Chloroplast Genome Research Articles

The Whole Mitochondrial Genome Sequence of Dendrobium loddigesii Rolfe, an Endangered Orchid Species in China, Reveals a Complex Multi-Chromosome Structure.

Dendrobium loddigesii is a precious traditional Chinese medicine with high medicinal and ornamental value. However, the characterization of its mitochondrial genome is still pending. Here, we assembled the complete mitochondrial genome of D. loddigesii and discovered that its genome possessed a complex multi-chromosome structure. The mitogenome of D. loddigesii consisted of 17 circular subgenomes, ranging in size from 16,323 bp to 56,781 bp. The total length of the mitogenome was 513,356 bp, with a GC content of 43.41%. The mitogenome contained 70 genes, comprising 36 protein-coding genes (PCGs), 31 tRNA genes, and 3 rRNA genes. Furthermore, we detected 403 repeat sequences as well as identified 482 RNA-editing sites and 8154 codons across all PCGs. Following the sequence similarity analysis, 27 fragments exhibiting homology to both the mitogenome and chloroplast genome were discovered, accounting for 9.86% mitogenome of D. loddigesii. Synteny analysis revealed numerous sequence rearrangements in D. loddigesii and the mitogenomes of related species. Phylogenetic analysis strongly supported that D. loddigesii and D. Amplum formed a single clade with 100% bootstrap support. The outcomes will significantly augment the orchid mitochondrial genome database, offering profound insights into Dendrobium's intricate mitochondrial genome architecture.

Unveiling the complete chloroplast genome of tribulus macropterus var. Arabicus (hosni) al-hemaid & j. Thomas: genome structure, comparative analysis and phylogeny

The present investigation unveiled the first complete chloroplast (cp) genome of Tribulus macropterus var. arabicus (Hosni) Al-Hemaid & J. Thomas (Zygophyllaceae), a medicinal herb, indigenous to Saudi Arabia. The cp genome, comprising a length of 158,179 bp and a GC content of 35.8%, exhibited the typical circular quadripartite arrangement of flowering plants, including two inverted repeat regions (25842 bp) separated by a large single-copy (88873 bp) and a small single-copy region (17622 bp). Genome annotation unraveled 132 genes, comprising of 87 protein-coding genes, 37 tRNAs and eight rRNAs. A comparative plastomics approach demonstrated a very similar genome structure and gene organization in closely related taxa. Whole-genome alignment indicated that the inverted repeat regions exhibited greater conservation when compared to the single copy zones. Repeat analysis of the cp genome identified 80 simple sequence repeats, with the majority (64) being mononucleotides. Among the longer repeats, forward repeats were frequent (20) followed by palindromic and reverse repeats. The nucleotide diversity endeavor identified some hypervariable sites (rpl22, cemA, trnL-UAG) in the small and large single copies which would offer opportunities to design molecular markers for potential application in taxonomic identification. Phylogenetic analysis with rbcL barcode elucidated the distinct position of T. macropterus var. arabicus compared to T. macropterus within Zygophyllaceae and further validated the assembly. The findings of this investigation provide significant insights into biological fields, particularly enhancing the current understanding of the genetic and evolutionary variations within Zygophyllaceae. Bangladesh J. Plant Taxon. 31(1): 1-14, 2024 (June)

Dendrobium tetrapterum, a cryptic species in the D. lindleyi alliance (Orchidaceae; Dendrobiinae): evidence from morphological and molecular data

Dendrobium tetrapterum, a cryptic species in the D. lindleyi alliance, is described and illustrated. Detailed morphological comparisons indicate that it is similar to D. lindleyi and D. jenkinsii but can be distinguished by four morphological characters, namely petals without (vs. with) claw, slit (vs. entire) transverse septum at lip base, anther cap with (vs. without) indentation on each side and a rhombic (vs. pentagonal–octagonal or oblong) pseudobulb cross-section. Combined with the geographical distribution and whole plastid genome data, we confirm that D. tetrapterum is not a natural hybrid of the other two species, but a separate species.

Morphological and functional evolution of gametophytes in epilithic Hymenasplenium murakami-hatanakae (Aspleniaceae): The fifth family capable of producing the independent gametophytes

The fern independent gametophytes that can maintain populations by vegetative reproduction without conspecific sporophytes have been considered an unusual phenomenon found in some epiphytic or epilithic species of Hymenophyllaceae, Pteridaceae, Lomariopsidaceae, and Polypodiaceae. By chance, the discovery of mysterious strap-like gametophytes on Izu-Oshima Island, Japan, has led to the hypothesis that Hymenasplenium murakami-hatanakae, a fern species belonging to Aspleniaceae, can also form independent gametophytes. Our investigation revealed gametophyte populations of H. murakami-hatanakae on three islands in the Izu Islands. Based on chloroplast DNA analysis of the gametophyte and sporophyte populations, the gametophytes were found to be maintained by vegetative reproduction without a new supply of spores from sporophytes. A comparison of the surrounding vegetation at the collection sites showed that environmental factors such as light and humidity may influence the maintenance of gametophyte populations. These results clearly show that H. murakami-hatanakae is one of the ferns capable of forming independent gametophytes. This is the first report of independent gametophytes from the suborder Aspleniineae (eupolypod II). The discovery of the independent gametophyte within a phylogenetic lineage previously thought not to form independent gametophytes will provide important insights into the morphological and functional evolution of gametophytes in ferns.

The genome sequence of the chlorophyte Pseudopediastrum boryanum CCAP 291/2 (Turpin) E. Hegewald 2005

We present a genome assembly from a colony of Pseudopediastrum boryanum (CCAP 291/2) (Chlorophyta; Chlorophyceae; Spaeropleales; Hydrodictyaceae). The genome sequence is 183.3 megabases in span. Most of the assembly is scaffolded into 20 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 44.62 kilobases and 205.69 kilobases in length, respectively.

The genome sequence of the chlorophyte Marvania coccoides CCAP 251/1B (Naumann) Henley, Hironaka, Guillou, M. Buchheim, J. Buchheim, M. Fawley & K. Fawley 2004

We present a genome assembly from a culture of Marvania coccoides (CCAP 251/1B) (Chlorophyta; Trebouxiophyceae; Chlorellales; Chlorellaceae). The genome sequence is 22.3 megabases in span. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 49.04 kilobases and 99.87 kilobases in length, respectively.

Iris luojiensis (Iridaceae), a new species from southwest China

Iris luojiensis Z.Y. Wang, H.W. Huang and R. Li sp. nov. from southwest China is described and illustrated. This species occurs on shrub slopes in mountainous regions of southwest China. Iris luojiensis is morphologically similar to Iris japonica Thunb., Iris calcicola Z. C. Lu, Z.P. Huang and Yan Liu and Iris wattii Baker, but easily distinguished from them by its bluish‐violet flowers, 3–6 flowering‐stem branches, leaf size, particularly the upper leaves, and by only having two to three (seldom one) flowers per bract. A phylogenetic analysis based on the complete plastid genome supports the separation of I. luojiensis from other morphologically related species. According to morphological and molecular evidence, I. luojiensis can be placed in the I. sect. Lophiris.

Characterization of the DNA accessibility of chloroplast genomes in grasses

Although the chloroplast genome (cpDNA) of higher plants is known to exist as a large protein-DNA complex called ‘plastid nucleoid’, researches on its DNA state and regulatory elements are limited. In this study, we performed the assay for transposase-accessible chromatin sequencing (ATAC-seq) on five common tissues across five grasses, and found that the accessibility of different regions in cpDNA varied widely, with the transcribed regions being highly accessible and accessibility patterns around gene start and end sites varying depending on the level of gene expression. Further analysis identified a total of 3970 putative protein binding footprints on cpDNAs of five grasses. These footprints were enriched in intergenic regions and co-localized with known functional elements. Footprints and their flanking accessibility varied dynamically among tissues. Cross-species analysis showed that footprints in coding regions tended to overlap non-degenerate sites and contain a high proportion of highly conserved sites, indicating that they are subject to evolutionary constraints. Taken together, our results suggest that the accessibility of cpDNA has biological implications and provide new insights into the transcriptional regulation of chloroplasts.

Temporal dynamics of chloroplast biogenesis revealed initiation of photosynthesis-related gene expression and protein complexes during alfalfa seed germination

The chloroplast biogenesis occurs in cotyledon during alfalfa seed germination before true leaf formation, and is extremely important for the followed plant development and growth. In this study, we conducted a simulation of alfalfa seed germination in the soil by using tin foil and focused on 10 pivotal time points of chloroplast biogenesis in cotyledons before and after light exposure, which showed significant differences in multispectral images, and covered the whole process of chloroplast biogenesis from proplastid, etioplast to mature chloroplast. We revealed three phases that referred to the programmed involvements of photosynthesis promotion, ultrastructure maturity, transcriptomic expression, and protein complex construction, and observed distinct transcriptional expressions of genes from nuclear and chloroplast genomes. In phase I at dark germination before light exposure, chloroplast-encoded genes showed up-regulated expressions together with the importation of chloroplast proteins. In phase II for the first day after light exposure, nuclear-encoded genes’ expressions were initiated at 2 h after light exposure (E2h), followed by swift assembly of chloroplast thylakoid membrane protein complexes, and roaring Fv/Fm and contents of chlorophyll a, chlorophyll b and carotenoid. The initiation at E2h was pronounced by the observation of gradual accumulation of single lamella, and facilitated the formation of granum stacks (thylakoid) at E8h in phase II. In phase III from the second day after light exposure, chloroplast became gradually complete with the fully established photosynthetic capacity. Altogether, our results layed a theoretical foundation for enhancing potential photosynthetic efficiency in alfalfa and related species.

Identification of DNA Barcodes from rbcL Chloroplast DNA in Katokkon Chili (Capsicum annuum var. chinense) Origin of Tana Toraja, South Sulawesi

Katokkon chili (Capsicum annuum var. chinense) is a type of chili which are commonly found in Tana Toraja. It has a distinctive aroma, high spiciness, and a potential economic value but has not been widely identified and explored, thus, it is necessary to carry out molecular identification using DNA barcodes from chloroplast DNA. The aim of this study was to determine genetic variation and the results of constructing a phylogenetic tree from DNA sequences katokkon chili (C. annuum var. chinense) using the rbcL marker. This study used 6 samples of katokkon chilies (C. annuum var. chinense) and 3 outgroup samples (C. frutescens, C. chinense and C. baccatum). The stages of the research included total DNA isolation, qualitative and quantitative tests, PCR amplification using rbcL primers, and sequencing. Data analysis used is sequence alignment, phylogenetic, genetic distance matrix, haplotypes and phylogeography. The results showed genetic variation with 7 polymorphisms consisting of 4 singleton sites at the nucleotide base sequences of 6th, 525, 715 and 737, and 3 parsimony informative sites at the nucleotide base sequences 370, 616 and 902 and the haplotype distribution is divided into 4 haplotypes namely Hap_1 (A1, A2, A3, B1, B2 and B3), Hap_2 (C1), Hap_3 (C2), and Hap_3 (C3). The phylogenetic tree construction formed two clades, namely clade I consist of six samples of katokkon chilies (C. annuum var. chinense) and clade II consisting of three outgroup samples. Mark the highest bootstrap is 96 and the lowest bootstrap value is 29. Genetic distance matrix values are in the range of 0.000–0.005.

Complete chloroplast genomes and phylogenetic relationships of Pedicularis chinensis and Pedicularis kansuensis

The complete cp genomes of Pedicularis chinensis (GenBank accession number: OQ587614) and Pedicularis kansuensis (GenBank accession number: OQ587613) were sequenced, assembled, and annotated. Their chloroplast (cp) genome lengths were 146,452 bp, and 146,852 bp, respectively; 120 and 116 genes were identified, comprising 75 and 72 protein-coding genes (PCGs), 37 and 36 transfer RNA (tRNA) genes, and 8 and 8 ribosomal RNA (rRNA) genes, for P. chinensis and P. kansuensis, respectively. A simple sequence repeat (SSR) analysis revealed that the repetitive sequences were mainly composed of mononucleotide repeats (A/T motif) and dinucleotide repeats (AT/TA motif). Comparative genomics identified several variant genes (rpl22, rps19, rpl12, ycf1, trnH, psbA, and ndhH) and variant regions (trnS-GGA, trnV-UAC, ndhJ-trnV, ycf4-cemA, ndhE-nhdG, and rpl32-trnL) with a high Pi, indicating the potential to serve as deoxyribo nucleic acid (DNA) barcodes for Pedicularis species identification. The results show that the cp genomes of P. chinensis and P. kansuensis were the same as those of other plants in Pedicularis, with different degrees of AT preference for codons. Large differences in the number of SSRs and the expansion of the inverted repeat (IR) region showed strong variability and interspecific differentiation between these two species and other species represented in the genus Pedicularis. A phylogenetic analysis showed that P. kansuensis had the closest relationship with P. oliveriana, and P. chinensis had the closest relationship with P. aschistorhyncha. These results will facilitate the study of the phylogenetic classification and interspecific evolution of Pedicularis plants.

The Complete Chloroplast Genome of an Epiphytic Leafless Orchid, Taeniophyllum complanatum: Comparative Analysis and Phylogenetic Relationships

Taeniophyllum is a distinct taxon of epiphytic leafless plants in the subtribe Aeridinae of Orchidaceae. The differences in chloroplast genomes between extremely degraded epiphytic leafless orchids and other leafy orchids, as well as their origins and evolution, raise intriguing questions. Therefore, we report the chloroplast genome sequence of Taeniophyllum complanatum, including an extensive comparative analysis with other types of leafless orchids. The chloroplast genome of T. complanatum exhibited a typical quadripartite structure, and its overall structure and gene content were relatively conserved. The entire chloroplast genome was 141,174 bp in length, making it the smallest known chloroplast genome of leafless epiphytic orchids. It encoded a total of 120 genes, including repetitive genes, comprising 74 protein-coding genes, 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. A phylogenetic analysis was conducted on the chloroplast genomes of 43 species belonging to five subfamilies of Orchidaceae. The results showed that the five subfamilies were monophyly, with nearly all segments having a 100% bootstrap value. T. complanatum and Chiloschista were clustered together as a sister group to Phalaenopsis and occupied the highest position in the Epidendroideae. Phylogenetic analysis suggested that T. complanatum and other leafless orchids within the Orchidaceae evolved independently. This study may provide the foundation for research on phylogenetic and structural diversity in leafless epiphytic orchids, thereby enhancing the resources available for chloroplast genome studies in Orchidaceae.

Chloroplast Genomes Evolution and Phylogenetic Relationships of Caragana species.

Caragana sensu lato (s.l.) includes approximately 100 species that are mainly distributed in arid and semi-arid regions. Caragana species are ecologically valuable for their roles in windbreaking and sand fixation. However, the taxonomy and phylogenetic relationships of the genus Caragana are still unclear. In this study, we sequenced and assembled the chloroplast genomes of representative species of Caragana and reconstructed robust phylogenetic relationships at the section level. The Caragana chloroplast genome has lost the inverted repeat region and wascategorized in the inverted repeat loss clade (IRLC). The chloroplast genomes of the eight species ranged from 128,458 bp to 135,401 bp and contained 110 unique genes. All the Caragana chloroplast genomes have a highly conserved structure and gene order. The number of long repeats and simple sequence repeats (SSRs) showed significant variation among the eight species, indicating heterogeneous evolution in Caragana. Selective pressure analysis of the genes revealed that most of the protein-coding genes evolved under purifying selection. The phylogenetic analyses indicated that each section forms a clade, except the section Spinosae, which was divided into two clades. This study elucidated the evolution of the chloroplast genome within the widely distributed genus Caragana. The detailed information obtained from this study can serve as a valuable resource for understanding the molecular dynamics and phylogenetic relationships within Caragana.

Characterization and Comparative Analysis of Complete Chloroplast Genomes of Four Bromus (Poaceae, Bromeae) Species.

Bromus (Poaceae Bromeae) is a forage grass with high adaptability and ecological and economic value. Here, we sequenced Bromus ciliatus, Bromus benekenii, Bromus riparius, and Bromus rubens chloroplast genomes and compared them with four previously described species. The genome sizes of Bromus species ranged from 136,934 bp (Bromus vulgaris) to 137,189 bp (Bromus ciliates, Bromus biebersteinii), with a typical quadripartite structure. The studied species had 129 genes, consisting of 83 protein-coding, 38 tRNA-coding, and 8 rRNA-coding genes. The highest GC content was found in the inverted repeat (IR) region (43.85-44.15%), followed by the large single-copy (LSC) region (36.25-36.65%) and the small single-copy (SSC) region (32.21-32.46%). There were 33 high-frequency codons, with those ending in A/U accounting for 90.91%. A total of 350 simple sequence repeats (SSRs) were identified, with single-nucleotide repeats being the most common (61.43%). A total of 228 forward and 141 palindromic repeats were identified. No reverse or complementary repeats were detected. The sequence identities of all sequences were very similar, especially with respect to the protein-coding and inverted repeat regions. Seven highly variable regions were detected, which could be used for molecular marker development. The constructed phylogenetic tree indicates that Bromus is a monophyletic taxon closely related to Triticum. This comparative analysis of the chloroplast genome of Bromus provides a scientific basis for species identification and phylogenetic studies.

The chloroplast genome sequences of Ipomoea alba and I. obscura (Convolvulaceae): genome comparison and phylogenetic analysis

Ipomoea species have diverse uses as ornamentals, food, and medicine. However, their genomic information is limited; I. alba and I. obscura were sequenced and assembled. Their chloroplast genomes were 161,353 bp and 159,691 bp, respectively. Both genomes exhibited a quadripartite structure, consisting of a pair of inverted repeat (IR) regions, which are separated by the large single-copy (LSC) and small single-copy (SSC) regions. The overall GC content was 37.5% for both genomes. A total of 104 and 93 simple sequence repeats, 50 large repeats, and 30 and 22 short tandem repeats were identified in the two chloroplast genomes, respectively. G and T were more preferred than C and A at the third base position based on the Parity Rule 2 plot analysis, and the neutrality plot revealed correlation coefficients of 0.126 and 0.105, indicating the influence of natural selection in shaping the codon usage bias in most protein-coding genes (CDS). Genome comparative analyses using 31 selected Ipomoea taxa from Thailand showed that their chloroplast genomes are rather conserved, but the presence of expansion or contraction of the IR region was identified in some of these Ipomoea taxa. A total of five highly divergent regions were identified, including the CDS genes accD, ndhA, and ndhF, as well as the intergenic spacer regions psbI-atpA and rpl32-ccsA. Phylogenetic analysis based on both the complete chloroplast genome sequence and CDS datasets of 31 Ipomoea taxa showed that I. alba is resolved as a group member for series (ser.) Quamoclit, which contains seven other taxa, including I. hederacea, I. imperati, I. indica, I. nil, I. purpurea, I. quamoclit, and I. × sloteri, while I. obscura is grouped with I. tiliifolia, both of which are under ser. Obscura, and is closely related to I. biflora of ser. Pes-tigridis. Divergence time estimation using the complete chloroplast genome sequence dataset indicated that the mean age of the divergence for Ipomoeeae, Argyreiinae, and Astripomoeinae, was approximately 29.99 Mya, 19.81 Mya, and 13.40 Mya, respectively. The node indicating the divergence of I. alba from the other members of Ipomoea was around 10.06 Mya, and the split between I. obscura and I. tiliifolia is thought to have happened around 17.13 Mya. The split between the I. obscura accessions from Thailand and Taiwan is thought to have taken place around 0.86 Mya.

The chloroplast genomes of two medicinal species (Veronica anagallis-aquatica L. and Veronica undulata Wall.) and its comparative analysis with related Veronica species

Veronica anagallis-aquatica L. and Veronica undulata Wall. are widely used ethnomedicinal plants in China. The two species have different clinical efficacies, while their extremely similar morphology and unclear interspecific relationship make it difficult to accurately identify them, leading to increased instances of mixed usage. This article reports on the complete chloroplast genomes sequence of these two species and their related Veronica species to conduct a comparative genomics analysis and phylogenetic construction. The results showed that the chloroplast (cp) genomes of Veronica exhibited typical circular quadripartite structures, with total lengths of 149,386 to 152,319 base pairs (bp), and GC content of 37.9 to 38.1%, and the number of genes was between 129–134. The total number of simple sequence repeats (SSRs) in V. anagallis-aquatica and V. undulata is 37 and 36, while V. arvensis had the highest total number of 56, predominantly characterized by A/T single bases. The vast majority of long repeat sequence types are forward repeats and palindromic repeats. Selective Ka/Ks values showed that three genes were under positive selection. Sequence differences often occur in the non-coding regions of the large single-copy region (LSC) and small single-copy region (SSC), with the lowest sequence variation in the inverted repeat regions (IR). Seven highly variable regions (trnT-GGU-psbD, rps8-rpl16, trnQ-UUG, trnN-GUU-ndhF, petL, ycf3, and ycf1) were detected, which may be potential molecular markers for identifying V. anagallis-aquatica and V. undulata. The phylogenetic tree indicates that there is a close genetic relationship between the genera Veronica and Neopicrorhiza, and V. anagallis-aquatica and V. undulata are sister groups. The molecular clock analysis results indicate that the divergence time of Veronica may occur at ∼ 9.09 Ma, and the divergence time of these two species occurs at ∼ 0.48 Ma. It is speculated that climate change may be the cause of Veronica species diversity and promote the radiation of the genus. The chloroplast genome data of nine Veronica specie provides important insights into the characteristics and evolution of the chloroplast genome of this genus, as well as the phylogenetic relationships of the genus Veronica.

Insights into structure, codon usage, repeats, and RNA editing of the complete mitochondrial genome of Perilla frutescens (Lamiaceae)

Perilla frutescens (L.) Britton, a member of the Lamiaceae family, stands out as a versatile plant highly valued for its unique aroma and medicinal properties. Additionally, P. frutescens seeds are rich in Îś-linolenic acid, holding substantial economic importance. While the nuclear and chloroplast genomes of P. frutescens have already been documented, the complete mitochondrial genome sequence remains unreported. To this end, the sequencing, annotation, and assembly of the entire Mitochondrial genome of P. frutescens were hereby conducted using a combination of Illumina and PacBio data. The assembled P. frutescens mitochondrial genome spanned 299,551 bp and exhibited a typical circular structure, involving a GC content of 45.23%. Within the genome, a total of 59 unique genes were identified, encompassing 37 protein-coding genes, 20 tRNA genes, and 2 rRNA genes. Additionally, 18 introns were observed in 8 protein-coding genes. Notably, the codons of the P. frutescens mitochondrial genome displayed a notable A/T bias. The analysis also revealed 293 dispersed repeat sequences, 77 simple sequence repeats (SSRs), and 6 tandem repeat sequences. Moreover, RNA editing sites preferentially produced leucine at amino acid editing sites. Furthermore, 70 sequence fragments (12,680 bp) having been transferred from the chloroplast to the mitochondrial genome were identified, accounting for 4.23% of the entire mitochondrial genome. Phylogenetic analysis indicated that among Lamiaceae plants, P. frutescens is most closely related to Salviamiltiorrhiza and Platostoma chinense. Meanwhile, inter-species Ka/Ks results suggested that Ka/Ks <1\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$<1$$\\end{document} for 28 PCGs, indicating that these genes were evolving under purifying selection. Overall, this study enriches the mitochondrial genome data for P. frutescens and forges a theoretical foundation for future molecular breeding research.

Production of biologically active human basic fibroblast growth factor (hFGFb) using Nicotiana tabacum transplastomic plants.

We generated transplastomic tobacco lines that stably express a human Basic Fibroblast Growth Factor (hFGFb) in their chloroplasts stroma and purified a biologically active recombinant hFGFb. MAIN: The use of plants as biofactories presents as an attractive technology with the potential to efficiently produce high-value human recombinant proteins in a cost-effective manner. Plastid genome transformation stands out for its possibility to accumulate recombinant proteins at elevated levels. Of particular interest are recombinant growth factors, given their applications in animal cell culture and regenerative medicine. In this study, we produced recombinant human Fibroblast Growth Factor (rhFGFb), a crucial protein required for animal cell culture, in tobacco chloroplasts. We successfully generated two independent transplastomic lines that are homoplasmic and accumulate rhFGFb in their leaves. Furthermore, the produced rhFGFb demonstrated its biological activity by inducing proliferation in HEK293T cell lines. These results collectively underscore plastid genome transformation as a promising plant-based bioreactor for rhFGFb production.

Complete Organelle Genome of the Desiccation-Tolerant (DT) Moss Tortula atrovirens and Comparative Analysis of the Pottiaceae Family.

Tortula atrovirens (Sm.) Lindb. is an important component of biological soil crusts and possesses an extraordinary tolerance against desiccation in dryland habitats. However, knowledge of the organelle genome of this desiccation-tolerant (DT) moss is still lacking. Here, we assembled the first reported Tortula organelle genome and conducted a comprehensive analysis within the Pottiaceae family. T. atrovirens exhibited the second largest chloroplast genome (129,646 bp) within the Pottiaceae, whereas its mitogenome (105,877 bp) and those of other mosses were smaller in size compared to other land plants. The chloroplast and mitochondrial genomes of T. atrovirens were characterized by the expansion of IR boundaries and the absence of homologous recombination-mediated by large repeats. A total of 57 RNA editing sites were detected through mapping RNA-seq data. Moreover, the gene content and order were highly conserved among the Pottiaceae organelle genomes. Phylogenetic analysis showed that bryophytes are paraphyletic, with their three lineages (hornworts, mosses, and liverworts) and vascular plants forming successive sister clades. Timmiella anomala is clearly separated from the monophyletic Pottiaceae, and T. atrovirens is closely related to Syntrichia filaris within the Pottioideae. In addition, we detected four hypervariable regions for candidate-molecular markers. Our findings provide valuable insights into the organelle genomes of T. atrovirens and the evolutionary relationships within the Pottiaceae family, facilitating future discovery of DT genetic resources from bryophytes.

Comparative Analysis of Chloroplast Genome Variation and Evolutionary Analysis of the Endangered Species Dendrobium flexicaule and its Relative Species

Globally, the genus Dendrobium (Family: Orchidaceae) exhibits widespread distribution, predominantly occupying the tropical and subtropical areas of Asia. Although the chloroplast genomes (cpDNAs) of certain Dendrobium species have been documented, the evolutionary relationships among these species remain largely unexplored. In this pioneering investigation, a comprehensive analysis of the complete cpDNAs from Dendrobium species is presented, including Dendrobium flexicaule along with three closely related taxa (D. nobile, D. officinale, and D. huoshanense). The size of the novel complete cpDNAs ranged from 150,529 to 152,588 bp, and their cpDNA structure exhibits a unique quadrifoliate structure reminiscent of female quadrivalents, including large single copy, small single copy (SSC), and inverted repeat regions. A total of 175 simple sequence repeats were identified in the D. flexicaule cpDNA. A few pseudogenes of the NA(D)H dehydrogenase-like (NDH) genes were found in the annotated cpDNAs of the four Dendrobium species. Within the shared pseudogenes ndhF and ndhG, ndhF frequently undergoes mutations. Additionally, the phylogenetic analysis showed that D. flexicaule and D. scoriarum were close sister species. The research findings provide crucial genetic information for the molecular phylogenetic system of D. flexicaule.