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Abstract Bract coloration is one of the key ornamental traits in Bougainvillea, yet research has predominantly focused on phenotypic color traits and pigment composition, with limited understanding of the molecular mechanisms underlying color formation. This gap hinders the improvement and innovation in bract coloration. To elucidate the regulatory mechanisms of bract coloration in Bougainvillea and to enhance the utilization of its germplasm resources, this study employed the Illumina Novaseq 6000 sequencing platform to conduct transcriptomic sequencing on 21 samples of bracts exhibiting seven distinct phenotypes. Comparative analysis against Nr, Pfam, EggNOG, GO, and KEGG databases annotated 90,279 unigenes. The highest annotation rates were achieved with the Nr (40.13%), GO (30.44%), and EggNOG (25.64%) databases. Among the species annotated, Beta vulgaris (20.08%) and Chenopodium quinoa (14.58%) shared the highest homology with Bougainvillea bract transcriptomes. WGCNA analysis identified 12 positively correlated tissue-specific modules, of which 2 are related to bract color formation. By comparing transcriptome data and genes within these specific modules against the KEGG database, a total of 321 unigenes associated with bract color formation in Bougainvillea were discovered. Among these, 220 unigenes are involved in anthocyanin synthesis, 43 unigenes are involved in betalain synthesis, 23 unigenes are annotated as Chlorophyll a-b binding protein genes, and 35 unigenes participate in carotenoid synthesis. Quantitative real-time PCR (qRT-PCR) validation of 16 differentially expressed genes (DEGs) including PAL2, CHS1, ANS, BZ1, 6GT, CDOPA5GT, ANR, CHS2, and DOPA, revealed significant expression differences among magenta, yellow, white, and cherry-colored bracts, suggesting their potential as candidate genes for bract color development. This study not only enriches the transcriptomic data of Bougainvillea but also identifies genes associated with bract coloration, providing a valuable theoretical basis for future gene cloning, genetic engineering, and breeding efforts in Bougainvillea.

The genus Neocinnamomum is considered to be one of the most enigmatic groups in Lauraceae, mainly distributed in tropical and subtropical regions of Southeast Asia. The genus contains valuable oilseed and medicinal tree species. However, there are few studies on the genus Neocinnamomum at present, and its interspecific relationship is still unclear. In order to explore the genetic structure and evolutionary characteristics of the Neocinnamomum chloroplast genome and to resolve the species relationships within the genus, comparative genomic and phylogenetic analyses were performed on the whole chloroplast genome sequences of 51 samples representing seven Neocinnamomum taxa. The whole Neocinnamomum chloroplast genome size ranged from 150,753-150,956 bp, with a GC content of 38.8%-38.9%. A total of 128 genes were annotated within the Neocinnamomum chloroplast genome, including 84 protein coding genes, 8 rRNA genes, and 36 tRNA genes. Between 71-82 SSRs were detected, among which A/T base repeats were the most common. The chloroplast genome contained a total of 31 preferred codons. Three highly variable regions, trnN-GUU-ndhF, petA-psbJ, and ccsA-ndhD, were identified with Pi values > 0.004. Based on the whole chloroplast genome phylogenetic tree, the phylogenetic relationships among the seven Neocinnamomum taxa were determined. N. delavayi and N. fargesii were the most closely related species, and N. lecomtei was identified as the most basal taxon. In this study, the characteristics and sequence variation of the chloroplast genomes of seven Neocinnamomum taxa were revealed, and the genetic relationship among the species was clarified. The results of this study will provide a reference for subsequent molecular marker development and phylogenetic research of Neocinnamomum.

Eriobotrya (Rosaceae) is an economically important genus with around 30 species. It is widely distributed in tropical and warm temperate regions of Asia, with most of its species in China, Myanmar, and Vietnam. However, Eriobotrya is often confused with the smaller genus Rhaphiolepis, and the phylogenetic relationships between the two genera are controversial. Here we present phylogenetic analyses of 38 newly generated Eriobotrya and Rhaphiolepis nrDNA together with 16 sequences of nrDNA and 28 sequences of ITS obtained from GenBank, representing 28 species of Eriobotrya and 12 species of Rhaphiolepis, in order to reconstruct highly supported relationships for the two genera. Contrary to previous research based on limited sampling, our results highlight the monophyly of Eriobotrya as well as Rhaphiolepis. The topology recovered here is consistent with key morphological synapomorphies such as the persistent sepals in Eriobotrya. Our findings show that increased sampling of taxa can provide a more robust phylogeny through reducing phylogenetic error and increasing overall phylogenetic accuracy.

Species within the Genus Catalpa are mostly semievergreen or deciduous trees with opposite or whorled leaves. C. bungei, C. fargesii f. duclouxii and C. fargesii are sources of traditional precious wood in China, known as the “kings of wood”. Due to a lack of phenotypic and molecular studies and insufficient sequence information, intraspecific morphological differences, common DNA barcodes and partial sequence fragments cannot clearly reveal the phylogenetic or intraspecific relationships within Catalpa. Therefore, we sequenced the complete chloroplast genomes of six taxa of the genus Catalpa and analyzed their basic structure and evolutionary relationships. The chloroplast genome of Catalpa shows a typical tetrad structure with a total length ranging from 157,765 bp (C. fargesii) to 158,355 bp (C. ovata). The length of the large single-copy (LSC) region ranges from 84,599 bp (C. fargesii) to 85,004 bp (C. ovata), that of the small single-copy (SSC) region ranges from 12,662 bp (C. fargesii) to 12,675 bp (C. ovata), and that of the inverted repeat (IR) regions ranges from 30,252 bp (C. fargesii) to 30,338 bp (C. ovata). The GC content of the six chloroplast genomes were 38.1%. In total, 113 unique genes were detected, and there were 19 genes in IR regions. The 113 genes included 79 protein-coding genes, 30 tRNA genes and four rRNA genes. Five hypervariable regions (trnH-psbA, rps2-rpoC2, rpl22, ycf15-trnl-CAA and rps15) were identified by analyzing chloroplast nucleotide polymorphisms, which might be serve as potential DNA barcodes for the species. Comparative analysis showed that single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) were highly diverse in the six species. Codon usage patterns were highly similar among the taxa included in the present study. In addition to the stop codons, all codons showed a preference for ending in A or T. Phylogenetic analysis of the entire chloroplast genome showed that all taxa within the genus Catalpa formed a monophyletic group, clearly reflecting the relationships within the genus. This study provides information on the chloroplast genome sequence, structural variation, codon bias and phylogeny of Catalpa, which will facilitate future research efforts.

Brassaiopsis angustifolia K.M. Feng belongs to the family Araliaceae, and is an endangered shrub species in southwest China. Despite the importance of this species, the plastid genome has not been sequenced and analyzed. In this study, the complete plastid genome of B. angustifolia was sequenced, analyzed, and compared to the eight species in the Araliaceae family. Our study reveals that the complete plastid genome of B. angustifolia is 156,534 bp long, with an overall GC content of 37.9%. The chloroplast genome (cp) encodes 133 genes, including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. All protein-coding genes consisted of 21,582 codons. Among the nine species of Araliaceae, simple sequence repeats (SSRs) and five large repeat sequences were identified with total numbers ranging from 37 to 46 and 66 to 78, respectively. Five highly divergent regions were successfully identified that could be used as potential genetic markers of Brassaiopsis and Asian Palmate group. Phylogenetic analysis of 47 plastomes, representing 19 genera of Araliaceae and two related families, was performed to reconstruct highly supported relationships for the Araliaceae, which highlight four well-supported clades of the Hydrocotyle group, Greater Raukaua group, Aralia-Panax group, and Asian Palmate group. The genus Brassaiopsis can be divided into four groups using internal transcribed spacer (ITS) data. The results indicate that plastome and ITS data can contribute to investigations of the taxonomy, and phylogeny of B. angustifolia. This study provides a theoretical basis for species identification and future biological research on resources of the genus Brassaiopsis.

Mangifera plants are tropical fruits that have high economic value and scientific utility. However, the chloroplast genome characteristics and phylogenetic relationships among Mangifera species remain unclear. In this work, we reconstructed maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees using 11 newly sequenced chloroplast genomes as well as six existing genomes obtained from the National Center for Biotechnology Information (NCBI) database. The chloroplast genomes all had a typical quadripartite structure, with lengths ranging from 157,368 to 158,942 bp. The GC-content in the genomes ranged from 37.8% to 37.9%. We found conserved boundaries comprised of two inverted repeats (IRs), large single-copy (LSC) regions, and small single-copy (SSC) regions. Nucleotide polymorphism analysis revealed three hypervariable regions (ycf4-cemA, rps18-rpl20, and rpl32-ndhF) in the LSC and SSC regions, which could potentially be used as DNA barcodes for Mangifera species. According to our phylogenetic analysis, Mangifera plants were clustered into three clades. Among them, all five samples of M. indica formed a monophyletic group in Clade Ⅰ. Clade Ⅱ included seven Mangifera species and could be further divided into five subclades with 100% branch support values. Clade Ⅲ included two M. persiciforma samples that formed a monophyletic group. Taken together, these results provide a theoretical basis for species determination, in addition to shedding light on the evolution of Mangifera.

Pourthiaea is of great ornamental value because it produces white flowers in spring and summer, red fruit in autumn, and their fruit does not fall in winter. In order to explore the genetic structure and evolutionary characteristics of the chloroplast genome of Pourthiaea, comparative genomics analysis and phylogenetic analysis were conducted using ten published chloroplast genomes of Pourthiaea from the NCBI database. The results showed that the chloroplast genomes of the ten species of Pourthiaea showed typical circular tetrad structures, and the genome sizes were all within the range of 160,159–160,401 bp, in which the large single copy was 88,047–88,359 bp, the small single copy was 19,234–19,338 bp, and the lengths of a pair of inverted repeats were 26,341–26,401 bp. The GC contents ranged from 36.5% to 36.6%. A total of 1017 SSR loci were identified from the chloroplast genomes of the ten species of Pourthiaea, including six types of nucleotide repeats. The gene types and gene distribution of the IR boundary regions of the chloroplast genomes of different species of Pourthiaea were highly conservative, with little variation. Through the sequence alignment of chloroplast genomes, it was found that the chloroplast genomes of the ten species of Pourthiaea were generally highly conservative. The variation mainly occurred in the spacer regions of adjacent genes. Through nucleic acid diversity analysis, three hypervariable regions were screened at Pi > 0.006, namely trnQ(UUC)-psbk-psbl, accD-psal, and ndhF-rpl32-trnL (UAG). Phylogenetic analysis showed that the ten species of the genus Pourthiaea were clustered in the same branch and formed sister groups with the genus Stranvaesia, and that the support rate for the monophyly of the genus Pourthiaea was high. This study can serve as a reference for the breeding, genetic evolution, and phylogeny of Pourthiaea.

Rosa lucieae is one of the famous wild ancestors of cultivated roses and plays a very important role in horticultural research, but there is still a lack of research on the R. lucieae chloroplast genome. In this study, we used the Illumina MiSeq platform for sequencing, assembly, and annotation to obtain the R. lucieae chloroplast genome sequencing information and compared genomics, selection stress analysis, and phylogenetic analysis with 12 other chloroplast genomes of Rosa. The R. lucieae cpDNA sequence has a total length of 156,504 bp, and 130 genes are annotated. The length of all 13 studied chloroplast genomes is 156,333~157,385 bp. Their gene content, gene sequence, GC content, and IR boundary structure were highly similar. Five kinds of large repeats were detected that numbered 100~116, and SSR sequences ranged from 78 to 90 bp. Four highly differentiated regions were identified, which can be used as potential genetic markers for Rosa. Selection stress analysis showed that there was significant positive selection among the 18 genes. The phylogenetic analysis of R. lucieae and R. cymose, R. maximowicziana, R. multiflora, and R. pricei showed the closest relationship. Overall, our results provide a more comprehensive understanding of the systematic genomics and comparative genomics of Rosa.

Illigera grandiflora, a kind of traditional medicinal liana, belongs to the Illigera Blume of the Hernandiaceae. In this study, we reported the characteristics of complete plastome for I. grandiflora. Its total plastome was 156,138 bp in length, comprising a large single-copy region(LSC) of 84,931 bp, a small single-copy region (SSC) of 18,544 bp, and a pair of inverted repeat (IR) regions of 26,549 bp. The overall GC content was 39.16% (LSC, 37.77%; SSC, 33.89%; IR, 43.21%). The plastome encoded 134 genes, including 83 protein-coding genes, 42 transfer RNA genes, and 10 ribosomal RNA genes. The relationships in our phylogeny showed that the two Illigera species are located in the same clade, with Hernandia nymphaeifolia being the next sister group, followed by Wilkiea huegeliana.

The genus Pyrus, comprising several popular fruit crops worldwide, includes over 30 tree species. Here we determined the complete plastid genome sequence of Pyrus betulaefolia. The plastome consists of 160,184 bp, including a pair of inverted repeats (IRs) with a length of 26,384 bp separated by a large single-copy region (LSC) and a small single-copy region (SSC) of 88,121 bp and 19,295 bp, respectively. Further phylogenetic analyze was conducted using 11 complete plastid genomes of Rosaceae with KVM + F + I model, which supports Pyrus betulaefolia as a sister to all other eight Pyrus taxa with published plastomes.

Eriobotrya malipoensis Kuan is an important wild woody evergreen tree within the genus Eriobotrya Lindl belonging the family Rosaceae. To better determine its phylogenetic location with respect to the other Eriobotrya species, the complete plastome of E. malipoensis was sequenced. The whole plastome is 159,313 bp in length, consisting of a pair of inverted repeat (IR) regions of 26,344 bp, one large single-copy (LSC) region of 87,270 bp, and one small single-copy (SSC) region of 19,355 bp. The overall G + C content of the whole plastome is 36.7%. Further, maximum likelihood phylogenetic analyse (TVM + F+R2 model) was conducted using 14 complete plastome of the Rosaceae. Our phylogeny supports the relationships: sisterhood of the E. malipoensis and E. fragrans Champ, flowed E. japonica Lindl.

Eriobotrya fragrans Champion ex Bentham is a potential medicinal plant of the genus Eriobotrya Lindl in the family Rosaceae. To better determine its phylogenetic location with respect to the other Rosaceae species, the complete chloroplast genome of E. fragrans was sequenced. The whole E. fragrans chloroplast genome is 159,286 bp in length, consisting of a pair of inverted repeat (IR) regions of 26,343 bp, one large single-copy (LSC) region of 87,301 bp, and one small single-copy (SSC) region of 19,299 bp. The overall GC content of the whole chloroplast genome is 36.7%. Further, phylogenetic analysis using maximum likelihood with TVM + F+R2 model strongly supports the relationship: sisterhood of E. fragrans and E. japonica, followed by three species of Pyrus L.

Cinnamomum burmanni (Nees et T. Nees) Blume is a valuable aromatic timber tree of the genus Cinnamomum Tree in the family Lauraceae. To better determine its phylogenetic location with respect to the other Cinnamomum species, the complete chloroplast genome of C. burmanni was sequenced. The total chloroplast genome size is 152,775 bp, consisting of a pair of inverted repeats (IRa/b) with a length of 20,092 bp separated by a large single-copy region (LSC) and a small single-copy region (SSC) which are 93,687 and 18,903 bp, respectively. The overall GC content of the cp genome is 39.1%. Further, maximum-likelihood phylogenetic analysis with K3Pu + F+I model was performed using eleven complete plastomes of the Lauraceae, which revealed that C. burmanni is closely related to C. verum.

Being a sister species of Saccharomyces cerevisiae, Saccharomyces uvarum shows great potential regarding the future of the wine industry. The sulfite tolerance of most S. uvarum strains is poor, however. This is a major flaw that limits its utility in the wine industry. In S. cerevisiae, FZF1 plays a positive role in the transcription of SSU1, which encodes a sulfite efflux transport protein that is critical for sulfite tolerance. Although FZF1 has previously been shown to play a role in sulfite tolerance in S. uvarum, there is little information about its action mechanism. To assess the function of FZF1, two over-expression vectors that contained different FZF1 genes, and one FZF1 silencing vector, were constructed and introduced into a sulfite-tolerant S. uvarum strain using electroporation. In addition, an FZF1-deletion strain was constructed. Both of the FZF1-over-expressing strains showed an elevated tolerance to sulfite, and the FZF1-deletion strain showed the opposite effect. Repression of FZF1 transcription failed, however, presumably due to the lack of alleles of DCR1 and AGO. The qRT-PCR analysis was used to examine changes in transcription in the strains. Surprisingly, neither over-expressing strain promoted SSU1 transcription, although MET4 and HAL4 transcripts significantly increased in both sulfite-tolerance increased strains. We conclude that FZF1 plays a different role in the sulfite tolerance of S. uvarum compared to its role in S. cerevisiae.

The genus Neocinnamomumis considered to be one of themost enigmatic groups in Lauraceae, mainlydistributedintropical andsubtropical regionsofSoutheastAsia. The genus contains valuable oilseed andmedicinal tree species. However, there are few studies on the genus Neocinnamomum at present, and its interspecific relationship is still unclear. In order to explore the genetic structure and evolutionary characteristics of the Neocinnamomum chloroplast genome and to resolve the species relationships within the genus, comparative genomic and phylogenetic analyses were performed on the whole chloroplast genome sequences of 51 samples representing seven Neocinnamomum taxa. The whole Neocinnamomumchloroplast genome size ranged from150,753-150,956 bp, with a GC content of 38.8%-38.9%. A total of 128 genes were annotated within the Neocinnamomumchloroplast genome, including 84 protein coding genes, 8 rRNA genes, and 36 tRNA genes. Between 71-82 SSRs were detected, among which A/T base repeatswere themost common. The chloroplast genome contained a total of 31preferredcodons. Threehighly variableregions, trnN-GUU-ndhF, petA-psbJ, and ccsA-ndhD, were identified with Pi values > 0.004. Based on the whole chloroplast genome phylogenetic tree, the phylogenetic relationships among the seven Neocinnamomum taxa were determined. N. delavayi and N. fargesii were the most closely related species, and N. lecomtei was identified as the most basal taxon. In this study, the characteristics and sequence variation of the chloroplast genomes of seven Neocinnamomum taxa were revealed, and the genetic relationship among the species was clarified. The results of this study will provide a reference for subsequent molecular marker development and phylogenetic research of Neocinnamomum. [ABSTRACT FROM AUTHOR]