes of Ranunculaceae species indicates that Trollius farreri and Anemone taipaiensis are closely related to their congeneric species, respectively. The phylogenetic relationships are inconsistent with the current classification of Ranunculaceae.

The complete chloroplast genome of Parnassia wightiana (Celastraceae).

The infrageneric relationships of the genus Parnassia were not clearly identified due to limited available genetic data. In this study, we presented the complete chloroplast genome of Parnassia wightiana for future phylogenetic study. The plastome of P. wightiana was 152,043 bp in length, with a large single-copy region (LSC) of 82,737 bp and a small single-copy region (SSC) of 19,030 bp, separated by a pair of inverted repeat regions (IRs) of 25,138 bp. It contained 134 genes, including 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 2 pseudogenes. The overall GC content was 37.1%, while the corresponding values in the LSC, SSC, and IR region were 35.0%, 30.8%, and 42.9%, respectively. The phylogenetic analysis supported the monophyly of Parnassia.

The complete chloroplast genome sequence of Cypripedium tibeticum King Ex Rolfe (Orchidaceae).

In this study, we determined the complete chloroplast genome of Cypripedium tibeticum, an endangered species in China. The plastome is 159,223 bp in length, with a large single-copy region (LSC) of 86,537 bp, a small single-copy region (SSC) of 17,552 bp, and a pair of inverted repeat regions (IRs) of 27,567 bp each. It contains 133 genes, including 87 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The overall GC content was 36.9%, while the corresponding values in the LSC, SSC, and IR regions are 34.6, 30.4, and 42.6%, respectively. The phylogenetic analysis showed that C. tibeticum was closely related to its congeners and the classification of five subfamilies of Orchidaceae was also highly supported.

Climatic and Soil Factors Shape the Demographical History and Genetic Diversity of a Deciduous Oak (Quercus liaotungensis) in Northern China.

Past and current climatic changes have affected the demography, patterns of genetic diversity, and genetic structure of extant species. The study of these processes provides valuable information to forecast evolutionary changes and to identify conservation priorities. Here, we sequenced two functional nuclear genes and four chloroplast DNA regions for 105 samples from 21 populations of Quercus liaotungensis across its distribution range. Coalescent-based Bayesian analysis, approximate Bayesian computation (ABC), and ecological niche modeling (ENM) were integrated to investigate the genetic patterns and demographical history of this species. Association estimates including Mantel tests and multiple linear regressions were used to infer the effects of geographical and ecological factors on temporal genetic variation and diversity of this oak species. Based on multiple loci, Q. liaotungensis populations clustered into two phylogenetic groups; this grouping pattern could be the result of adaptation to habitats with different temperature and precipitation seasonality conditions. Demographical reconstructions and ENMs suggest an expansion decline trend of this species during the Quaternary climatic oscillations. Association analyses based on nuclear data indicated that intraspecific genetic differentiation of Q. liaotungensis was clearly correlated with ecological distance; specifically, the genetic diversity of this species was significantly correlated with temperature seasonality and soil pH, but negatively correlated with precipitation. Our study highlights the impact of Pleistocene climate oscillations on the demographic history of a tree species in Northern China, and suggests that climatic and soil conditions are the major factors shaping the genetic diversity and population structure of Q. liaotungensis.

Comparative Plastid Genomes of Primula Species: Sequence Divergence and Phylogenetic Relationships.

Compared to traditional DNA markers, genome-scale datasets can provide mass information to effectively address historically difficult phylogenies. Primula is the largest genus in the family Primulaceae, with members distributed mainly throughout temperate and arctic areas of the Northern Hemisphere. The phylogenetic relationships among Primula taxa still maintain unresolved, mainly due to intra- and interspecific morphological variation, which was caused by frequent hybridization and introgression. In this study, we sequenced and assembled four complete plastid genomes (Primula handeliana, Primula woodwardii, Primula knuthiana, and Androsace laxa) by Illumina paired-end sequencing. A total of 10 Primula species (including 7 published plastid genomes) were analyzed to investigate the plastid genome sequence divergence and their inferences for the phylogeny of Primula. The 10 Primula plastid genomes were similar in terms of their gene content and order, GC content, and codon usage, but slightly different in the number of the repeat. Moderate sequence divergence was observed among Primula plastid genomes. Phylogenetic analysis strongly supported that Primula was monophyletic and more closely related to Androsace in the Primulaceae family. The phylogenetic relationships among the 10 Primula species showed that the placement of P. knuthiana-P. veris clade was uncertain in the phylogenetic tree. This study indicated that plastid genome data were highly effective to investigate the phylogeny.

Development of Chloroplast and Nuclear DNA Markers for Chinese Oaks (Quercus Subgenus Quercus) and Assessment of Their Utility as DNA Barcodes.

Chloroplast DNA (cpDNA) is frequently used for species demography, evolution, and species discrimination of plants. However, the lack of efficient and universal markers often brings particular challenges for genetic studies across different plant groups. In this study, chloroplast genomes from two closely related species (Quercus rubra and Castanea mollissima) in Fagaceae were compared to explore universal cpDNA markers for the Chinese oak species in Quercus subgenus Quercus, a diverse species group without sufficient molecular differentiation. With the comparison, nine and 14 plastid markers were selected as barcoding and phylogeographic candidates for the Chinese oaks. Five (psbA-trnH, matK-trnK, ycf3-trnS, matK, and ycf1) of the nine plastid candidate barcodes, with the addition of newly designed ITS and a single-copy nuclear gene (SAP), were then tested on 35 Chinese oak species employing four different barcoding approaches (genetic distance-, BLAST-, character-, and tree-based methods). The four methods showed different species identification powers with character-based method performing the best. Of the seven barcodes tested, a barcoding gap was absent in all of them across the Chinese oaks, while ITS and psbA-trnH provided the highest species resolution (30.30%) with the character- and BLAST-based methods, respectively. The six-marker combination (psbA-trnH + matK-trnK + matK + ycf1 + ITS + SAP) showed the best species resolution (84.85%) using the character-based method for barcoding the Chinese oaks. The barcoding results provided additional implications for taxonomy of the Chinese oaks in subg. Quercus, basically identifying three major infrageneric clades of the Chinese oaks (corresponding to Groups Quercus, Cerris, and Ilex) referenced to previous phylogenetic classification of Quercus. While the morphology-based allocations proposed for the Chinese oaks in subg. Quercus were challenged. A low variation rate of the chloroplast genome, and complex speciation patterns involving incomplete lineage sorting, interspecific hybridization and introgression, possibly have negative impacts on the species assignment and phylogeny of oak species.