Complete Plastome Sequence Research Articles

Characterization of the complete plastome of Dysphania botrys, a candidate plant for cancer treatment

Dysphania botrys belongs to Amaranthaceae and distributes in North Europe, Asia, and North America. It is a medicinal plant with diuretic, antispasmodic, carminative, antidiarrhoeic properties, and a candidate plant for cancer treatment. However, few studies focused on its phylogeny, and its taxonomic status is still controversial. To better understand the evolution of this species, the complete plastome of D. botrys was obtained by next-generation sequencing. It is the first plastome to be sequenced and reported in the genus Dysphania. The plastome is 152,055 bp in length, which consists of a large single-copy region (LSC, 83,769 bp; GC content: 34.7%), a small single-copy region (SSC, 17,916 bp; GC content: 30.1%), and a pair of inverted repeat regions (IRs, 25,185 bp; GC content: 42.7%). It harbors 112 unique genes, including 78 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes with an overall G + C content of 36.8%. The phylogeny of Amaranthaceae based on the complete plastome sequences of 13 taxa showed that D. botrys belong to subfamily Chenopodioideae. Chenopodioideae, together with Betoideae formed a sister clade to the three subfamilies (Salicornioideae, Suaedoideae, and Salsoloideae), and this sister clade formed an evolutionary sister clade to Amaranthoideae. Our data will largely enrich the genetic information of Dysphania botrys and facilitate future studies on its evolutionary status.

Complete plastome sequence of Atalantia kwangtungensis (Rutaceae): an endemic “near threatened” shrub in South China

Atalantia kwangtungensis (Rutaceae) is a small shrub (1–2 m tall) distributed in moist and shady places throughout evergreen broad-leaved forests having altitudes that range from 100 to 400 m in West Guangdong, Southeast Guangxi, Hainan province of China. It has been ranked as a near threatened (NT) species in China. Here, we report and characterize the complete plastid genome sequence of A. kwangtungensis in an effort to provide genomic resources useful for its conservation. The complete plastome is 160,248 bp in length and contains the typical structure and gene content of angiosperm plastomes, including two inverted repeat (IR) regions of 27,151 bp, a large single-copy (LSC) region of 87,483 bp and a small single-copy (SSC) region of 18,463 bp. The plastome contains 110 genes, consisting of 77 unique protein-coding genes (ycf1 is a pseudogene), 29 unique tRNA genes, and 4 unique rRNA genes. The overall A/T content in the plastome of A. kwangtungensis is 61.6%. Phylogenetic analyses were performed using the entire plastome, including spacers, introns, etc., and we determined that A. kwangtungensis and Merrillia caloxylon were closely related. The complete plastome sequence of A. kwangtungensis will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies in Sapindales.

Complete plastome sequence of Hoya pottsii Traill and Hoya liangii Tsiang (Apocynaceae)

Hoya is the largest genus (about 350–450 species) within Apocynaceae. It is a subshrub or liana, epiphytic or epilithic. Most species grow in tropical and subtropical South and Southeast Asia. Here we report and characterize the complete plastid genome sequence of Hoya pottsii Traill and Hoya liangii Tsiang in an effort to provide genomic resources useful for promoting its systematics research. The complete plastome of H. pottsii is 161,565 bp in length, including two Inverted Repeat (IR) regions of 24,657 bp, a Large Single-Copy (LSC) region of 92,532 bp, and a Small Single-Copy (SSC) region of 19,719 bp. The plastome contains 115 genes, consisting of 81 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes. The overall A/T content in the plastome of H. pottsii is 62.40%. The complete plastome of H. liangii is 162,989 bp in length, including two IR regions of 24,841 bp, a LSC region of 93,292 bp, and a SSC region of 20,015 bp. The plastome contains 115 genes, consisting of 81 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes. The overall A/T content in the plastome of H. pottsii is 62.30%. The complete plastome sequence of H. pottsii and H. liangii will provide a useful resource for the conservation genetics of the two species as well as for the phylogenetic studies of Hoya.

Complete plastome sequences of Diospyros maclurei Merr. and Diospyros hainanensis Merr. (Ebenaceae): two endemic species in Hainan Province, China

Diospyros is the largest genus (about 485 species) in Ebenaceae. It is a deciduous or evergreen tree or shrub. It grows in pantropical and extending into temperate regions. Here, we report and characterize the complete plastid genome sequences of D. maclurei Merr. and D. hainanensis Merr. in an effort to provide genomic resources useful for promoting their systematics research and potential economic development. The complete plastome of D. maclurei is 157,946 bp in length, including two Inverted Repeat (IR) regions of 26,081 bp, a Large Single-Copy (LSC) region of 87,387 bp, and a Small Single-Copy (SSC) region of 18,397 bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA genes, and four unique rRNA genes. The overall A/T content in the plastome of D. maclurei is 62.60%. The complete plastome of D. hainanensis is 157,999 bp in length, including two Inverted Repeat (IR) regions of 26,077 bp, a Large Single-Copy (LSC) region of 87,523 bp, and a Small Single-Copy (SSC) region of 18,322 bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA genes, and four unique rRNA genes. The overall A/T content in the plastome of D. hainanensis is 62.60%. The complete plastome sequences of D. Maclurei and D. hainanensis will provide a useful resource for the conservation genetics of the two species as well as for the phylogenetic studies of Diospyros.

Complete plastome sequence of Piper laetispicum (Piperaceae): An endemic plant species in South China

Piper laetispicum is dioecious climbers woody with 10 m tall, which is an endemic species in China. It grows on trees or rocks in forests (100–600 m) in Guangdong and Hainan Province of China. Here, we report and characterize the complete plastid genome sequence of P. laetispicum in an effort to provide genomic resources useful for promoting its conservation. The complete plastome is 161,721 bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 27,125 bp, a large single copy (LSC) region of 89,224 bp and a small single copy (SSC) region of 18,247 bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA gene, and four unique rRNA genes. The overall A/T content in the plastome of P. laetispicum is 61.70%. The complete plastome sequence of P. laetispicum will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies for Piper.

Complete plastome sequence of Changiostyrax dolichocarpa (Styracaeae): An endangered (EN) plant species endemic to China

Changiostyrax dolichocarpa is a critically endangered plant species occurring in central and southeastern China. Although the systematic position of Changiostyrax was still unclear, morphological characters, plastid and nSSR evidence supported that C. dolichocarpa should be separated from Sinojackia (Styracaceae). Here, we report and characterize the complete plastid genome sequence of C. dolichocarpa in an effort to provide genomic resources useful for promoting its conservation. The complete plastome is 158,821 bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 26,000 bp, a large single copy (LSC) region of 88,038 bp and a small single copy (SSC) region of 18,784 bp. The plastome contains 120 genes, consisting of 83 unique protein-coding genes, 37 unique tRNA gene, and eight unique rRNA genes. The overall A/T content in the plastome of C. dolichocarpa is 62.70%. The complete plastome sequence of C. dolichocarpa will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies for Changiostyrax.

Complete plastome sequence of Hydnocarpus hainanensis Merr (Achariaceae): an endemic ‘vulnerable’ tree in South China

Hydnocarpus hainanensis Merr. is an evergreen tree with a height of 6–12 m and a diameter at breast height of 50 cm. It is distributed in Guangxi, Guizhou, Hainan, South of Yunnan Province of China. Here, we report and characterize the complete plastid genome sequence of H. hainanensis in an effort to provide genomic resources useful for promoting its conservation and systematics research. The plastome of H. hainanensis is found to possess a total length 163,330 bp with the typical quadripartite structure of angiosperms, containing two inverted repeats (IRs) of 26,870 bp, a large single copy (LSC) region of 91,510 bp and a small single copy (SSC) region of 18,080 bp. The plastome contains 111 genes, consisting of 78 unique protein-coding genes (seven of which are duplicated in the IR: rps12, rps7, ndhB, ycf2, rpl23, rpl2, and rps19), 29 unique tRNA genes (seven of which are duplicated in the IR, i.e. trnNGUU, trnRACG, trnAUGC, trnlGAU, trnVGAC, trnLCAA, and trnlCAU) and four unique rRNA genes (5S rRNA, 4.55S rRNA, 23S rRNA, and 16S rRNA). The overall A/T content in the plastome of H. hainanensis is 63.70%. The phylogenetic analysis indicated that H. hainanensis is close to Salix rorida within Malpighiales. The complete plastome sequence of H. hainanensis will provide a useful resource for the conservation genetics of the one species as well as for the phylogenetic studies of Achariaceae.

Complete plastome sequence of Nepenthes mirabilis (Nepenthaceae): a “vulnerable” herb in China

Nepenthes mirabilis (Nepenthaceae) is an erect or climbing (0.5–2 m tall) herb distributed in Africa (Madagascar), south and southeast Asia, North Australia and Pacific Islands (Caroline Islands). There is only one species in China. It grows in wet and sandy soils places throughout forests, grasslands, swamps, mountains, roadsides, wastelands having altitudes that sea level to 400 m. It has been ranked as a VU (Vulnerable) species in China. Here we report and characterize the complete plastid genome sequence of N. mirabilis in an effort to provide genomic resources useful for its conservation. The complete plastome is 155,755 bp in length and contains the typical structure and gene content of angiosperm plastomes, including two Inverted Repeat (IR) regions of 26,415 bp, a Large Single-Copy (LSC) region of 84,997 bp and a Small Single-Copy (SSC) region of 17,928 bp. The plastome contains 113 genes, consisting of 77 unique protein-coding genes, three pseudogenes, 29 unique tRNA genes, and four unique rRNA genes. The overall A/T content in the plastome of N. mirabilis is 62.8%. Phylogenetic analyses were performed using the entire plastome, including spacers, introns, etc., and we determined that N. mirabilis 32 and Dionaea muscipula were closely related. The complete plastome sequence of N. 33 mirabilis will provide a useful resource for the conservation genetics of this species as 34 well as for the phylogenetic studies in Caryophyllales.

Complete plastome sequence of Vatica mangachapoi (Dipterocarpaceae): a vulnerable (VU) plant species in Southeast Asia

Vatica mangachapoi is a tree up to 20 m tall with white resinous. It is distributed in China (Hainan province), Indonesia, Malaysia (N Borneo), Philippines, Thailand, and Vietnam. It grows in forests on hills and mountain slopes below 700 metres. Its durable wood is used for making boats and building bridges and houses. It has been ranked as a VU (Vulnerable) species in China. Here we report and characterize the complete plastid genome sequence of V. mangachapoi in an effort to provide genomic resources useful for promoting its conservation and phylogenetic research. The complete plastome is 151,538 bp in length and contains the typical structure and gene content of angiosperm plastome, including two Inverted Repeat (IR) regions of 23,921 bp, a Large Single-Copy (LSC) region of 83,587 bp and a Small Single-Copy (SSC) region of 20,109 bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA gene, and 4 unique rRNA genes. The overall A/T content in the plastome of V. mangachapoi is 62.80%. The phylogenetic analysis indicated that V. mangachapoi and V. odorata is closely related and as an independent branch in Malvales in our study. The complete plastome sequence of V. mangachapoi will provide a useful resource for the conservation genetics of this species and for the phylogenetic studies for Vatica.

Accurate authentication of Dendrobium officinale and its closely related species by comparative analysis of complete plastomes

Owing to its great medicinal and ornamental values, Dendrobium officinale is frequently adulterated with other Dendrobium species on the market. Unfortunately, the utilization of the common DNA markers ITS, ITS2, and matK+rbcL is unable to distinguish D. officinale from 5 closely related species of it (D. tosaense, D. shixingense, D. flexicaule, D. scoriarum and D. aduncum). Here, we compared 63 Dendrobium plastomes comprising 40 newly sequenced plastomes of the 6 species and 23 previously published plastomes. The plastomes of D. officinale and its closely related species were shown to have conserved genome structure and gene content. Comparative analyses revealed that small single copy region contained higher variation than large single copy and inverted repeat regions, which was mainly attributed to the loss/retention of ndh genes. Furthermore, the intraspecific sequence variability among different Dendrobium species was shown to be diversified, which necessitates a cautious evaluation of genetic markers specific for different Dendrobium species. By evaluating the maximum likelihood trees inferred from different datasets, we found that the complete plastome sequence dataset had the highest discriminatory power for D. officinale and its closely related species, indicating that complete plastome sequences can be used to accurately authenticate Dendrobium species.

Complete plastome sequence of Dracaena cambodiana (Asparagaceae): a species considered “Vulnerable” in Southeast Asia

Dracaena cambodiana (Asparagaceae) is a treelike plant ranging from 3 to 10 m tall. It grows in low-elevation forests (0–300 m) having dry and sandy soils. It is distributed in Southern Hainan Island in China and other Southeast Asian countries (e.g. Cambodia, Laos, Thailand and Vietnam). The dried resin can be used medicinally as a substitute for that of Dracaena cochinchinensis. It has been ranked as a Vulnerable (VU) species in China. Here we report and characterize the complete plastid genome sequence of D. cambodiana. The complete plastome is 156,697 bp in length. It contains the typical structure and gene content of angiosperm plastomes, including two Inverted Repeat (IR) regions of 26,526 bp, a Large Single-Copy (LSC) region of 84,988 bp and a Small Single-Copy (SSC) region of 18,657 bp. The plastome contains 113 genes, consisting of 76 unique protein-coding genes, 30 unique tRNA genes, four unique rRNA genes and three pseudogenes (i.e. matK, infA, ndhF). The overall A/T content in the plastome of D. cambodiana is 62.4%. We performed phylogenetic analyses using the entire plastome, including spacers, introns, etc., and we determined that D. cambodiana and Maianthemum bicolor were closely related. The complete plastome sequence of D. cambodiana will provide a useful resource for the conservation genetics of this species as well as for phylogenetic studies in Asparagales.

The complete plastome sequence of Rubus takesimensis endemic to Ulleung Island, Korea: Insights into molecular evolution of anagenetically derived species in Rubus (Rosaceae)

Previous phylogenetic studies have suggested that Rubus takesimensis (Rosaceae), which is endemic to Ulleung Island, Korea, is closely related to R. crataegifolius, which is broadly distributed across East Asia. A recent phylogeographic study also suggested the possible polyphyletic origins of R. takesimensis from multiple source populations of its continental progenitor R. crataegifolius in China, Japan, Korea, and the Russian Far East. However, even though the progenitor-derivative relationship between R. crataegifolius and R. takesimensis has been established, little is known about the chloroplast genome (i.e., plastome) evolution of anagenetically derived species on oceanic islands and their continental progenitor species. In the present study, we characterized the complete plastome of R. takesimensis and compared it to those of R. crataegifolius and four other Rubus species. The R. takesimensis plastome was 155,760 base pairs (bp) long, a total of 46 bp longer than the plastome of R. crataegifolius (28 from LSC and 18 from SSC). No structural or content rearrangements were found between the species pairs. Four highly variable intergenic regions (rpl32/trnL, rps4/trnT, trnT/trnL, and psbZ/trnG) were identified between R. takesimensis and R. crataegifolius. Compared to the plastomes of other congeneric species (R. corchorifolius, R. fockeanus, and R. niveus), six highly variable intergenic regions (ndhC/psaC, rps16/trnQ, trnK/rps16, trnL/trnF, trnM/atpE, and trnQ/psbK) were also identified. A total of 116 simple sequence repeats (SSRs), including 48 mononucleotide, 64 dinucleotide, and four trinucleotide repeat motifs were characterized in R. takesimensis. The plastome resources generated by the present study will help to elucidate plastome evolution within the genus and to resolve phylogenetic relationships within highly complex and reticulated lineages. Phylogenetic analysis supported both the monophyly of Rubus and the sister relationship between R. crataegifolius and R. takesimensis.

Complete chloroplast genome sequence of Scurrula notothixoides (Loranthaceae): a hemiparasitic shrub in South China

Scurrula notothixoides (Loranthaceae) is a hemiparasitic shrub distributed in forest margins of Southeast Asian countries. Here, we report and characterize the complete plastid genome sequence of S. notothixoides in an effort to provide genomic resources useful for the phylogenetic studies for Santalales. The complete plastome is 123,810 bp in length and contains the typical structure and gene content of angiosperm plastomes, including two inverted repeat (IR) regions of 23,101 bp, a large single copy (LSC) region of 71,448 bp and a small single copy (SSC) region of 6160 bp. The plastome contains 88 genes, consisting of 61 unique protein-coding genes, 23 unique tRNA genes and four unique rRNA genes. The overall A/T content in the plastome of S. notothixoides is 62.7%. Phylogenetic analyses were performed using the entire plastome, including spacers, introns, etc. and we recovered that S. notothixoides and Taxillus sutchuenensis was closely related. The complete plastome sequence of S. notothixoides will provide a useful resource for the phylogenetic studies for Santalales.

Complete plastome sequences from Bertholletia excelsa and 23 related species yield informative markers for Lecythidaceae.

Premise of the StudyThe tropical tree family Lecythidaceae has enormous ecological and economic importance in the Amazon basin. Lecythidaceae species can be difficult to identify without molecular data, however, and phylogenetic relationships within and among the most diverse genera are poorly resolved.MethodsTo develop informative genetic markers for Lecythidaceae, we used genome skimming to de novo assemble the full plastome of the Brazil nut tree (Bertholletia excelsa) and 23 other Lecythidaceae species. Indices of nucleotide diversity and phylogenetic signal were used to identify regions suitable for genetic marker development.ResultsThe B. excelsa plastome contained 160,472 bp and was arranged in a quadripartite structure. Using the 24 plastome alignments, we developed primers for 10 coding and non‐coding DNA regions containing exceptional nucleotide diversity and phylogenetic signal. We also developed 19 chloroplast simple sequence repeats for population‐level studies.DiscussionThe coding region ycf1 and the spacer rpl16‐rps3 outperformed plastid DNA markers previously used for barcoding and phylogenetics. Used in a phylogenetic analysis, the matrix of 24 plastomes showed with 100% bootstrap support that Lecythis and Eschweilera are polyphyletic. The plastomes and primers presented in this study will facilitate a broad array of ecological and evolutionary studies in Lecythidaceae.

Complete Plastome Sequencing Reveals an Extremely Diminished SSC Region in HemiparasiticPedicularis ishidoyana(Orobanchaceae)

The species within Orobanchaceae cover all forms of parasitism from full autotrophy to holoparasitism. Although parasitic species have gone through dramatic genome changes, the plastomes of land plants generally contain highly conserved structures. We investigated the complete plastome sequence of hemiparasitic Pedicularis ishidoyana, belonging to the largest genus in Orobanchaceae, and compared it with the highly rearranged genomes of other taxa in that family. This plastome comprises a total of 152 571 bp, with two inverted repeats (IRs) of 35 281 bp, a large single-copy region (LSC) of 81 982 bp, and an extremely reduced small single-copy (SSC) region of 27 bp. Although IR expansion and SSC contraction have been reported in the plastomes of other hemiparasitic species in Orobanchaceae, the IR region of P. ishidoyana is extremely expanded, resulting in a very small SSC region. This genome contains 101 genes that encode 67 proteins, four rRNAs, 30 tRNAs, and 22 duplicated genes in the IR region. In contrast to other hemi- or holoparasitic members of Orobanchaceae, genes in the ndh family in P. ishidoyana (except ndhE) have lost their function through pseudogenization (six genes) or deletion (four genes). Therefore, it seems that the degradation of this gene family in P. ishidoyana has occurred independently. Phylogenetic analysis, including all parasitic types, strongly supports the conclusion that P. ishidoyana diverged early from autotrophs and is sister to holoparasitic taxa. Our results suggest that these hemiparasitic Pedicularis plants might represent an early stage of parasitism that has developed stepwise in this family from non-parasites to holoparasites.

Complete plastome sequencing from Toona (Meliaceae) and phylogenomic analyses within Sapindales.

Premise of the Study Toona (Meliaceae, Sapindales) is a small genus of five species of trees native from southern and eastern Asia to New Guinea and Australia. Complete plastomes were sequenced for three Toona species to provide a basis for future plastome genetic studies in threatened species of Toona. In addition, plastome structural evolution and phylogenetic relationships across Sapindales were explored with a larger data set of 29 Sapindales plastomes (including members of six out of nine families).MethodsThe plastomes were determined using the Illumina sequencing platform; the phylogenetic analyses were conducted using maximum likelihood by RAxML.ResultsThe lengths of three Toona plastomes range from 159,185 to 158,196 bp. A total of 113 unique genes were found in each plastome. Across Sapindales, plastome gene structure and content were largely conserved, with the exception of the contraction of the inverted repeat region to exclude ycf1 in some species of Rutaceae and Sapindaceae, and the movement of trnI‐GAU and trnA‐UGC to a position outside the inverted repeat region in some Rutaceae species.DiscussionThe three Toona plastomes possess the typical structure of angiosperm plastomes. Phylogenomic analysis of Sapindales recovered a mostly strongly supported phylogeny of Sapindales, including most of the backbone relationships, with some improvements compared to previous targeted‐gene analyses.

Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae).

Hybridization, incomplete lineage sorting, and phylogenetic error produce similar incongruence patterns, representing a great challenge for phylogenetic reconstruction. Here, we use sequence capture data and multiple species tree and species network approaches to resolve the backbone phylogeny of the Neotropical genus Lachemilla, while distinguishing among sources of incongruence. We used 396 nuclear loci and nearly complete plastome sequences from 27 species to clarify the relationships among the major groups of Lachemilla, and explored multiple sources of conflict between gene trees and species trees inferred with a plurality of approaches. All phylogenetic methods recovered the four major groups previously proposed for Lachemilla, but species tree methods recovered different topologies for relationships between these four clades. Species network analyses revealed that one major clade, Orbiculate, is likely of ancient hybrid origin, representing one of the main sources of incongruence among the species trees. Additionally, we found evidence for a potential whole genome duplication event shared by Lachemilla and allied genera. Lachemilla shows clear evidence of ancient and recent hybridization throughout the evolutionary history of the group. Also, we show the necessity to use phylogenetic network approaches that can simultaneously accommodate incomplete lineage sorting and gene flow when studying groups that show patterns of reticulation.

Organellar phylogenomics inform systematics in the green algal family Hydrodictyaceae (Chlorophyceae) and provide clues to the complex evolutionary history of plastid genomes in the green algal tree of life.

Phylogenomic analyses across the green algae are resolving relationships at the class, order, and family levels and highlighting dynamic patterns of evolution in organellar genomes. Here we present a within-family phylogenomic study to resolve genera and species relationships in the family Hydrodictyaceae (Chlorophyceae), for which poor resolution in previous phylogenetic studies, along with divergent morphological traits, have precluded taxonomic revisions. Complete plastome sequences and mitochondrial protein-coding gene sequences were acquired from representatives of the Hydrodictyaceae using next-generation sequencing methods. Plastomes were characterized, and gene order and content were compared with plastomes spanning the Sphaeropleales. Single-gene and concatenated-gene phylogenetic analyses of plastid and mitochondrial genes were performed. The Hydrodictyaceae contain the largest sphaeroplealean plastomes thus far fully sequenced. Conservation of plastome gene order within Hydrodictyaceae is striking compared with more dynamic patterns revealed across Sphaeropleales. Phylogenetic analyses resolve Hydrodictyon sister to a monophyletic Pediastrum, though the morphologically distinct P. angulosum and P. duplex continue to be polyphyletic. Analyses of plastid data supported the neochloridacean genus Chlorotetraëdron as sister to Hydrodictyaceae, while conflicting signal was found in the mitochondrial data. A phylogenomic approach resolved within-family relationships not obtainable with previous phylogenetic analyses. Denser taxon sampling across Sphaeropleales is necessary to capture patterns in plastome evolution, and further taxa and studies are needed to fully resolve the sister lineage to Hydrodictyaceae and polyphyly of Pediastrum angulosum and P. duplex.

The Complete Plastome Sequence of an Antarctic Bryophyte Sanionia uncinata (Hedw.) Loeske.

Organellar genomes of bryophytes are poorly represented with chloroplast genomes of only four mosses, four liverworts and two hornworts having been sequenced and annotated. Moreover, while Antarctic vegetation is dominated by the bryophytes, there are few reports on the plastid genomes for the Antarctic bryophytes. Sanionia uncinata (Hedw.) Loeske is one of the most dominant moss species in the maritime Antarctic. It has been researched as an important marker for ecological studies and as an extremophile plant for studies on stress tolerance. Here, we report the complete plastome sequence of S. uncinata, which can be exploited in comparative studies to identify the lineage-specific divergence across different species. The complete plastome of S. uncinata is 124,374 bp in length with a typical quadripartite structure of 114 unique genes including 82 unique protein-coding genes, 37 tRNA genes and four rRNA genes. However, two genes encoding the α subunit of RNA polymerase (rpoA) and encoding the cytochrome b6/f complex subunit VIII (petN) were absent. We could identify nuclear genes homologous to those genes, which suggests that rpoA and petN might have been relocated from the chloroplast genome to the nuclear genome.

Plastid super-barcodes as a tool for species discrimination in feather grasses (Poaceae: Stipa)

Present study was designed to verify which or if any of plastome loci is a hotspot region for mutations and hence might be useful for molecular species identification in feather grasses. 21 newly sequenced complete plastid genomes representing 19 taxa from the genus of Stipa were analyzed in search of the most variable and the most discriminative loci within Stipa. The results showed that the problem with selecting a good barcode locus for feather grasses lies in the very low level of genetic diversity within its plastome. None of the single chloroplast loci is polymorphic enough to play a role of a barcode or a phylogenetic marker for Stipa. The biggest number of taxa was successfully identified by the analysis of 600 bp long DNA fragment comprising a part of rbcL gene, the complete rbcL-rpl23 spacer and a part of rpl23 gene. The effectiveness of multi-locus barcode composed of six best-performing loci for Stipa (ndhH, rpl23, ndhF-rpl32, rpl32-ccsA, psbK-psbI and petA-psbJ) didn’t reach 70% of analyzed taxa. The analysis of complete plastome sequences as a super-barcode for Stipa although much more effective, still didn’t allow for discrimination of all the analyzed taxa of feather grasses.