Comparative genomics and phylogenetic analysis of chloroplast genomes of Asian Caryodaphnopsis taxa (Lauraceae).

The genus Caryodaphnopsis, a member of the Lauraceae family, is characterized by seeds that are rich in oil, as well as highly exploitable fruits and wood. The Asian taxa within this genus exhibit complex morphological variations, posing challenges to their accurate classification and impeding their effective use and development as a resource. In this study, we sequenced the chloroplast genomes of 31 individuals representing nine Asian taxa within the Caryodaphnopsis genus. Our primary objectives were to reveal structural variations in these chloroplast genomes through comparative analyses and to infer the species' phylogenetic relationships. Our findings revealed that all chloroplast genomes had a tetrad structure, ranged in length from 148,828 to 154,946 bp, and harbored 128-131 genes. Notably, contraction of the IR region led to the absence of some genes in eight taxa. A comprehensive analysis identified 1267 long repetitive sequences and 2176 SSRs, 286 SNPs, and 135 indels across the 31 chloroplast genomes. The Ka/Ks ratio analysis indicated potential positive selection on the matK, rpl22, and rpoC2 genes. Furthermore, we identified six variable regions as promising barcode regions. Phylogenetic analysis grouped the nine Asian taxa into six branches, with C. henryi forming the basal group from which three distinct complexes emerged. This study contributes significantly to the current understanding of the evolutionary dynamics and phylogenetic relationships within the genus Caryodaphnopsis. Furthermore, the identified molecular markers hold potential for molecular barcoding applications in population genetics, providing valuable tools for future research and conservation efforts within this diverse genus.

Comparative and phylogenetic analysis of complete chloroplast genomes from seven Neocinnamomum taxa (Lauraceae).

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.

The complete plastid genome of the endangered shrub Brassaiopsis angustifolia (Araliaceae): Comparative genetic and phylogenetic analysis.

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.

Comparative Analysis of Chloroplast Genome Structure and Phylogenetic Relationships Among Six Taxa Within the Genus Catalpa (Bignoniaceae).

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.

Increasing Taxa Sampling Provides New Insights on the Phylogenetic Relationship Between Eriobotrya and Rhaphiolepis.

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.

The complete plastome sequence of Illigera grandiflora.

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 complete plastome sequence of a subtropical tree Pyrus betulaefolia (Rosaceae).

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.

Complete plastome of a subtropical tree Eriobotrya malipoensis (Rosaceae) in Yunnan.

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.

The complete chloroplast genome sequence of Eriobotrya fragrans.

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.

The chloroplast genome of aromatic plants Cinnamomum burmanni (Lauraceae).

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.

Functional Analysis of the FZF1 Genes of Saccharomyces uvarum.

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.

Development and characterization of novel EST-SSR markers for Speranskia tuberculata (Euphorbiaceae).

PREMISE OF THE STUDY: The first set of expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed and characterized for Speranskia tuberculata (Euphorbiaceae), a traditional medicinal plant endemic to northern China, to explore the effects of recent habitat fragmentation on the genetic diversity and structure of this species. METHODS AND RESULTS: In this study, a total of 18 novel polymorphic microsatellite (EST-SSR) markers were developed for S. tuberculata using high-throughput transcriptome sequencing. Analysis of 24 individuals of S. tuberculata from four natural populations revealed their robust polymorphic reliability. The number of alleles per locus ranged from two to 11, while the expected and observed heterozygosity per marker varied from 0.187 to 0.827 and 0.042 to 0.917, respectively. Of these markers, 13 showed good amplification results in the closely related species S. cantonensis. CONCLUSIONS: These newly generated SSR markers are expected to provide novel tools for genetic studies of S. tuberculata, which will contribute to the conservation and sustainable use of the species' wild genetic resources.

Development and characterization of EST-SSR markers in Bombax ceiba (Malvaceae).

PREMISE OF THE STUDY: Bombax ceiba (Malvaceae), commonly known as silk cotton tree, is a multipurpose tree species of tropical forests. Novel expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed and characterized for the species using transcriptome analysis. METHODS AND RESULTS: A total of 33 new EST-SSR markers were developed for B. ceiba, of which 13 showed polymorphisms across the 24 individuals from four distant populations tested in the study. The results showed that the number of alleles per polymorphic locus ranged from two to four, and the expected heterozygosity and observed heterozygosity per locus varied from 0.043 to 0.654 and from 0 to 0.609, respectively. CONCLUSIONS: These newly developed EST-SSR markers can be used in phylogeographic and population genetic studies to investigate the origin of B. ceiba populations. Furthermore, these EST-SSR markers could also greatly promote the development of molecular breeding studies pertaining to silk cotton tree.

[The zonal characteristics and cultivated types difference of functional components in brown rice for core collection of Yunnan rice].

The zonal characteristics and cultivated types difference of functional components in brown rice of 907 accessions for primary core collection for rice landrace from 16 prefectures of five rice regions in Yunnan Province were determined by ultraviolet spectrophotometry of DU640 type from BECKMAN. The analytical results showed that the contents mg x (100 g)(-1) of total flavone in brown rice is 306.98 +/- 192.75, the content of upland (341.74 +/- 185.11) is the most significantly higher than that of lowland (290.41 +/- 193.72), that of the glutinous (315.54 +/- 197.64) is significantly higher than non-glutinous (171.68 +/- 11.76), that of early-mid (318.25 +/- 197.93) is the most significantly higher than late (282.12 +/- 178.11), that of red rice (379.22 +/- 197.70) and purple rice (365.61 +/- 195.44) are the most significantly higher than white rice (216.96 +/- 142.11), and that of nuda (332.68 +/- 196.22) is significantly higher than non-nuda (300. 48 +/- 191.14). Among five rice regions, in turn III (327.13) > LL (324.23) > IV (273.11) > V (270.16) > I (258.26), namely it is the most significantly highest (p < 0.01) for contents of total flavone from South Yunnan (II, III) than that of middle Yunnan; It is the most significantly highest from Simao prefecture than that of 8 prefectures, but it is the most significantly low from Baoshan prefecture than that of 7 prefectures. The contents mg x (100 g)(-1) of g-amino butyric acid (GABA) in brown rice is 7.43 +/- 2.53, the content of lowland (7.59 +/- 2. 56) is the most significantly higher than that of upland (7.09 +/- 2.45), that of non-glutinous (8.55 +/- 2.88) is the most significantly higher than glutinous (7.10 +/- 2.32), that of late (7.88 +/- 2.64) is the most significantly higher than early-mid (7.23 +/- 2.45), that of white rice (8.38 +/- 2.66) is the most significantly higher than red rice (6.63 +/- 2.14) and purple rice (7.34 +/- 2.18); Among five rice regions in turn II (7.69) > I (7.40) > IV (7.39) > III (7.33) > V (6.64), viz. the content of GABA from South Yunnan single/double cropping rice region is clearly higher than that of Northwest Yunnan cold highland japonica rice region; It is significant difference of GABA content in brown rice for that Simao prefecture South Yunnan and Yuxi as well as Baoshan prefecture, at least than that of 5 prefectures. The contents (%) of resistant starch in brown rice is 0.75 +/- 0.29, the contents of indica (0.78 +/- 0.35) is significantly higher than japonica (0.74 +/- 0.24), that of glutinous (0.78 +/- 0.31) is the most significantly higher than non-glutinous (0. 67 +/- 0.22), that of late (0.77 +/- 0. 35) is the most significantly higher than early-mid (0.75 +/- 0.26), that of red rice (0.81 +/- 0.30) and purple rice (0.70 +/- 0.30) is the most significantly higher than white rice (0.69 +/- 0.27); Among five rice regions in turn I (0.83) > II (0.79) > III (0.76) > V (0. 55) > IV (0.50), namely it is the highest (p < 0.01) for contents of resistant starch from the middle and South Yunnan province (I, II, III) than that of northern rice regions (V, IV), and the lowest for contents of resistant starch of Lijiang prefecture of northwestern and Zaotong of northeastern in this province compared to that of 13 prefectures except Diqing prefectures. These results not only reveal the most significant difference between lowland versus upland, glutinous versus nonglutinous, early/mid rice and red/purple versus white rice based on the contents of total flavone and resistant starch as well as g-amino butyric acid (GABA) in brown rice (p < 0.01), and no significant difference between indica and japonica, awn and no-awn, and common rice and aromatic/soft rice, but also elucidate obvious zonal characteristics of three functional components in brown rice of Yunnan rice. The above results provided theory bases for the genetic breeding and production of functional rice and solve the problems of chronic for human being.