Genome-Wide Identification and Characterization of TCP Gene Family Members in Melastoma candidum.

It has been confirmed that the plant-specific Teosinte-branched 1/Cycloidea/Proliferating (TCP) gene family plays a pivotal role during plant growth and development. M. candidum is a native ornamental species and has a wide range of pharmacodynamic effects. However, there is still a lack of research on TCP's role in controlling M. candidum's development, abiotic stress responses and hormone metabolism. A comprehensive description of the TCP gene family in M. candidum is urgently needed. In this study, we used the HMMER search method in conjunction with the BLASTp method to identify the members of the TCP gene family, and a total of 35 TCP genes were identified. A domain analysis further confirmed that all 35 TCPs contained a TCP superfamily, a characteristic involved in dimerization and DNA binding that can be found in most genes from this gene family, suggesting that our identification was effective. As a result of the domain conservation analysis, the 35 TCP genes could be classified into two classes, TCP-P and TCP-C, based on the conservative regions of 55 and 59 amino acids, respectively. Gene-duplication analysis revealed that most TCP genes were present in duplication events that eventually led to TCP gene expansion in M. candidum. All the detected gene pairs had a Ka/Ks value of less than one, suggesting that purification selection is the most important factor that influences the evolution of TCP genes. Phylogenetic analysis of three species displayed the evolutionary relationship of TCP genes across different species and further confirmed our results. The real-time quantitative PCR (qRT-PCR) results showed that McTCP2a, McTCP7a, McTCP10, McTCP11, McTCP12a, McTCP13, McTCP16, McTCP17, McTCP18, McTCP20 and McTCP21 may be involved in leaf development; McTCP4a, McTCP1, McTCP14, McTCP17, McTCP18, McTCP20, McTCP22 and McTCP24 may be involved in flower development; and McTCP2a, McTCP3, McTCP5a, McTCP6, McTCP7a, McTCP9, McTCP11, McTCP14 and McTCP16 may be involved in seed development. Our results dissect the TCP gene family across the genome of M. candidum and provide valuable information for exploring TCP genes to promote molecular breeding and property improvement of M. candidum in the future.

The complete mitochondrial genome of Bauhinia variegata (Leguminosae).

The mitogenome of Bauhinia variegate was assembled and characterized in this study. The mitogenome size was 437,271 bp, and its GC content was 45.5%. 36 protein-coding genes, 17 tRNAs and 3 rRNAs were annotated in the mitogenome. A total of 12 MTPTs, ranging from 71 bp to 3562 bp, were identified in the mitogenome and covered 1.46% (6373 bp) of the mitogenome. Phylogenetic analysis of 15 species of Leguminosae based on 23 core protein-coding genes showed that B. variegata was sister to Tylosema esculentum, another member from the subfamily Cercidoideae. The mitogenome of B. variegata provides a valuable genetic resource for further phylogenetic studies of this family.

Lagerstroemiastenophylla (Lythraceae), a new species from China.

Lagerstroemiastenophylla, a new species from southeastern Shaanxi Province and northwestern Hubei Province of China is described. Morphologically, L.stenophylla resembles L.subcostata, but it differs in having 4-angular, subalate branchlets, elliptic-lanceolate, or narrowly elliptic leaves, and relatively larger flowers.

Chromosomal-level genome assembly of Melastoma candidum provides insights into trichome evolution.

Melastoma, consisting of ~100 species diversified in tropical Asia and Oceania in the past 1-2 million years, represents an excellent example of rapid speciation in flowering plants. Trichomes on hypanthia, twigs and leaves vary markedly among species of this genus and are the most important diagnostic traits for species identification. These traits also play critical roles in contributing to differential adaptation of these species to their own habitats. Here we sequenced the genome of M. candidum, a common, erect-growing species from southern China, with the aim to provide genomic insights into trichome evolution in this genus. We generated a high-quality, chromosome-level genome assembly of M. candidum, with the genome size of 256.2 Mb and protein-coding gene number of 40,938. The gene families specific to, and significantly expanded in Melastoma are enriched for GO terms related to trichome initiation and differentiation. We provide evidence that Melastoma and its sister genus Osbeckia have undergone two whole genome duplications (WGDs) after the triplication event (γ) shared by all core eudicots. Preferential retention of trichome development-related transcription factor genes such as C2H2, bHLH, HD-ZIP, WRKY, and MYB after both WGDs might provide raw materials for trichome evolution and thus contribute to rapid species diversification in Melastoma. Our study provides candidate transcription factor genes related to trichome evolution in Melastoma, which can be used to evolutionary and functional studies of trichome diversification among species of this genus.

Long non-coding RNA-mediated competing endogenous RNA regulatory network during flower development and color formation in Melastoma candidum.

M. candidum, an evergreen shrubby flower known for its superior adaptation ability in South China, has gained increased attention in garden applications. However, scant attention has been paid to its flower development and color formation process at the non-coding RNA level. To fill this gap, we conducted a comprehensive analysis based on long non-coding RNA sequencing (lncRNA-seq), RNA-seq, small RNA sequencing (sRNA-seq), and widely targeted metabolome detection of three different flower developmental stages of M. candidum. After differentially expressed lncRNAs (DElncRNAs), differentially expressed mRNAs (DEmRNAs), differentially expressed microRNAs (DEmiRNAs), and differentially synthesized metabolites (DSmets) analyses between the different flower developmental stages, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted to identify some key genes and metabolites in flavonoid, flavone, anthocyanin, carotenoid, and alkaloid-related GO terms and biosynthetic pathways. Three direct-acting models, including antisense-acting, cis-acting, and trans-acting between lncRNAs and mRNAs, were detected to illustrate the direct function of lncRNAs on target genes during flower development and color formation. Based on the competitive endogenous RNA (ceRNA) regulatory theory, we constructed a lncRNA-mediated regulatory network composed of DElncRNAs, DEmiRNAs, DEmRNAs, and DSmets to elucidate the indirect role of lncRNAs in the flower development and color formation of M. candidum. By utilizing correlation analyses between DERNAs and DSmets within the ceRNA regulatory network, alongside verification trials of the ceRNA regulatory mechanism, the study successfully illustrated the significance of lncRNAs in flower development and color formation process. This research provides a foundation for improving and regulating flower color at the lncRNA level in M. candidum, and sheds light on the potential applications of non-coding RNA in studies of flower development.

Chromosomal-level genome assembly of the orchid tree Bauhinia variegata (Leguminosae; Cercidoideae) supports the allotetraploid origin hypothesis of Bauhinia.

Cercidoideae, one of the six subfamilies of Leguminosae, contains one genus Cercis with its chromosome number 2n = 14 and all other genera with 2n = 28. An allotetraploid origin hypothesis for the common ancestor of non-Cercis genera in this subfamily has been proposed; however, no chromosome-level genomes from Cercidoideae have been available to test this hypothesis. Here, we conducted a chromosome-level genome assembly of Bauhinia variegata to test this hypothesis. The assembled genome is 326.4 Mb with the scaffold N50 of 22.1 Mb and contains 37,996 protein-coding genes. The Ks distribution between gene pairs in the syntenic regions indicates two whole-genome duplications (WGDs): one is B. variegata-specific, and the other is shared among core eudicots. Although Ks between gene pairs generated by the recent WGD in Bauhinia is greater than that between Bauhinia and Cercis, the WGD was not detected in Cercis, which can be explained by an accelerated evolutionary rate in Bauhinia after divergence from Cercis. Ks distribution and phylogenetic analysis for gene pairs generated by the recent WGD in Bauhinia and their corresponding orthologs in Cercis support the allopolyploidy origin hypothesis of Bauhinia. The genome of B. variegata also provides a genomic resource for dissecting genetic basis of its ornamental traits.

Characterization of the complete chloroplast genome sequence of Sarcandra glabra (Chloranthales).

Sarcandra glabra is a perennial evergreen subshrub, with high ornamental and medicinal value. Using the Illumina high-throughput sequencing data, its chloroplast genome is well assembled and characterized. The complete chloroplast genome is 158,872 bp in length with a typical quadripartite structure: a pair of inverted repeats (IRs) of 26,122 bp for each, an 88,182 bp large single-copy (LSC) region and an 18,445 bp small single-copy (SSC) region. It was composed of 128 genes and they were identified 84 coding genes, 8 rRNA genes, 36 tRNA genes. Phylogenetic analysis confirmed that the position of S. glabra lay within the order Chloranthales instead of Piperales simply according to classical morphological taxonomy.

The complete chloroplast genome sequence of Butea monosperma (Fabaceae).

Butea monosperma, an importantmedicinal plantin Fabaceae, is mainly distributed in southern Asia. In this study, we reported the complete chloroplast (cp) genome of B. monosperma assembled with Illumina sequencing data. The whole cp genome of this species is 151,925 bp in length, consisting of two inverted repeat regions (IR, 25,083 bp), one large single-copy region (LSC, 83,541 bp), and one small single-copy region (SSC, 18,218 bp).A total of 128 genes were annotated for the chloroplast genome, including 83 protein-coding genes, 37 tRNAs and 8 rRNAs. Phylogenetic analysis indicated that B. monosperma was closely related to the genus Lespedeza.

Characterization of the complete chloroplast genome of ornamental plant, Bougainvillea peruviana (Nyctaginaceae).

Bougainvillea peruviana is a widely domesticated ornamental plant species. However, studies on B. peruviana are limited. In this study, we reported the complete chloroplast (cp) genome of B. peruviana. The cp genome is 154,465 bp in length, containing a large single-copy (LSC) of 85,563 bp and a small single-copy (SSC) of 18,050 bp, which are separated by a pair of inverted repeats (IRs) of 25,426 bp, each. A total of 132 genes, including 86 protein-coding genes, 38 tRNA genes, and eight rRNA genes, were predicted. The overall GC content for the cp genome is 36.5%. The maximum-likelihood tree constructed based on cp genome sequences showed that B. peruviana is placed under Nyctaginaceae and is diverged before Bougainvillea glabra and Bougainvillea spectabilis under strong bootstrap support.

The complete chloroplast genome of Uvaria macrophylla Roxb. (Annonaceae).

Uvaria macrophylla (Annonaceae) is an erect shrub with multiple medicinal properties. In this study, we report the complete chloroplast genome of U. macrophylla, assembled from whole-genome high-throughput sequencing reads, as a resource for future studies on the phylogeny and evolution of Annonaceae. The chloroplast genome was 192,782 bp in length, with a large single-copy (LSC) region of 83,581 bp, a small single-copy (SSC) region of 3,741 bp, separated by two inverted repeat (IR) regions of 52,730 bp each. It was predicted to contain 151 genes, with an overall GC content of 38.7%. Phylogenetic analysis of 105 protein-coding sequences of 13 plant plastomes showed that U. macrophylla is closest to Annona cherimola.

The complete chloroplast genome of Laurocerasus zippeliana (Rosaceae).

Laurocerasus zippeliana is a widely known landscape plant with high adaptability. We report herein the complete chloroplast genome sequence of L. zippeliana assembled from Illumina high-throughput sequencing data. With a total length of 158,940 bp, the complete chloroplast genome was a typical quadripartite circle: two inverted repeats (IRs) of 26,339 bp for each, a large single-copy (LSC) region of 87,339 bp, and a small single-copy (SSC) region of 18,923 bp. A total of 110 unique genes were identified, consisting of 78 protein-coding genes, 28 tRNA genes, and 4 rRNA genes. Phylogenetic analysis confirmed the position of L. zippeliana within the order Rosales.

The complete chloroplast genome sequence of Moringa oleifera Lam. (Moringaceae).

The plant family Moringaceae contains only one genus, Moringa, and Moringa oleifera is widely cultivated for its young seed pods and leaves used as vegetables and for traditional herbal medicine. In this study, we report the complete chloroplast genome of M. oleifera, assembled from whole-genome high-throughput sequencing reads, as a resource for future studies on the phylogeny and evolution of Moringaceae. The chloroplast genome was 160,600 bp in length, with a large single-copy (LSC) region of 88,577 bp, a small single-copy (SSC) region of 18,883 bp, separated by two inverted repeat (IR) regions of 26,570 bp each. It was predicted to contain 131 genes, with an overall GC content of 36.78%. Phylogenetic analysis of 71 protein-coding sequences of 13 plant plastomes showed that M. oleifera is closest to Carica papaya.

The complete chloroplast genome of the lipstick tree, Bixa Orellana (Bixaceae).

Bixa orellana is a small tree known for its red, oil-soluble pigment contained in the seed coat that is used as a natural dye and food coloring. In this study, we assembled and characterized the complete chloroplast genome of B. orellana as a resource for future genetic studies. With a total length of 159,825 bp, the chloroplast genome comprised of a large single-copy (LSC) region of 89,476 bp, a small single-copy (SSC) region of 19,617 bp, and two inverted repeat (IR) regions of 25,356 bp each. A total of 127 genes were predicted, consisting of 83 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Phylogenetic analysis confirmed the position of B. orellana within the order Malvales.

The complete chloroplast genome of Reevesia thyrsoidea (Malvaceae).

Reevesia thyrsoidea Lindl. is an important ornamental plant with horticultural, industrial, and timber usages. In this study, we reported a complete chloroplast genome of R. thyrsoidea, which was quadripartite and 161,786 bp in size, including two inverted repeats (25,466 bp for each) that separated one large single-copy (90,565 bp) and one small single-copy (20,289 bp) regions. The chloroplast genome contained 131 unique genes (86 protein-coding, 37 tRNA, and 8 rRNA), and 17 of them were double copies. Phylogenetic analysis using the chloroplast genome data indicated that R. thyrsoidea was sister to the species in the family Malvaceae.

Endangered but genetically stable-Erythrophleum fordii within Feng Shui woodlands in suburbanized villages.

Feng Shui woodlands are naturally or artificially formed green areas in southern China. They are precious for maintaining ecosystem balance in modern semiurban environments. However, they are generally small and geographically isolated from each other, and the status of genetic diversity of the plant species within them has been almost neglected. Therefore, we studied the genetic diversity of the endangered Erythrophleum fordii in eight Feng Shui woodlands (a total of 1,061 individuals) in Guangzhou, a large city in southern China, using microsatellites. For comparison, one population with 33 individuals sampled in a nature reserve was also studied. Although our results indicate that significant demographic declines occurred historically in E. fordii, such declines have not resulted in consistent reductions in genetic variation over generations in Feng Shui populations in the recent past, and the levels of genetic variation in these populations were higher than or comparable to the genetic variation of the population in the nature reserve. In addition, our parentage and paternity analyses indicated widespread and potential long-distance pollen flow within one Feng Shui woodland, indicating the presence of an unbroken pollination network, which would at least partially alleviate the genetic erosion due to habitat fragmentation and the unequal gene contributions of E. fordii parents to their progenies when favorable recruitment habitats are absent under most of the parent trees. Overall, our results suggest that E. fordii in Feng Shui woodlands may not be driven to extinction in the near future. Nevertheless, uncontrolled fast urban development with a lack of awareness of Feng Shui woodlands will cause the local extinction of E. fordii, which has already happened in some Feng Shui woodlands.

The complete chloroplast genome of a commercially exploited ornamental plant, Bougainvillea glabra (Caryophyllales: Nyctaginaceae).

Bougainvillea glabra is an ornamental plant that is domesticated in many tropical and sub-tropical countries. The focus on its breeding programmes has overshadowed genetic studies of this important species. In this study, we reported on the complete chloroplast (cp) genome of B. glabra. The cp genome is 154,763 bp in size, comprised of a large single copy (LSC) region of 85,921 bp, a small single copy (SSC) region of 18,018 bp, and a pair of inverted repeat (IR) regions of 25,412 bp each. A total of 131 genes were predicted, including 37 tRNA, 8 rRNA, and 86 protein-coding genes. Phylogenetic analysis revealed that B. glabra is placed under Nyctaginaceae and sister to B. spectabilis under a strong bootstrap support.

Similar Morphologies but Different Origins: Hybrid Status of Two More Semi-creeping Taxa of Melastoma.

Inferring the origins of hybrid taxa based on morphology alone is difficult because morphologically similar hybrids can arise from hybridization between different populations of the same parental species or be produced by hybridization of different parental species. In this study, we investigated the origins of two semi-creeping taxa in Melastoma, which are morphologically similar to a natural hybrid, M. intermedium, by sequencing a chloroplast intergenic spacer, nuclear ribosomal internal transcribed spacer and two low-copy nuclear genes (tpi and cam) in these taxa and their putative parental species. Our sequence analysis provides compelling evidence for the hybrid status of the two semi-creeping taxa: one originating from hybridization between M. dodecandrum and M. malabathricum, and the other between M. dodecandrum and M. normale. The origins of these hybrids are therefore clearly different from M. intermedium, and morphological similarity for the three hybrids is most likely due to their origins from hybridization between the same creeping species M. dodecandrum and a different erect species in each of the three cases. We also observed low rate of introgression from M. normale to M. dodecandrum, and genetic exchange between them may transfer adaptive traits to M. dodecandrum. Rare occurrence of these two hybrids may be due to small range overlaps between parental species in one case, and different flowering periods between parental species in the other.

Extensive hybridization and introgression between Melastoma candidum and M. sanguineum.

Natural hybridization can lead to various evolutionary outcomes in plants, including hybrid speciation and interspecific gene transfer. It can also cause taxonomic problems, especially in plant genera containing multiple species. In this study, the hybrid status of Melastoma affine, the most widespread taxon in this genus, and introgression between its putative parental species, M. candidum and M. sanguineum, were assessed on two sites, Hainan and Guangdong, using 13 SSR markers and sequences of a chloroplast intergenic spacer. Bayesian-based STRUCTURE analysis detected two most likely distinct clusters for the three taxa, and 76.0% and 73.9% of the morphologically identified individuals of M. candidum and M. sanguineum were correctly assigned, respectively. 74.5% of the M. affine individuals had a membership coefficient to either parental species between 0.1 and 0.9, suggesting admixture between M. candidum and M. sanguineum. Furthermore, NewHybrids analysis suggested that most individuals of M. affine were F2 hybrids or backcross hybrids to M. candidum, and that there was extensive introgression between M. candidum and M. sanguineum. These SSR data thus provides convincing evidence for hybrid origin of M. affine and extensive introgression between M. candidum and M. sanguineum. Chloroplast DNA results were consistent with this conclusion. Much higher hybrid frequency on the more disturbed Guangdong site suggests that human disturbance might offer suitable habitats for the survival of hybrids, a hypothesis that is in need of further testing.

Development and characterization of microsatellite markers for Melastoma dodecandrum (Melastomataceae).

PREMISE OF THE STUDY: Microsatellite markers were developed for Melastoma dodecandrum to investigate the genetic diversity of this species and to detect hybridization and introgression in Melastoma. • METHODS AND RESULTS: Fourteen microsatellite loci were characterized by screening primers developed using two simple sequence repeat (SSR)-enriched libraries. Based on the genotyping of two natural populations, 13 loci were polymorphic and the number of alleles per locus ranged from two to 15. The observed and expected heterozygosities for the 13 loci ranged from 0.235 to 0.941 and 0.219 to 0.922, respectively. Cross-species amplification was successful for all 14 loci in each of two congeneric species, M. candidum and M. sanguineum. • CONCLUSIONS: These polymorphic SSR markers could be used as multilocus molecular makers to study the population genetics of M. dodecandrum, as well as hybridization and introgression among Melastoma species.