Analysis Of Plastid Genomes Research Articles

GENETIC DIVERSITY AND DIGITAL DOCUMENTATION OF KAZAKHSTAN'S FLORA

Kazakhstan, with its expansive and diverse climate zones, boasts a rich and varied flora, featuring around 6,000 vascular species, including approximately 10% that are endemic. Effective management and study of this diverse flora requires continuous monitoring and inventory using advanced botanical, molecular genetic and bioinformatics techniques. This research focuses on exploring the genetic diversity within Kazakhstan's flora and establishing a comprehensive information database. Under Program 0237/PTF (2015-2017), efforts began to assess the genetic diversity of endemic, rare, endangered, and economically significant plant species of Kazakhstan. As part of grant АР05131621, an open-access web resource was developed, offering botanical and genetic data on Kazakhstan's flora. This database includes detailed botanical information on around 500 species. Ongoing research into the genetic diversity of different genera such as Juniperus, Tulipa, Allium, Iris, Salsola, and etc. promises to provide valuable insights into their population structure, phylogenetic relationships, and conservation strategies. Notably, this research has also initiated the first comparative analysis of plastid genomes in Kazakhstan. This research has been funded by the Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan (AP23490860, AP23483825, AP14870612, АР14869593, AP09259027, 0237/PTF-14, and АР05131621).

Comparative and phylogenetic analyses of plastid genomes of the medicinally important genus Alisma (Alismataceae).

Alisma L. is a medicinally important genus of aquatic and wetland plants consisting of c. 10 recognized species. However, largely due to polyploidy and limited taxon and gene sampling, the phylogenomic relationships of Alisma remain challenging. In this study, we sequenced 34 accessions of Alismataceae, including eight of the ten species of Alisma, one species of Echinodorus and one species of Luronium, to perform comparative analyses of plastid genomes and phylogenetic analyses. Comparative analysis of plastid genomes revealed high sequence similarity among species within the genus. Our study analyzed structural changes and variations in the plastomes of Alisma, including IR expansion or contraction, and gene duplication or loss. Phylogenetic results suggest that Alisma is monophyletic, and constitutes four groups: (1) A. lanceolatum and A. canaliculatum; (2) the North American clade of A. subcordatum and A. triviale; (3) A. wahlenbergii and A. gramineum; and (4) A. plantago-aquatica from Eurasia and northern Africa with the eastern Asian A. orientale nested within it. Hence the results challenge the recognition of A. orientale as a distinct species and raise the possibility of treating it as a synonym of the widespread A. plantago-aquatica. The well-known Alismatis Rhizoma (Zexie) in Chinese medicine was likely derived from the morphologically variable Alisma plantago-aquatica throughout its long history of cultivation in Asia. The plastome phylogenetic results also support the tetraploid A. lanceolatum as the likely maternal parent of the hexaploid eastern Asian A. canaliculatum.

Comparative analysis of plastid genomes reveals rearrangements, repetitive sequence features, and phylogeny in the Annonaceae.

The Annonaceae stands as the most species rich family in the Magnoliales, a basal group of angiosperms. Widely distributed in tropical and subtropical regions, it holds significant ecological and economic value. The plastid genome (plastome) is often employed in studies related to plant phylogenetics, comparative genomics, evolutionary biology, and genetic engineering. Nonetheless, research progress on plastid genomics in the Annonaceae has been relatively slow. In this study, we analyzed the structure and repetitive sequence features of plastomes from 28 Annonaceae species. Among them, Mitrephora tomentosa and Desmos chinensis were newly sequenced, with sizes of 160,157 bp and 192,167 bp, and GC contents of 38.3% and 38.4%, respectively. The plastome size in the Annonaceae ranged from 158,837 bp to 202,703 bp, with inverted repeat (IR) region sizes ranging from 64,621 bp to 25,861 bp. Species exhibiting expansion in the IR region showed an increase in plastome size and gene number, frequent boundary changes, different expansion modes (bidirectional or unidirectional), and an increase in repetitive sequences. Specifically, a large number of dispersed repetitive sequences lead to an increase in the size of the LSC region in Goniothalamus tamirensis. Phylogenetic analysis revealed Annonoideae and Malmeoideae as monophyletic groups and sister clades, with Cananga odorata outside of them, followed by Anaxagorea javanica. This research uncovers the structural variation characteristics of plastomes in the Annonaceae, providing valuable information for understanding the phylogeny and plastome evolution of Annonaceae.

Transcriptome and comparative chloroplast genome analysis of Taxus yunnanensis individuals with high and low paclitaxel yield

Paclitaxel is a potent anti-cancer drug that is mainly produced through semi-synthesis, which still requires plant materials as precursors. The content of paclitaxel and 10-deacetyl baccatin III (10-DAB) in Taxus yunnanensis has been found to differ from that of other Taxus species, but there is little research on the mechanism underlying the variation in paclitaxel content in T. yunnanensis of different provenances. In this experiment, the contents of taxoids and precursors in twigs between a high paclitaxel-yielding individual (TG) and a low paclitaxel-yielding individual (TD) of T. yunnanensis were compared, and comparative analyses of transcriptomes as well as chloroplast genomes were performed. High-performance liquid chromatography (HPLC) detection showed that 10-DAB and baccatin III contents in TG were 18 and 47 times those in TD, respectively. Transcriptomic analysis results indicated that genes encoding key enzymes in the paclitaxel biosynthesis pathway, such as taxane 10-β-hydroxylase (T10βH), 10-deacetylbaccatin III 10-O-acetyltransferase (DBAT), and debenzoyl paclitaxel N-benzoyl transferase (DBTNBT), exhibited higher expression levels in TG. Additionally, qRT-PCR showed that the relative expression level of T10βH and DBAT in TG were 29 and 13 times those in TD, respectively. In addition, six putative transcription factors were identified that may be involved in paclitaxel biosynthesis from transcriptome data. Comparative analysis of plastid genomes showed that the TD chloroplast contained a duplicate of rps12, leading to a longer plastid genome length in TD relative to TG. Fifteen mutation hotspot regions were identified between the two plastid genomes that can serve as candidate DNA barcodes for identifying high-paclitaxel-yield individuals. This experiment provides insight into the difference in paclitaxel accumulation among different provenances of T. yunnanensis individuals.

Complete mitochondrial genome of the endangered Prunus pedunculata (Prunoideae, Rosaceae) in China: characterization and phylogenetic analysis.

Prunus pedunculata (Prunoideae: Rosaceae), a relic shrub with strong resistance and multiple application values, is endangered in China. Extensive research had been devoted to gene expression, molecular markers, plastid genome analysis, and genetic background investigations of P. pedunculata. However, the mitochondrial genome of this species has not been systematically described, owing to the complexity of the plant mitogenome. In the present research, the complete mitochondrial genome of P. pedunculata was assembled, annotated, and characterized. The genomic features, gene content and repetitive sequences were analyzed. The genomic variation and phylogenetic analysis have been extensively enumerated. The P. pedunculata mitogenome is a circular molecule with a total length of 405,855 bp and a GC content of 45.63%, which are the smallest size and highest GC content among the known Prunus mitochondrial genomes. The mitogenome of P. pedunculata encodes 62 genes, including 34 unique protein-coding genes (PCGs, excluding three possible pseudogenes), three ribosomal RNA genes, and 19 transfer RNA genes. The mitogenome is rich in repetitive sequences, counting 112 simple sequence repeats, 15 tandem repeats, and 50 interspersed repetitive sequences, with a total repeat length of 11,793 bp, accounting for 2.91% of the complete genome. Leucine (Leu) was a predominant amino acid in PCGs, with a frequency of 10.67%, whereas cysteine (Cys) and tryptophan (Trp) were the least adopted. The most frequently used codon was UUU (Phe), with a relative synonymous codon usage (RSCU) value of 1.12. Selective pressure was calculated based on 20 shared PCGs in the mitogenomes of the 32 species, most of which were subjected to purifying selection (Ka/Ks < 1), whereas ccmC and ccmFn underwent positive selection. A total of 262 potential RNA editing sites in 26 PCGs were identified. Furthermore, 56 chloroplast-derived fragments were ascertained in the mitogenome, ranging from 30 to 858 bp, and were mainly located across IGS (intergenic spacer) regions or rRNA genes. These findings verify the occurrence of intracellular gene transfer events from the chloroplast to the mitochondria. Furthermore, the phylogenetic relationship of P. pedunculata was supported by the mitogenome data of 30 other taxa of the Rosaceae family. Understanding the mitochondrial genome characteristics of P. pedunculata is of great importance to promote comprehension of its genetic background and this study provides a basis for the genetic breeding of Prunus.

Bulbophyllum wolongense , a New Orchidaceae Species from Sichuan Province in China, and Its Plastome Comparative Analysis

A new orchid species, Bulbophyllum wolongense , from the Wolong National Nature Reserve (Sichuan, China), is proposed and described . Using the nuclear ribosomal DNA (nrDNA) and complete plastome sequences, we examined the phylogenetic position of this species and explored the plastome variation among the species of genus Bulbophyllum . The plastome of B. wolongense had a length of 157,496 bp and encoded 132 genes. Comparative plastid genome analysis revealed that the plastome length of B. wolongense was within the length range of other Bulbophyllum plastomes, and the plastome of B. wolongense was relatively conserved in structure compared to other Bulbophyllum plastomes that presented some genes ( ndh , accD , and trnL-UAA ) loss or pseudogenization, a small inversion, and inverted repeat boundary expansions. Furthermore, phylogenetic analyses of 17 Bulbophyllum whole plastomes, 67 shared protein-coding genes from 17 Bulbophyllum whole plastomes, and 4 DNA (ITS, Xdh , matK , and psbA - trnH ) concatenated sequences from 127 Bulbophyllum species, all strongly supported that B. wolongense is a member of the Cirrhopetalum alliance and most likely in B. sect. Brachyantha . Further comparative morphological analysis showed that B. wolongense is clearly morphologically distinguishable from its closely related species in the phylogenetic tree.

Parental origins of the cultivated tetraploid sour cherry (Prunus cerasus L.)

Societal impact statementSour cherry (Prunus cerasus L.) is an agriculturally valuable tree that produces fruits used in a range of culinary dishes, beverages, and other products. The progenitor species and number of origins of sour cherry remain unresolved. Here, we performed phylogenetic analyses of plastid genomes and nuclear genes from nine wild species and three historically important sour cherry cultivars. Our analyses identified Prunus fruticosa and Prunus avium as the closest extant relatives of the progenitor species of tetraploid sour cherry. Furthermore, our analyses revealed P. fruticosa as the likely maternal contributor. These findings and transcriptomic datasets should serve as valuable new resources to guide future breeding efforts in sour cherry.

Hopping or Jumping on the Cliffs: The Unusual Phylogeographical and Demographic Structure of an Extremely Narrow Endemic Mediterranean Plant.

Several past and recent climatic and geological events have greatly influenced the current distribution of coastal species around the Mediterranean Basin. As a consequence, the reconstruction of the distributional history of these species is challenging. In this study, we used both chloroplast and nuclear SNPs to assess the levels of genetic differentiation, contemporary/historical levels of gene flow, and demographic history for the three only known (one mainland and two insular) populations of Eokochia saxicola, a rare Mediterranean coastal rocky halophyte. Plastid genome analysis revealed very low intraspecific haplotype variation and partial admixture among Capri and Palinuro populations with at least two independent colonization events for the Strombolicchio islet. Nuclear SNPs variation consistently identified three distinct genetic clusters corresponding to our sampling localities. Furthermore, strong genetic isolation was confirmed by both historical and contemporary levels of migration among the three populations. The DIYABC analysis identified two introductions temporally separated from Palinuro to Capri (ca.25 Mya) and subsequently to Strombolicchio (ca.09 Mya) as the most likely hypothesis for the current distribution of E. saxicola. Regardless of their small population sizes, all study sites supported high-genetic diversity maintained by outcrossing and random mating between individuals owing largely to wind pollination, an exclusive trait among Mediterranean narrow endemics. In conclusion, the patterns observed confirm that some Mediterranean endemics are not necessarily “evolutionary dead-ends” but rather represent species that have extensive demographic stability and a strong evolutionary legacy.

Comparative Analysis of Plastid Genomes in the Non-photosynthetic Genus Thismia Reveals Ongoing Gene Set Reduction.

Heterotrophic plants provide intriguing examples of reductive evolution. This is especially evident in the reduction of their plastid genomes, which can potentially proceed toward complete genome loss. Several milestones at the beginning of this path of degradation have been described; however, little is known about the latest stages of plastome reduction. Here we analyze a diversity of plastid genomes in a set of closely related non-photosynthetic plants. We demonstrate how a gradual loss of genes shapes the miniaturized plastomes of these plants. The subject of our study, the genus Thismia, represents the mycoheterotrophic monocot family Thismiaceae, a group that may have experienced a very ancient (60–80 mya) transition to heterotrophy. In all 18 species examined, the plastome is reduced to 14–18 kb and is highly AT-biased. The most complete observed gene set includes accD, seven ribosomal protein genes, three rRNA, and two tRNA genes. Different clades of Thismia have undergone further gene loss (complete absence or pseudogenization) compared to this set: in particular, we report two independent losses of rps2 and rps18.

Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica).

Species of the genus Nicotiana (Solanaceae), commonly referred to as tobacco plants, are often cultivated as non-food crops and garden ornamentals. In addition to the worldwide production of tobacco leaves, they are also used as evolutionary model systems due to their complex development history tangled by polyploidy and hybridization. Here, we assembled the plastid genomes of five tobacco species: N. knightiana, N. rustica, N. paniculata, N. obtusifolia and N. glauca. De novo assembled tobacco plastid genomes had the typical quadripartite structure, consisting of a pair of inverted repeat (IR) regions (25,323–25,369 bp each) separated by a large single-copy (LSC) region (86,510–86,716 bp) and a small single-copy (SSC) region (18,441–18,555 bp). Comparative analyses of Nicotiana plastid genomes with currently available Solanaceae genome sequences showed similar GC and gene content, codon usage, simple sequence and oligonucleotide repeats, RNA editing sites, and substitutions. We identified 20 highly polymorphic regions, mostly belonging to intergenic spacer regions (IGS), which could be suitable for the development of robust and cost-effective markers for inferring the phylogeny of the genus Nicotiana and family Solanaceae. Our comparative plastid genome analysis revealed that the maternal parent of the tetraploid N. rustica was the common ancestor of N. paniculata and N. knightiana, and the later species is more closely related to N. rustica. Relaxed molecular clock analyses estimated the speciation event between N. rustica and N. knightiana appeared 0.56 Ma (HPD 0.65–0.46). Biogeographical analysis supported a south-to-north range expansion and diversification for N. rustica and related species, where N. undulata and N. paniculata evolved in North/Central Peru, while N. rustica developed in Southern Peru and separated from N. knightiana, which adapted to the Southern coastal climatic regimes. We further inspected selective pressure on protein-coding genes among tobacco species to determine if this adaptation process affected the evolution of plastid genes. These analyses indicate that four genes involved in different plastid functions, including DNA replication (rpoA) and photosynthesis (atpB, ndhD and ndhF), came under positive selective pressure as a result of specific environmental conditions. Genetic mutations in these genes might have contributed to better survival and superior adaptations during the evolutionary history of tobacco species.

Structural, evolutionary and phylogenomic features of the plastid genome of Carya illinoinensis cv. Imperial

The economically most important nut tree species in the world belong to family Juglandaceae, tribe Jungladeae. Evolutive investigations concerning species from this tribe are important for understanding the molecular basis driving the evolution and systematics of these species. In this study, we release the complete plastid genome of C. illinoinensis cv. Imperial. Using an IonTorrent NGS platform we generated 8.5 ´ 10 8 bp of raw sequences, enabling the assemblage of the complete plastid genome of this species. The plastid genome is 160,818 bp long, having a quadripartite structure with an LSC of 90,041 bp, an SSC of 18,791 bp and two IRs of 25,993 bp. A total of 78 protein-coding, 37 tRNA-coding, and 8 rRNA-coding regions were predicted. Bias in synonymous codon usage was detected in cultivar Imperial and three tRNA-coding regions were identified as hotspots of nucleotide divergence, with high estimations of dN/dS ratio. The high fraction of SSR loci prospected in non-coding regions may provide informative genetic markers, useful to a wide range of genetic researches. Despite the significant structural differences among plastid genomes, the phylogenetic relationships among species is supported by the whole plastid genome analysis, supporting the monophyly of subtribes Caryinae and Juglandinae within family Juglandaceae.

The complete plastid genome and phylogenetic analysis of Codium fragile

Codium fragile, a nutrient-rich green algae that is both edible and medicinal, it is called a ‘rat tail’ because of its unique shape, it can reach up to a metre in length and has the functions of clearing heat and detoxifying, detumescence and water, and repelling insects. The plastid genome sequence of C. fragile is 83,422 bp. A total of 105 genes were determined, including 77 protein-encoding genes, 3 rRNA genes, and 25 tRNA genes. Phylogenetic analysis showed that C. fragile clustered together into a single branch with C. simulans and Codium sp. 'arenicola' as sister branches. The plastid genome analysis will help the understanding of Chlorophyta evolution.

The complete plastid genome and phylogenetic analysis of Gracilaria edulis

Gracilaria edulis, a marine red macroalgae, is a rich source of sulfated polysaccharides, carbohydrate, vitamins, and minerals, and showed multiple bioactivities such as antibacterial, antitumour, and cholinesterase inhibitory activity. The plastid genome sequence of G. edulis is 179,410 bp. A total of 235 genes were determined, including 201 protein-encoding genes, 30 tRNA genes, 3 rRNA genes, 1 ribonuclease gene, and 1 intron inserted into the trnM gene. Phylogenetic analysis showed that G. edulis clustered together with Gracilaria salicornia, Gracilaria tenuistipitata var. liui and Gracilaria chilensis. The plastid genome analysis will help in the understanding of Gracilaria evolution.

Comparative plastid genomics of Synurophyceae: inverted repeat dynamics and gene content variation

BackgroundThe Synurophyceae is one of most important photosynthetic stramenopile algal lineages in freshwater ecosystems. They are characterized by siliceous scales covering the cell or colony surface and possess plastids of red-algal secondary or tertiary endosymbiotic origin. Despite their ecological and evolutionary significance, the relationships amongst extant Synurophyceae are unclear, as is their relationship to most other stramenopiles.ResultsHere we report a comparative analysis of plastid genomes sequenced from five representative synurophycean algae. Most of these plastid genomes are highly conserved with respect to genome structure and coding capacity, with the exception of gene re-arrangements and partial duplications at the boundary of the inverted repeat and single-copy regions. Several lineage-specific gene loss/gain events and intron insertions were detected (e.g., cemA, dnaB, syfB, and trnL).ConclusionsUnexpectedly, the cemA gene of Synurophyceae shows a strong relationship with sequences from members of the green-algal lineage, suggesting the occurrence of a lateral gene transfer event. Using a molecular clock approach based on silica fossil record data, we infer the timing of genome re-arrangement and gene gain/loss events in the plastid genomes of Synurophyceae.

The Plastid Genome of Deschampsia cespitosa (Poaceae).

Plastid genome analysis of non-model organisms provides valuable information for basic research e.g., molecular evolutionary genomics, phylogeny and phylogeography. Deschampsia cespitosa is the most widespread species of the genus and it is a common grass that is found across Eurasia and North America. Scattered populations in regions of appropriate ecological conditions are also found in Australia, New Zealand and southern South America, where it is sympatric with D. antarctica. We analyzed the plastid genome of a sample of Deschampsia cespitosa of the Austrian Alps using high-throughput sequencing. The plastid (cp) genome shows the typical quadripartite structure with a length of 135,340 bp, comprising a large single-copy (LSC) region of 79,992 bp, a small single-copy (SSC) region of 12,572 bp and two inverted repeats (IR) regions of 21,388 bp each. It contains 115 genes, including 85 protein-coding genes, four ribosomal RNA genes and 30 transfer RNA genes. The GC content (%), number of repeats and microsatellites, RNA editing sites and codon usage were highly similar to those of D. antarctica. The results of this present study highlight the extremely conserved nature of the cp genome in this group, since the comparison involved individuals separated by about 13,000 km, from the Alps to Antarctica.

Evolutionary Analysis of Plastid Genomes of Seven Lonicera L. Species: Implications for Sequence Divergence and Phylogenetic Relationships.

Plant plastomes play crucial roles in species evolution and phylogenetic reconstruction studies due to being maternally inherited and due to the moderate evolutionary rate of genomes. However, patterns of sequence divergence and molecular evolution of the plastid genomes in the horticulturally- and economically-important Lonicera L. species are poorly understood. In this study, we collected the complete plastomes of seven Lonicera species and determined the various repeat sequence variations and protein sequence evolution by comparative genomic analysis. A total of 498 repeats were identified in plastid genomes, which included tandem (130), dispersed (277), and palindromic (91) types of repeat variations. Simple sequence repeat (SSR) elements analysis indicated the enriched SSRs in seven genomes to be mononucleotides, followed by tetra-nucleotides, dinucleotides, tri-nucleotides, hex-nucleotides, and penta-nucleotides. We identified 18 divergence hotspot regions (rps15, rps16, rps18, rpl23, psaJ, infA, ycf1, trnN-GUU-ndhF, rpoC2-rpoC1, rbcL-psaI, trnI-CAU-ycf2, psbZ-trnG-UCC, trnK-UUU-rps16, infA-rps8, rpl14-rpl16, trnV-GAC-rrn16, trnL-UAA intron, and rps12-clpP) that could be used as the potential molecular genetic markers for the further study of population genetics and phylogenetic evolution of Lonicera species. We found that a large number of repeat sequences were distributed in the divergence hotspots of plastid genomes. Interestingly, 16 genes were determined under positive selection, which included four genes for the subunits of ribosome proteins (rps7, rpl2, rpl16, and rpl22), three genes for the subunits of photosystem proteins (psaJ, psbC, and ycf4), three NADH oxidoreductase genes (ndhB, ndhH, and ndhK), two subunits of ATP genes (atpA and atpB), and four other genes (infA, rbcL, ycf1, and ycf2). Phylogenetic analysis based on the whole plastome demonstrated that the seven Lonicera species form a highly-supported monophyletic clade. The availability of these plastid genomes provides important genetic information for further species identification and biological research on Lonicera.

Dynamic evolution of inverted repeats in Euglenophyta plastid genomes

Photosynthetic euglenids (Euglenophyta) are a monophyletic group of unicellular eukaryotes characterized by the presence of plastids, which arose as the result of the secondary endosymbiosis. Many Euglenophyta plastid (pt) genomes have been characterized recently, but they represented mainly one family – Euglenaceae. Here, we report a comparative analysis of plastid genomes from eight representatives of the family Phacaceae. Newly sequenced plastid genomes share a number of features including synteny and gene content, except for genes mat2 and mat5 encoding maturases. The observed diversity of intron number and presence/absence of maturases corroborated previously suggested correlation between the number of maturases in the pt genome and intron proliferation. Surprisingly, pt genomes of taxa belonging to Discoplastis and Lepocinclis encode two inverted repeat (IR) regions containing the rDNA operon, which are absent from the Euglenaceae. By mapping the presence/absence of IR region on the obtained phylogenomic tree, we reconstructed the most probable events in the evolution of IRs in the Euglenophyta. Our study highlights the dynamic nature of the Euglenophyta plastid genome, in particular with regards to the IR regions that underwent losses repeatedly.

Cryptic divergences in the genus Pisum L. (peas), as revealed by phylogenetic analysis of plastid genomes

Organellar genomes may shed light on complicated patterns of plant evolution at inter- and intraspecies level. Primary structure of plastid genomes sequenced in this study and taken from public databases was characterised and compared in 22 diverse, mostly wild representatives of the genus Pisum (peas). Phylogenetic trees reconstructed via Bayesian approach on the basis of entire plastid genomes resembled those reconstructed on the basis of a nuclear gene His5 coding for a minor histone H1 subtype. They reveal Pisum fulvum as an early divergence of the genus but do not support other taxonomical subdivisions. The positions of three accessions, classified as P. sativum subsp. elatius (the wild subspecies of the common pea), appeared quite unexpected. On the entire plastid genome tree, two accessions, from the Black Sea area of Turkey and Georgia, clustered with representatives of another species, P. fulvum, while the other, from Greece, was the first divergence of the P. sativum branch. We suppose these unusual plastid genomes to be ancient lineages ascending to a ‘missing link’ between P. fulvum and P. sativum, represented by accession Pe 013 from Turkey. Accessions with common pea appearance but deeply diverged plastids could occur through occasional crossing of diverged pea lines in the past and biparental plastid inheritance, both events being possible in peas.

Plastid genome analysis of three Nemaliophycidae red algal species suggests environmental adaptation for iron limited habitats.

The red algal subclass Nemaliophycidae includes both marine and freshwater taxa that contribute to more than half of the freshwater species in Rhodophyta. Given that these taxa inhabit diverse habitats, the Nemaliophycidae is a suitable model for studying environmental adaptation. For this purpose, we characterized plastid genomes of two freshwater species, Kumanoa americana (Batrachospermales) and Thorea hispida (Thoreales), and one marine species Palmaria palmata (Palmariales). Comparative genome analysis identified seven genes (ycf34, ycf35, ycf37, ycf46, ycf91, grx, and pbsA) that were different among marine and freshwater species. Among currently available red algal plastid genomes (127), four genes (pbsA, ycf34, ycf35, ycf37) were retained in most of the marine species. Among these, the pbsA gene, known for encoding heme oxygenase, had two additional copies (HMOX1 and HMOX2) that were newly discovered and were reported from previously red algal nuclear genomes. Each type of heme oxygenase had a different evolutionary history and special modifications (e.g., plastid targeting signal peptide). Based on this observation, we suggest that the plastid-encoded pbsA contributes to the iron controlling system in iron-deprived conditions. Thus, we highlight that this functional requirement may have prevented gene loss during the long evolutionary history of red algal plastid genomes.

Comparative analyses of plastid genomes from fourteen Cornales species: inferences for phylogenetic relationships and genome evolution

BackgroundThe Cornales is the basal lineage of the asterids, the largest angiosperm clade. Phylogenetic relationships within the order were previously not fully resolved. Fifteen plastid genomes representing 14 species, ten genera and seven families of Cornales were newly sequenced for comparative analyses of genome features, evolution, and phylogenomics based on different partitioning schemes and filtering strategies.ResultsAll plastomes of the 14 Cornales species had the typical quadripartite structure with a genome size ranging from 156,567 bp to 158,715 bp, which included two inverted repeats (25,859–26,451 bp) separated by a large single-copy region (86,089–87,835 bp) and a small single-copy region (18,250–18,856 bp) region. These plastomes encoded the same set of 114 unique genes including 31 transfer RNA, 4 ribosomal RNA and 79 coding genes, with an identical gene order across all examined Cornales species. Two genes (rpl22 and ycf15) contained premature stop codons in seven and five species respectively. The phylogenetic relationships among all sampled species were fully resolved with maximum support. Different filtering strategies (none, light and strict) of sequence alignment did not have an effect on these relationships. The topology recovered from coding and noncoding data sets was the same as for the whole plastome, regardless of filtering strategy. Moreover, mutational hotspots and highly informative regions were identified.ConclusionsPhylogenetic relationships among families and intergeneric relationships within family of Cornales were well resolved. Different filtering strategies and partitioning schemes do not influence the relationships. Plastid genomes have great potential to resolve deep phylogenetic relationships of plants.