cpDNA Genome Research Articles

Dryopteris microlepioides, a new synonym of Trichoneuron microlepioides (Dryopteridaceae)

When reviewing the species diversity of Dryopteridaceae from Vietnam, we noticed the name Dryopteris microlepioides Christensen (1934: 102) is taxonomically uncertain and to be treated (Hassler 1994–2024). Dryopteris microlepioides was described based on two collections from northern Vietnam and was thought to be a distinct species superficially resembling Microlepia speluncae (Linnaeus 1753: 1093) Moore (1857: 93) (Christensen 1934). Since its publication in 1934, this name had been neglected by authors who treated Dryopteris Adanson (1763: 20) for the fern flora or species diversity of Vietnam (e.g., Tardieu-Blot & Christensen 1938, 1941; Pham 1999; Phan 2010). At the first sight of the type specimens of D. microlepioides, the senior author (SYD) was aware of D. microlepioides representing the same taxon with Trichoneuron microlepioides Ching (1965: 119) described from southern Yunnan, China, because this taxon is morphologically unique by having the microlepioid frond habit (especially with copious pale hairs on both surfaces) and the dryopterioid sori (reniform, medial on abaxial surface of lamina) (Fig. 1). Phylogenetically, the sample of this species from northern Vietnam, which was identified as T. microlepioides by Liu et al. (2016), was resolved to be sister to Polystichopsis (Smith 1875: 217) Holttum (1947: 147) in Dryopteridaceae subfam. Polybotryoideae based on the analysis of three cpDNA sequences (rbcL, atpA, and atpB) (Liu et al. 2016). In recent years, we also collected this taxon in northern Vietnam (paratype locality of D. microlepioides) and southern Yunnan, China, and conducted phylogenetic analysis based on cpDNA genome (not presenting here). Our analysis resolved one sample from Vietnam (Dong 4598) and two collections from Yunnan (Dong 4801 and Zuo 5093) clustered together, identifying no any significant difference between them. The three samples in the phylogenetic tree formed a sister relationship in high supporting values with Polystichopsis as the result in Liu et al. (2016). This result provides further evidence supporting the same species of D. microlepioides Christensen (1934) with T. microlepioides Ching (1965).

Molecular Profile of Cogongrass [Imperata cylindrica (L.) Raeusch] in Java Island Based on trnT(UGU)-trnL(UAA) IGS Sequences

Cogongrass is one of the top ten problem-causing weeds in the world that is invasively spread over many tropical and subtropical regions, including Java Island, the Republic of Indonesia. The wide distribution is possibly related to their adaptability to almost all terrestrial habitats from various altitudes, which may lead to a high level of genetic variation. This study aimed to assess the genetic variation and phylogenetic relationship of cogongrass in Java Island using an intergenic spacer (IGS) sequence in the cpDNA genome, i.e. trnT(UGU)-trnL(UAA), as the molecular marker of high mutation rate. Plant samples were collected randomly from five different sites on the island. These were subjected to total genomic DNA extraction. The DNAs obtained were then used as PCR templates to amplify trnT(UGU)-trnL(UAA) IGS using a pair of universal primers. The PCR products were sequenced for genetic analysis. It was shown that an extremely high genetic variation with respect to the haplotype diversity of cogongrass in Java Island was observed. Nevertheless, a very low nucleotide diversity was obtained revealing a considerably close genetic relationship among the samples. Anatomical data regarding stomata number and length were found to correspond to the high level of genetic variation, but it was not the case with the stomata index.

The Phylogeny ofErrazurizia(Fabaceae: Amorpheae) and Description of the New Monotypic GenusPictarena

Abstract—Errazurizia(Fabaceae) is a genus comprised of four species of New World desert shrubs with an ambiguous evolutionary history. Prior studies determined the North American species ofErrazuriziawere polyphyletic and the relationship ofE. rotundatawith other genera in the tribe Amorpheae remained undetermined. The sole South American species, which is also the type species, has never been included in a molecular study. We inferred the phylogenetic relationships ofErrazuriziaand six closely related genera using data from the cpDNA genome and nrDNA cistron from reference guided assemblies. Maximum likelihood and Bayesian analyses found two of the North American and the South American species were a monophyletic group, but thatE. rotundatawas sister to the monotypic genusParryella. Gland and pollen surface characters confirm the close relationship betweenP. filifoliaandE. rotundata. Cytonuclear discordance yielded partially incongruent tree topologies, and while the cpDNA phylogeny indicated a monophyleticAmorphawas sister to theE. rotundataandP. filifoliaclade, the nrDNA cistron phylogeny recovered a paraphyleticAmorpha, withA. californicasister to theE. rotundataandP. filifoliaclade. Molecular and morphological evidence support the elevation ofE. rotundatato its own monotypic genus,Pictarena. The new genusPictarenais defined by subsessile, suborbicular leaflets, mammiform leaflet glands, spicate inflorescences, and flowers with either all petals absent or rarely with a banner petal. ElevatingE. rotundatatoPictarenaresolves the confusing classification of the species, an imperiled endemic known only from four localities in northern Arizona and lends support for continued conservation.

Complete Chloroplast Genome Sequence of a New Variety of Brasenia schreberi: Genome Characteristics, Comparative Analysis, and Phylogenetic Relationships

This study sequenced and assembled the chloroplast (cp) genome of Brasenia schreberi cv. ‘Mahu Chuncai’, a novel variety of B. schreberi rich in nutrients with distinctive characteristics, unlike other varieties in China. The cpDNA genome of ‘Mahu Chuncai’ has a typical quadripartite structure, with a full length of 158,973 bp, including 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenetic analysis revealed that all species can be divided into three main clades. Results from inverted repeats (IR) boundary analysis revealed substantial differences between Brasenia and Cabomba species. The cpDNA genome of B. schreberi identified was strongly related to Brasenia species but appeared to be a distant relative of Cabomba aquatica more than other species in Cabombaceae. In contrast with the species from Cabombaceae, ‘Mahu Chuncai’ was a close relative of B. schreberi MN315507.1, which was a distant relative of C. aquatica MG720559.1. Furthermore, we found four potential molecular markers, i.e., ycf1 in the IR region, psbT in the LSC region, and ndhF and rps15 in the SSC region. Collectively, our findings confirm the phylogenetic evolution and cultivation origin of B. schreberi. We identified genetic characteristics and nucleotide diversity hotspots, which provides a theoretical basis for additional research on variety identification, germplasm resources, and molecular breeding of the precious vegetable.

Complete chloroplast genomes of Asparagus aethiopicus L., A. densiflorus (Kunth) Jessop 'Myers', and A. cochinchinensis (Lour.) Merr.: Comparative and phylogenetic analysis with congenerics.

Asparagus species are widely used for medicinal, horticultural, and culinary purposes. Complete chloroplast DNA (cpDNA) genomes of three Asparagus specimens collected in Hong Kong-A. aethiopicus, A. densiflorus 'Myers', and A. cochinchinensis-were de novo assembled using Illumina sequencing. Their sizes ranged from 157,069 to 157,319 bp, with a total guanine-cytosine content of 37.5%. Structurally, a large single copy (84,598-85,350 bp) and a small single copy (18,677-18,685 bp) were separated by a pair of inverted repeats (26,518-26,573 bp). In total, 136 genes were annotated for A. aethiopicus and A. densiflorus 'Myers'; these included 90 mRNA, 38 tRNA, and 8 rRNA genes. Further, 132 genes, including 87 mRNA, 37 tRNA, and 8 rRNA genes, were annotated for A. cochinchinensis. For comparative and phylogenetic analysis, we included NCBI data for four congenerics, A. setaceus, A. racemosus, A. schoberioides, and A. officinalis. The gene content, order, and genome structure were relatively conserved among the genomes studied. There were similarities in simple sequence repeats in terms of repeat type, sequence complementarity, and cpDNA partition distribution. A. densiflorus 'Myers' had distinctive long sequence repeats in terms of their quantity, type, and length-interval frequency. Divergence hotspots, with nucleotide diversity (Pi) ≥ 0.015, were identified in five genomic regions: accD-psaI, ccsA, trnS-trnG, ycf1, and ndhC-trnV. Here, we summarise the historical changes in the generic subdivision of Asparagus. Our phylogenetic analysis, which also elucidates the nomenclatural complexity of A. aethiopicus and A. densiflorus 'Myers', further supports their close phylogenetic relationship. The findings are consistent with prior generic subdivisions, except for the placement of A. racemosus, which requires further study. These de novo assembled cpDNA genomes contribute valuable genomic resources and help to elucidate Asparagus taxonomy.

Comparison of Auxenochlorella protothecoides and Chlorella spp. Chloroplast Genomes: Evidence for Endosymbiosis and Horizontal Virus-like Gene Transfer

Resequencing of the chloroplast genome (cpDNA) of Auxenochlorella protothecoides UTEX 25 was completed (GenBank Accession no. KC631634.1), revealing a genome size of 84,576 base pairs and 30.8% GC content, consistent with features reported for the previously sequenced A. protothecoides 0710, (GenBank Accession no. KC843975). The A. protothecoides UTEX 25 cpDNA encoded 78 predicted open reading frames, 32 tRNAs, and 4 rRNAs, making it smaller and more compact than the cpDNA genome of C. variabilis (124,579 bp) and C. vulgaris (150,613 bp). By comparison, the compact genome size of A. protothecoides was attributable primarily to a lower intergenic sequence content. The cpDNA coding regions of all known Chlorella species were found to be organized in conserved colinear blocks, with some rearrangements. The Auxenochlorella and Chlorella species genome structure and composition were similar, and of particular interest were genes influencing photosynthetic efficiency, i.e., chlorophyll synthesis and photosystem subunit I and II genes, consistent with other biofuel species of interest. Phylogenetic analysis revealed that Prototheca cutis is the closest known A. protothecoides relative, followed by members of the genus Chlorella. The cpDNA of A. protothecoides encodes 37 genes that are highly homologous to representative cyanobacteria species, including rrn16, rrn23, and psbA, corroborating a well-recognized symbiosis. Several putative coding regions were identified that shared high nucleotide sequence identity with virus-like sequences, suggestive of horizontal gene transfer. Despite these predictions, no corresponding transcripts were obtained by RT-PCR amplification, indicating they are unlikely to be expressed in the extant lineage.

Complete chloroplast genome of Toona ciliata Roem. var. pubescens (Franch.) Hand.-Mazz (Meliaceae), ‘Chinese mahogany’

Toona ciliata var. pubescens is classified as Toona subgenus of Meliaceae family, which belongs to a large deciduous tree species. It is also a kind of precious timber tree species and has a certain medicinal value. Here, the first complete chloroplast genome (cpDNA) sequence of T. ciliata var. pubescens was determined using the Illumina sequencing platform. The cpDNA genome is 159,481 bp in length, containing a large single-copy region (LSC) of 87,176 bp and a small single-copy region (SSC) of 18,381 bp, which were separated by a pair of inverted repeats (IRs) regions of 26,962 bp. The genome contains 138 genes, including 90 protein-coding genes, eight ribosomal RNA genes, and 40 transfer RNA genes. The phylogenetic analysis based on 19 cpDNA genomes showed a close relationship with Toona ciliate.

The complete chloroplast genome sequence of Tussilago farfara (Asteraceae)

Tussilago farfara is a member of the family Asteraceae. In this paper, we reported the complete chloroplast (cp) genome sequence of T. farfara. The results showed that T. farfara complete chloroplast genome comprises 151,325 bp, containing a largen single copy (LSC) region of 83,370 bp, a small single copy (SSC) region of 18,273 bp, and a pair of inverted repeats (IRs) region of 24,841 bp. The genome has a GC content of 37.4%. The LSC, SSC, and IR regions represent 35.5%, 30.6%, and 43.0% of the T. farfara chloroplast genome length. We annotated 132 genes, comprising 87 protein-coding genes (PCGs), eight rRNA genes, and 36 tRNA genes. A phylogenetic analysis based on 31 cpDNA genomes suggested that the T. farfara is closely related to Farfugium japonicum.

DNA Barcoding and Phylogenomic Analysis of the Genus Fritillaria in China Based on Complete Chloroplast Genomes.

The Fritillaria is an extremely complicated genus in taxonomy and phylogeny, which contains numerous medicinal species in China. Both traditional characteristic-based taxonomy and universal DNA barcodes (ITS, trnH-psbA, and rbcL) are difficult to effectively identify the species. Here, we generated a large dataset of chloroplast genomes from multiple accessions per species of Fritillaria to evaluate their effectiveness in species discrimination. Moreover, phylogeny of species in China was explored based on the complete chloroplast genomes, and then divergence times of each node were estimated. The results showed that all 21 species in Fritillaria here (including two suspicious species) could be correctly discriminated using cpDNA genomes except F. cirrhosa, which suggested that DNA super-barcode could greatly enhance species discriminatory resolution for complicated genera. Furthermore, four regions (ycf1, matK-trnG-GCC, rpoC1, and matK) gained remarkably higher resolution than that of other plastid regions, but only matK might be suitable to identify Fritillaria species in consideration of its lengths. Phylogenomic analysis showed that the subgenus Fritillaria in China was divided into four major clades with obvious geographic structure. Among them, Clade I, mainly distributed in southwest China, was a young and complicated group. Moreover, according to the analysis, taxonomic treatments of the two suspicious species, namely “F. omeiensis” and “F. hupehensis” in Flora of China (2000) are questionable and might need further revision. Molecular dating revealed that both origin and divergence of subgenus Fritillaria, as well as its four major clades, were significantly associated with geological and climatic fluctuations during the Middle to Late Miocene. This study would enrich case studies of DNA super-barcode and provide new insights on speciation, lineage diversification, and biogeography of the Fritillaria in China.

Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (Castanea)

Chloroplast (cp) DNA genomes are traditional workhorses for studying the evolution of species and reconstructing phylogenetic relationships in plants. Species of the genus Castanea (chestnuts and chinquapins) are valued as a source of nuts and timber wherever they grow, and chestnut species hybrids are common. We compared the cp genomes of C. mollissima, C. seguinii, C. henryi, and C. pumila. These cp genomes ranged from 160,805 bp to 161,010 bp in length, comprising a pair of inverted repeat (IR) regions (25,685 to 25,701 bp) separated by a large single-copy (LSC) region (90,440 to 90,560 bp) and a small single-copy (SSC) region (18,970 to 19,049 bp). Each cp genome encoded the same 113 genes; 82–83 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. There were 18 duplicated genes in the IRs. Comparative analysis of cp genomes revealed that rpl22 was absent in all analyzed species, and the gene ycf1 has been pseudo-genized in all Chinese chestnuts except C. pumlia. We analyzed the repeats and nucleotide substitutions in these plastomes and detected several highly variable regions. The phylogenetic analyses based on plastomes confirmed the monophyly of Castanea species.

Assessment of the Physico-chemico and Microbiological changes during Nipa (Nypa fruticans) Sap Fermentation collected from different sites in Cagayan province, Philippines

Background/Objectives: Sap from Nypa fruticans are used as feedstock for a bioethanol national program to establish a sustainable and productive village-scale bioethanol industry. The study aimed to establish the physicochemical, microbiological, and molecular characteristics of nipa sap. Methods/Statistical Analysis: Nipa sap samples were collected from three sampling sites at different fermentation time. Physico-chemical parameters such as pH, titratable acidity, and total soluble solids were determined and statistically analyzed using One-way Analysis of Variance and mean ± SD values. Molecular approaches were used to profile and identify yeast species naturally residing in the sap during fermentation and assess the genetic diversity of nipa palm in selected sampling locations. Findings: Sampling site and fermentation time significantly affect the levels of pH, titratable acids, and total soluble solids in the sap samples. Sugar concentration in nipa sap is affected by sampling site: as the sampling site nears the river, the amount of sugars become significantly greater. Molecular studies revealed that among the 12 isolates obtained, five of them (Y24S1, Y48S1, Y72S1, Y24S2, and Y24S3) showed 100% similarity to strain of Pichia occidentalis, three (Y48S2, Y48S3, and Y72S3) were similar (100%) to a strain of Saccharomyces cerevisiae (YPDW9), and the other two isolates (Y72S1 and Y48S3A) were identical to Naganishia randhawae strain HBUMO6885 and Tremellales sp. LM523 respectively with a 100% similarity. PCR amplification of their trnL–trnF cpDNA genome, BLAST and phylogenetic analyses reveals that all nipa plant samples were similar to Nypa fruticans. Applications: The generated information on the effect of sampling site on sugar content of nipa sap samples could be good input in selecting expansion sites for the establishment of nipa plantations. Furthermore, the identified yeast strains can be used as inoculant or starter culture to improve fermentation. Keywords: Physico-chemical parameter; yeasts molecular profiling; nipa sap fermentation; phylogenetic analysis; genetic diversity

The complete chloroplast genome sequence of Artemisia ordosica

Artemisia ordosica is one of the important plants in succession of psammophytes in sandy (desert), it is a high ecological, economic and scientific research value. The chloproplast is photosynthetic organelles that provide energy for green plants. In this study, we reported the complete chloroplast (cp) genome sequence of A. ordosica, which were assembled using high-throughput sequencing technology. The results showed that the total cpDNA genome of A. ordosica is 151,209 bp in length, consisting of a large single copy (LSC) region of 82,980 bp, a small single copy (SSC) region of 18,303 bp, and a pair of inverted repeat regions (IRa and IRb, 24,963 bp each). Among all genes, the content of GC is 37.4%. The LSC, SSC, and IRs are 58.44%, 12.10%, and 33.02% of the A. ordosica cpDNA genome length respectively. Furthermore, the genome contained a total of 113 genes, comprising 79 protein-coding genes, 4 rRNA genes, and 29 tRNA genes. A phylogenetic analysis based on 21cpDNA genomes suggested that the A.ordosica is closely related to A. scoparia.

The complete chloroplast genome sequence of Malva verticillata

Malva verticillata, which belongs to the family Malvaceae, is an herb with a wide ecological range and considerable economic and ecological value. herein this study, we determined the complete chloroplast (cp) genome of M. verticillata using Illumina sequencing. The total length of the cpDNA genome was 158,408 bp, including two copies of inverted repeats (IRs, 50,214 bp), a large single copy (LSC, 87,085 bp), and a small single copy (SSC, 21,109 bp). A total of 130 genes were annotated, including 36 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes, and 86 messenger RNA (mRNA) genes. Phylogenetic analysis showed that M. verticillata is closely related to Abelmoschus esculentus, and Hibiscus syriacus among Malvaceae species.

The complete chloroplast genome sequence of Elsholtzia densa, a herb with volatile aroma component

The complete chloroplast genome sequence of Elsholtzia densa was analysed. The results indicated that the size of the chloroplast genome was 149,095 bp in length with a large single-copy region (LSC) of 81,497 bp, a small single-copy region (SSC) of 17,364 bp, and a pair of inverted repeat (IR) regions of 25,117bp. The overall GC content of the cpDNA genome was 37.86%, while the corresponding values of the LSC, SSC, and IR regions were 35.96%, 31.92%, and 43.16%, respectively. A total of 132 functional genes were identified, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The maximum likelihood phylogenetic tree suggested that E. densa was closely related to the species in the family Labiatae.

The complete chloroplast genome sequence of an alpine wildflower, Philadelphus calvescens (Rehd.) S. M. Hwang (Saxifragaceae)

Philadelphus calvescens, belonging to the family Saxifragaceae, is a beautiful shrub with white fragrant flowers which is widely distributed in southwest China. In this study, we sequenced the complete chloroplast (cp) genome of P. calvescens to investigate its phylogenetic relationship in Saxifragaceae. Total length of the cpDNA genome was 157,237 bp, consisting of a large single copy (LSC) region of 86,481 bp, a small single copy (SSC) region of 18,728 bp, and a pair of inverted repeat regions (IRs, 26,014 bp). The genome contained 114 genes, namely 79 protein-coding genes, 31 tRNA genes, and 4 rRNA. The overall GC content was 37.8%. Phylogenetic analysis suggested that Philadelphus was closely related to Deutzia. The present study was the first report on complete cp genome of Philadelphus so it could afford important genetic information for further researches on the genus and related genera.

Peach chloroplast genome variation architecture and phylogenomic signatures of cpDNA introgression in Prunus

The complete chloroplast genome of peach provides essential information required for the assessment of phylogenetic relationships among Prunus species. Here, we compared the complete chloroplast DNA (cpDNA) genome between two peach cultivars and a wild relative, Prunus mira. The cpDNA genomes of the three peach specimens ranged from 157 330 to 157 744 bp in length and all contained 133 genes and 128 intergenic spacer (IGS) regions with an average GC content of 36.8%. The cpDNA genome of peach contained approximately 600 simple sequence repeats (SSRs), with hexa-nucleotide repeats being the most frequent microsatellites. Most SSRs have undergone divergence between cultivated and wild peaches. A total of 331 single nucleotide variants were identified in the cpDNA genomes. Fifty-one multiple-base pair indels were detected, which are mainly responsible for the cpDNA genome size variation. The cpDNA genomes contained 45 hypervariable regions, with 78% in the large single copy region (LSC). Phylogenomic analysis revealed that Prunus persica is more closely related to Prunus kansuensis than to other wild relatives, and a frequency of introgression of the chloroplast genome between Prunus species was deduced. Collectively, various genetic variations in the cpDNA genomes can serve as molecular markers for genomic studies of Prunus species, such as DNA barcoding, phylogeny, and systematics.

Whole Plastome Sequencing Within Silene Section Psammophilae Reveals Mainland Hybridization and Divergence With the Balearic Island Populations.

Reconstructing the phylogenetic relationships within Caryophyllaceae tribe Sileneae has been obscured by hybridization and incomplete lineage sorting. Silene is the largest genus in the Caryophyllaceae, and unraveling its evolutionary history has been particularly challenging. In order to infer the phylogenetic relationships among the five species in Silene section Psammophilae, we have performed a genome skimming approach to acquire the complete plastid genome (cpDNA), nuclear ribosomal cistron (nrDNA), and partial mitochondrial genome (mtDNA). We have included 26 populations, representing the range of each species' distribution. This section includes five morphologically similar species endemic to the Iberian Peninsula and Balearic Islands (Ibiza and Formentera), yet some of them occupy distinct edaphic habitats (e.g. maritime sands, calcareous sandstones). In addition to phylogeographic analyses, genetic structuring using the chloroplast data set was inferred with Discriminant Analysis of Principal Components (DAPC), analyses of molecular variance (AMOVA), and a partial Mantel test. Reference-guided assembly of 50 bp single-end and 250 bp paired-end Illumina reads produced the nearly complete cpDNA genome (154 kbp), partial mtDNA genome (from 81 to 114 kbp), and the nrDNA cistron (6.4 kbp). Selected variable regions of the cpDNA and mtDNA assemblies were confirmed by Sanger sequencing. Phylogenetic analyses of the mainland populations reveal incongruence among the three genomes. None of the three data sets produced relationships consistent with taxonomy or geography. In contrast, Silene cambessedesii, present in the Balearic Islands, is the only species that forms a strongly supported monophyletic clade in the cpDNA genome and is strongly differentiated with respect to the remaining taxa of the Iberian Peninsula. These results contrast with those obtained for mainland populations. Across the entire analysis, only one well-supported mainland clade of Silene littorea and Silene stockenii emerges from the southern region of the Iberian Peninsula. DAPC and AMOVA results suggest the absence of genetic structure among mainland populations of Silene section Psammophilae, whereas partial Mantel test discarded spatial correlation of genetic differentiation. The widespread incongruence between morphology-based taxonomic boundaries and phylogeography suggests a history of interspecific hybridization, in which only a substantial geographic barrier, like isolation by the Mediterranean Sea, was sufficient to create and maintain species boundaries in Silene section Psammophilae.

Complex Analyses of Short Inverted Repeats in All Sequenced Chloroplast DNAs.

Chloroplasts are key organelles in the management of oxygen in algae and plants and are therefore crucial for all living beings that consume oxygen. Chloroplasts typically contain a circular DNA molecule with nucleus-independent replication and heredity. Using “palindrome analyser” we performed complete analyses of short inverted repeats (S-IRs) in all chloroplast DNAs (cpDNAs) available from the NCBI genome database. Our results provide basic parameters of cpDNAs including comparative information on localization, frequency, and differences in S-IR presence. In a total of 2,565 cpDNA sequences available, the average frequency of S-IRs in cpDNA genomes is 45 S-IRs/per kbp, significantly higher than that found in mitochondrial DNA sequences. The frequency of S-IRs in cpDNAs generally decreased with S-IR length, but not for S-IRs 15, 22, 24, or 27 bp long, which are significantly more abundant than S-IRs with other lengths. These results point to the importance of specific S-IRs in cpDNA genomes. Moreover, comparison by Levenshtein distance of S-IR similarities showed that a limited number of S-IR sequences are shared in the majority of cpDNAs. S-IRs are not located randomly in cpDNAs, but are length-dependently enriched in specific locations, including the repeat region, stem, introns, and tRNA regions. The highest enrichment was found for 12 bp and longer S-IRs in the stem-loop region followed by 12 bp and longer S-IRs located before the repeat region. On the other hand, S-IRs are relatively rare in rRNA sequences and around introns. These data show nonrandom and conserved arrangements of S-IRs in chloroplast genomes.

The complete chloroplast genome of Amygdalus mira (Rosaceae) a threatened wild Chinese peach

Amygdalus mira (Koehne) Ricker (Basionym: Prunus mira Koehne) is a wild relative species of peach belonging to Rosaceae family. It is likely the oldest progenitor of peach and considered threatened or even on the verge of extinction, which requires urgent conservation attention. To contribute to such efforts, complete chloroplast genome of A. mira was assembled using Illumina Hiseq 2500 platform. The cpDNA genome is 157,330 bp in length and has a GC content of 36.80%, with a typical circular quadripartite structure comprising a pair of inverted repeats (IRA and IRB) separated by two single-copy regions. The cpDNA genome consisted of 88 coding sequences (CDS), 37 tRNAs and 8 rRNAs genes. 583 simple sequence repeat (SSR) motifs were identified, where hexa-nucleotide was the most common (27.7% of all SSRs). The complete cpDNA genome of A. mira will be of valuable data for the upcoming research on comparative population genomics of peach.

The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae

Zizania latifolia (Griseb.) Turcz. ex Stapf was once utilized as an important grain in ancient China and has been cultivated as an aquatic vegetable. Here, we report the complete Z. latifolia chloroplast genome sequence obtained through de novo assembly of Illumina paired-end reads generated by directly purified chloroplast (cp) DNA genome sequencing. The Z. latifolia cp genome is 136,501 bp in length, comprising a pair of 20,878-bp inverted repeat regions (IR) separated by small and large single copy regions (SSC and LSC) of 12,590 bp and 82,155 bp, respectively. The Z. latifolia cp genome encodes 110 unique genes (77 protein-coding genes, 29 tRNA genes, and 4 rRNA genes), of which 15 encompass introns. Sequence analysis identified a total of 39 direct/inverted repeats and 63 simple sequence repeats (SSR) with an average rate of 0.46 SSRs/kb. Our results revealed that the Z. latifolia cp genome is AT-rich (61.02%) and gene codon usage may be largely affected by a low GC content and codon usage bias for A, T-ending codons. We predicted 33 RNA editing sites in the chloroplast of Z. latifolia, all for C-to-U transitions. Comparative analyses with other available Oryzeae plastid genomes showed that the coding and IR sequences were more conserved than the single-copy and noncoding regions, suggesting that the indels should be cautiously employed in phylogenetic studies. Phylogenetic analysis of 52 complete grass chloroplast genomes including the reported Z. latifolia cp genome in this study yielded an identical tree topology as previous plastid-based trees, providing strong support for a sister relationship between Bambusoideae+Pooideae and Ehrhartoideae in the BEP (Bambusoideae, Ehrhartoideae, Pooideae) clade of the grass family.