Comparing and phylogenetic analysis chloroplast genome of three Achyranthes species

Characterization of the complete chloroplast genome sequence of Bassia scoparia (L.) A. J. Scott 1978 (Amaranthaceae) and its phylogenetic analysis

Bassia scoparia, an annual potherb belonging to the family Amaranthaceae, has been widely used in traditional Chinese and Japanese medicine for over 2000 years. Herein, we presented its complete chloroplast. The chloroplast genome sequence was 151,278 bp in length with a 36.6% content of GC. The genome showed the typical quadripartite structure, comprising a pair of inverted repeat (IR) regions (24,353 bp) separated by a large single-copy (LSC) region (84,067 bp) and a small single-copy (SSC) region (18,505 bp). This chloroplast genome harbored 133 predicted genes, including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The phylogenetic analysis indicated that B. scoparia was closely related to B. littorea. This newly sequenced chloroplast genome not only enhances our understanding of the genome of Bassia but also provides valuable insights for the evolutionary study of the family Amaranthaceae.

Assembly, annotation and analysis of the chloroplast genome of the Algarrobo tree Neltuma pallida (subfamily: Caesalpinioideae)

BACKGROUND

Neltuma pallida is a tree that grows in arid soils in northwestern Peru. As a predominant species of the Equatorial Dry Forest ecoregion, it holds significant economic and ecological value for both people and environment. Despite this, the species is severely threatened and there is a lack of genetic and genomic research, hindering the proposal of evidence-based conservation strategies.

RESULTS

In this work, we conducted the assembly, annotation, analysis and comparison of the chloroplast genome of a N. pallida specimen with those of related species. The assembled chloroplast genome has a length of 162,381 bp with a typical quadripartite structure (LSC-IRA-SSC-IRB). The calculated GC content was 35.97%. However, this is variable between regions, with a higher GC content observed in the IRs. A total of 132 genes were annotated, of which 19 were duplicates and 22 contained at least one intron in their sequence. A substantial number of repetitive sequences of different types were identified in the assembled genome, predominantly tandem repeats (> 300). In particular, 142 microsatellites (SSR) markers were identified. The phylogenetic reconstruction showed that N. pallida grouped with the other Neltuma species and with Prosopis cineraria. The analysis of sequence divergence between the chloroplast genome sequences of N. pallida, N. juliflora, P. farcta and Strombocarpa tamarugo revealed a high degree of similarity.

CONCLUSIONS

The N. pallida chloroplast genome was found to be similar to those of closely related species. With a size of 162,831 bp, it had the classical chloroplast quadripartite structure and GC content of 35.97%. Most of the 132 identified genes were protein-coding genes. Additionally, over 800 repetitive sequences were identified, including 142 SSR markers. In the phylogenetic analysis, N. pallida grouped with other Neltuma spp. and P. cineraria. Furthermore, N. pallida chloroplast was highly conserved when compared with genomes of closely related species. These findings can be of great potential for further diversity studies and genetic improvement of N. pallida.

Comparative Analysis of Codon Usage Patterns in Nuclear and Chloroplast Genome of Dalbergia (Fabaceae)

The Dalbergia plants are widely distributed across more than 130 tropical and subtropical countries and have significant economic and medicinal value. Codon usage bias (CUB) is a critical feature for studying gene function and evolution, which can provide a better understanding of biological gene regulation. In this study, we comprehensively analyzed the CUB patterns of the nuclear genome, chloroplast genome, and gene expression, as well as systematic evolution of Dalbergia species. Our results showed that the synonymous and optimal codons in the coding regions of both nuclear and chloroplast genome of Dalbergia preferred ending with A/U at the third codon base. Natural selection was the primary factor affecting the CUB features. Furthermore, in highly expressed genes of Dalbergia odorifera, we found that genes with stronger CUB exhibited higher expression levels, and these highly expressed genes tended to favor the use of G/C-ending codons. In addition, the branching patterns of the protein-coding sequences and the chloroplast genome sequences were very similar in the systematic tree, and different with the cluster from the CUB of the chloroplast genome. This study highlights the CUB patterns and features of Dalbergia species in different genomes, explores the correlation between CUB preferences and gene expression, and further investigates the systematic evolution of Dalbergia, providing new insights into codon biology and the evolution of Dalbergia plants.

Characterization of the Complete Chloroplast Genome Sequence of the Socotra Dragon`s Blood Tree (Dracaena cinnabari Balf.)

The Socotra dragon`s blood tree (Dracaena cinnabari Balf.) is endemic to the island of Socotra in Yemen. This iconic species plays an essential role in the survival of associated organisms, acting as an umbrella tree. Overexploitation, overgrazing by livestock, global climate change, and insufficient regeneration mean that the populations of this valuable species are declining in the wild. Although there are many studies on the morphology, anatomy, and physiology of D. cinnabari, no genomic analysis of this endangered species has been performed so far. Therefore, the main aim of this study was to characterize the complete chloroplast sequence genome of D. cinnabari for conservation purposes. The D. cinnabari chloroplast genome is 155,371 bp with a total GC content of 37.5%. It has a quadripartite plastid genome structure composed of one large single-copy region of 83,870 bp, one small single-copy region of 18,471 bp, and two inverted repeat regions of 26,515 bp each. One hundred and thirty-two genes were annotated, 86 of which are protein-coding genes, 38 are transfer RNAs, and eight are ribosomal RNAs. Forty simple sequence repeats have also been identified in this chloroplast genome. Comparative analysis of complete sequences of D. cinnabari chloroplast genomes with other species of the genus Dracaena showed a very high conservativeness of their structure and organization. Phylogenetic inference showed that D. cinnabari is much closer to D. draco, D. cochinchinensis, and D. cambodiana than to D. terniflora, D. angustifolia, D. hokouensis, and D. elliptica. The results obtained in this study provide new and valuable omics data for further phylogenetic studies of the genus Dracaena as well as enable the protection of genetic resources of highly endangered D. cinnabari.

Transcriptional Basis for Haustorium Formation and Host Establishment in Hemiparasitic Psittacanthus schiedeanus Mistletoes

The mistletoe Psittacanthus schiedeanus, a keystone species in interaction networks between plants, pollinators, and seed dispersers, infects a wide range of native and non-native tree species of commercial interest. Here, using RNA-seq methodology we assembled the whole circularized quadripartite structure of P. schiedeanus chloroplast genome and described changes in the gene expression of the nuclear genomes across time of experimentally inoculated seeds. Of the 140,467 assembled and annotated uniGenes, 2,000 were identified as differentially expressed (DEGs) and were classified in six distinct clusters according to their expression profiles. DEGs were also classified in enriched functional categories related to synthesis, signaling, homoeostasis, and response to auxin and jasmonic acid. Since many orthologs are involved in lateral or adventitious root formation in other plant species, we propose that in P. schiedeanus (and perhaps in other rootless mistletoe species), these genes participate in haustorium formation by complex regulatory networks here described. Lastly, and according to the structural similarities of P. schiedeanus enzymes with those that are involved in host cell wall degradation in fungi, we suggest that a similar enzymatic arsenal is secreted extracellularly and used by mistletoes species to easily parasitize and break through tissues of the host.

Chloroplast Genome of Lithocarpus dealbatus (Hook.f. & Thomson ex Miq.) Rehder Establishes Monophyletic Origin of the Species and Reveals Mutational Hotspots with Taxon Delimitation Potential

There is phylogenetic ambiguity in the genus Lithocarpus and subfamily Quercoideae (Family: Fagaceae). Lithocarpus dealbatus, an ecologically important tree, is the dominant species among the Quercoideae in India. Although several studies have been conducted on the species' regeneration and ecological and economic significance, limited information is available on its phylo-genomics. To resolve the phylogeny in Quercoideae, we sequenced and assembled the 161,476 bp chloroplast genome of L. dealbatus, which has a large single-copy section of 90,732 bp and a small single-copy region of 18,987 bp, separated by a pair of inverted repeat regions of 25,879 bp. The chloroplast genome contained 133 genes, of which 86 were protein-coding genes, 39 were transfer RNAs, and eight were ribosomal RNAs. Analysis of repeat elements and RNA editing sites revealed interspecific similarities within the Lithocarpus genus. DNA diversity analysis identified five highly diverged coding and noncoding hotspot regions in the four genera, which can be used as polymorphic markers for species/taxon delimitation across the four genera of Quercoideae viz., Lithocarpus, Quercus, Castanea, and Castanopsis. The chloroplast-based phylogenetic analysis among the Quercoideae established a monophyletic origin of Lithocarpus, and a closer evolutionary lineage with a few Quercus species. Besides providing insights into the chloroplast genome architecture of L. dealbatus, the study identified five mutational hotspots having high taxon-delimitation potential across four genera of Quercoideae.

Comparative analysis of chloroplast genomes reveals phylogenetic relationships and intraspecific variation in the medicinal plant Isodon rubescens

Isodon rubescens (Hemsley) H. Hara (Lamiaceae) is a traditional Chinese medicine plant that has been used to treat various human diseases and conditions such as inflammation, respiratory and gastrointestinal bacterial infections, and malignant tumors. However, the contents of the main active components of I. rubescens from different origins differ significantly, which greatly affected its quality. Therefore, a molecular method to identify and classify I. rubescens is needed. Here, we report the DNA sequence of the chloroplast genome of I. rubescens collected from Lushan, Henan province. The genome is 152,642 bp in length and has a conserved structure that includes a pair of IR regions (25,726 bp), a LSC region (83,527 bp) and a SSC region (17,663 bp). The chloroplast genome contains 113 unique genes, four rRNA genes, 30 tRNA genes, and 79 protein-coding genes, 23 of which contain introns. The protein-coding genes account for a total of 24,412 codons, and most of them are A/T biased usage. We identified 32 simple sequence repeats (SSRs) and 48 long repeats. Furthermore, we developed valuable chloroplast molecular resources by comparing chloroplast genomes from three Isodon species, and both mVISTA and DnaSP analyses showed that rps16-trnQ, trnS-trnG, and ndhC-trnM are candidate regions that will allow the identification of intraspecific differences within I. rubescens. Also 14 candidate fragments can be used to identify interspecific differences between species in Isodon. A phylogenetic analysis of the complete chloroplast genomes of 24 species in subfamily Nepetoideae was performed using the maximum likelihood method, and shows that I. rubescens clustered closer to I. serra than I. lophanthoides. Interestingly, our analysis showed that I. rubescens (MW018469.1) from Xianyang, Shaanxi Province (IR-X), is closer to I. serra than to the other two I. rubescens accessions. These results strongly indicate that intraspecific diversity is present in I. rubescens. Therefore, our results provide further insight into the phylogenetic relationships and interspecific diversity of species in the genus Isodon.

New plastomes of eight Ipomoea species and four putative hybrids from Eastern Amazon

Ipomoea is a large pantropical genus globally distributed, which importance goes beyond the economic value as food resources or ornamental crops. This highly diverse genus has been the focus of a great number of studies, enriching the plant genomics knowledge, and challenging the plant evolution models. In the Carajás mountain range, located in Eastern Amazon, the savannah-like ferruginous ecosystem known as canga harbors highly specialized plant and animal populations, and Ipomoea is substantially representative in such restrictive habitat. Thus, to provide genetic data and insights into whole plastome phylogenetic relationships among key Ipomoea species from Eastern Amazon with little to none previously available data, we present the complete plastome sequences of twelve lineages of the genus, including the canga microendemic I. cavalcantei, the closely related I. marabaensis, and their putative hybrids. The twelve plastomes presented similar gene content as most publicly available Ipomoea plastomes, although the putative hybrids were correctly placed as closely related to the two parental species. The cavalcantei-marabaensis group was consistently grouped between phylogenetic methods. The closer relationship of the I. carnea plastome with the cavalcantei-marabaensis group, as well as the branch formed by I. quamoclit, I. asarifolia and I. maurandioides, were probably a consequence of insufficient taxonomic representativity, instead of true genetic closeness, reinforcing the importance of new plastome assemblies to resolve inconsistencies and boost statistical confidence, especially the case for South American clades of Ipomoea. The search for k-mers presenting high dispersion among the frequency distributions pointed to highly variable coding and intergenic regions, which may potentially contribute to the genetic diversity observed at species level. Our results contribute to the resolution of uncertain clades within Ipomoea and future phylogenomic studies, bringing unprecedented results to Ipomoea species with restricted distribution, such as I. cavalcantei.

The chloroplast genome sequence and phylogenetic analysis of Apocynum venetum L

Apocynum venetum L. (Apocynaceae) is valuable for its medicinal compounds and fiber content. Native A. venetum populations are threatened and require protection. Wild A. venetum resources are limited relative to market demand and a poor understanding of the composition of A. venetum at the molecular level. The chloroplast genome contains genetic markers for phylogenetic analysis, genetic diversity evaluation, and molecular identification. In this study, the entire genome of the A. venetum chloroplast was sequenced and analyzed. The A. venetum cp genome is 150,878 bp, with a pair of inverted repeat regions (IRA and IRB). Each inverted repeat region is 25,810 bp, which consist of large (LSC, 81,951 bp) and small (SSC, 17,307 bp) single copy areas. The genome-wide GC content was 38.35%, LSC made up 36.49%, SSC made up 32.41%, and IR made up 43.3%. The A. venetum chloroplast genome encodes 131 genes, including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. This study identified the unique characteristics of the A. venetum chloroplast genome, which will help formulate effective conservation and management strategies as well as molecular identification approaches for this important medicinal plant.

Seven Complete Chloroplast Genomes from Symplocos: Genome Organization and Comparative Analysis

In the present study, chloroplast genome sequences of four species of Symplocos (S. chinensis for. pilosa, S. prunifolia, S. coreana, and S. tanakana) from South Korea were obtained by Ion Torrent sequencing and compared with the sequences of three previously reported Symplocos chloroplast genomes from different species. The length of the Symplocos chloroplast genome ranged from 156,961 to 157,365 bp. Overall, 132 genes including 87 functional genes, 37 tRNA genes, and eight rRNA genes were identified in all Symplocos chloroplast genomes. The gene order and contents were highly similar across the seven species. The coding regions were more conserved than the non-coding regions, and the large single-copy and small single-copy regions were less conserved than the inverted repeat regions. We identified five new hotspot regions (rbcL, ycf4, psaJ, rpl22, and ycf1) that can be used as barcodes or species-specific Symplocos molecular markers. These four novel chloroplast genomes provide basic information on the plastid genome of Symplocos and enable better taxonomic characterization of this genus.