Comparative and phylogenetic analysis of the complete chloroplast genomes of ten Pittosporum species from East Asia.

Pittosporum (Pittosporaceae) is famous as the ornamental and medical values, which is distributed tropical and subtropical regions of Eastern Hemisphere. The few phylogenetic studies have included samples from the Pacific Island, but the phylogenetic relationships of Asian species has not been studied. Here, the complete chloroplast (cp) genomes of ten Pittosporum species from East Asia were first sequenced and compared with those of the published species of this genus. Our results indicated that cp genomes of these species had a typical and conserved quadripartite structure. 131 genes were identical in order and orientation and no changes of inverted repeat (IR) occurred. However, the comparative analysis of cp genomes suggested that sequence divergence mainly appeared in non-coding or intergenic regions, in which several divergence hotspots were identified. By contrast, protein-coding genes showed the lowest variance under strong purifying selection. Phylogenetic analysis based on the cp genome sequences showed that the tested Pittosporum species were clustered into two major clades, in which the Asian species formed Clade I and the remaining species from Australia and New Zealand formed Clade II with high support values, which was consistent with the results of ITS data with low support values. These results suggested that cp genome is a robust phylogenetic indicator for deep nodes in the phylogeny of Pittosporum. Meanwhile, these results will provide the valuable information to better understand the phylogeny and biogeography of Pittosporum.

Comparative and phylogenetic analyses of the chloroplast genomes of Filipendula species (Rosoideae, Rosaceae).

Genus Filipendula (Rosoideae, Rosaceae) comprises about 15 species and mainly distributed in Northern Hemisphere. The phylogenetic relationships based on the nrITS marker are not consistent with the traditional taxonomic systems of the genus. Here, we first analysed the complete chloroplast (cp) genomes of seven Filipendula species (including two varieties of F. palmate). Our results indicated that the cp genomes of Filipendula species had few changes in size, ranging from 154,205 bp to 154,633 bp and the average of 36.63% GC content. A total of 126 annotated genes had the identical order and orientation, implying that the cp genome structure of Filipendula species was rather conserved. However, the cp genomes of Filipendula species exhibited structural differences, including gene loss, transposition and inversion when compared to those of other genera of Rosoideae. Moreover, SSRs with the different number were observed in the cp genome of each Filipendula species and sequence divergence mainly occurred in noncoding regions, in which four mutational hotspots were identified. In contrast, only two positive selection genes (matK and rps8) were found. Phylogenetic and molecular-dating analysis indicated that Filipendula species were divergent from other genera of Rosoideae at about 82.88 Ma. Additionally, Filipendula species from East Asia were split at about 9.64 Ma into two major clades. These results provide a basis for further studying the infrageneric classification of Filipendula.

Characterization and phylogenetic analyses of ten complete plastomes of Spiraea species.

BACKGROUND: Spiraea is a genus of deciduous shrubs that contains 80-120 species, is mainly distributed in the Northern Hemisphere and has diversified in East Asia. Spiraea species are cultivated as ornamental plants and some are used in traditional herbal medicine. Based on morphological characteristics and genetic markers, phylogenetic classification exhibits low discriminatory power. RESULTS: In present study, we assembled and characterized the chloroplast (cp) genomes of ten Spiraea species and comparatively analysed with five reported cp genomes of this genus. The cp genomes of the fifteen Spiraea species, ranging from 155,904 to 158,637 bp in length, were very conserved and no structural rearrangements occurred. A total of 85 protein-coding genes (PCGs), 37 tRNAs and 8 rRNAs were annotated. We also examined 1,010 simple sequence repeat (SSR) loci, most of which had A/T base preference. Comparative analysis of cp genome demonstrated that single copy and non-coding regions were more divergent than the inverted repeats (IRs) and coding regions and six mutational hotspots were detected. Selection pressure analysis showed that all PCGs were under purifying selection. Phylogenetic analysis based on the complete cp genome data showed that Spiraea formed a monophyletic group and was further divided into two major clades. Infrageneric classification in each clade was supported with a high resolution value. Moreover, the phylogenetic trees based on each individual mutational hotspot segment and their combined dataset also consisted of two major clades, but most of the phylogenetic relationships of interspecies were not well supported. CONCLUSIONS: Although the cp genomes of Spiraea species exhibited high conservation in genome structure, gene content and order, a large number of polymorphism sites and several mutation hotspots were identified in whole cp genomes, which might be sufficiently used as molecular markers to distinguish Spiraea species. Phylogenetic analysis based on the complete cp genome indicated that infrageneric classification in two major clades was supported with high resolution values. Therefore, the cp genome data of the genus Spiraea will be effective in resolving the phylogeny in this genus.

Molecular Structure and Phylogenetic Analyses of the Plastomes of Eight Sorbus Sensu Stricto Species.

Sorbus L. is a genus of controversy on its taxonomic concept due to great variations in morphological characteristics. Sorbus sensu stricto species, being monophyletic, are characterized as pinnate leaves. However, phylogenetic relationships of these species are somewhat fluid based on morphological characteristics and genetic markers. In this study, the chloroplast (cp) genomes of eight Sorbus s. str. species were characterized and compared with those of twelve released species in this genus. Our results indicated that the plastomes of the twenty Sorbus species had a conserved quadripartite structure, and 129 annotated genes had the same order and showed a good collinearity. Additionally, numerous SSRs were observed in the cp genome of each Sorbus species; most of the sequence variations appeared in non-coding regions, and four intergenic regions were identified as mutation spots. By contrast, protein-coding genes showed low variations under purifying selection. The phylogenetic and molecular-dating analysis showed that Sorbus was resolved into two major clades, in which S. americana forms one clade originating at 51.78 Ma, and the rest of Sorbus formed another clade, splitting at 36.77 Ma into two sister groups with high support values. These results provide a basis for further studying the phylogenetic relationship and biogeography of Sorbus species.

Comparative proteomic analysis between mature and germinating seeds in Paris polyphylla var. yunnanensis.

The long dormancy period of Paris polyphylla var. yunnanensis seeds affects the supply of this scarce plant, which is used as an important traditional Chinese medicine. Mature seeds with a globular embryo and germinating seeds with developed embryo were used to explore the mechanisms of seed germination in this species. The protein profiles between the mature and germinating seeds were compared using the isobaric tags for relative and absolute quantification (iTRAQ) approach. Of the 4,488 proteins identified, a total of 1,305 differentially expressed proteins (DEPs) were detected. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of these DEPs indicated that metabolic pathways and the biosynthesis of secondary metabolites were the two top pathways. Additionally, phytohormone quantification shows that the abscisic acid (ABA) level significantly decreased, whereas the GA3 level dramatically increased among nine endogenous gibberellins (GAs), resulting in a significant increase of the GA3/ABA ratio in germinating seeds. The biosynthesis pathways of carotenoid as a precursor for ABA production and GA were further analyzed, and showed that proteinic expressions of the candidate genes in the two pathways did not correlate with the transcriptional abundances. However, 9-cis-epoxycarotenoid dioxygenase (NCED), a rate limited enzyme for ABA biosynthesis, was significantly decreased in mRNA levels in germinating seeds. By contrast, gibberellin 20-oxidase (GA20ox), a key enzyme GA biosynthesis, exhibited the major increase in one copy and a slight decrease in three others at the protentional level in germinating seeds. Gibberellin 2-oxidase (GA2ox), an inactivate enzyme in bioactive GAs, has the tendency to down-regulate in mRNA or at the proteinic level in germinating seeds. Altogether, these results suggested that the analyses of ABA and GA levels, the GA3/ABA ratio, and the expressional patterns of their regulatory genes may provide a novel mechanistic understanding of how phytohormones regulate seed germination in P. polyphylla var. yunnanensis.

The complete chloroplast genome and phylogenetic analysis of Paris stigmatosa (Melanthiaceae).

Paris stigmatosa is a new described species of Melanthiaceae. In this study, the complete chloroplast (cp) genome sequence of P. stigmatosa was first reported and characterized. The cp genome is 165,623 bp in length and contains a pair of inverted repeats (IRs, 34,165 bp) separated by a large (84,327 bp) and small (12,966 bp) single-copy regions. A total of 113 genes were predicted, including 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The phylogenetic analysis suggested that P. stigmatosa is sister of the clade formed by P. marmorata and P. luquanensis.

The complete chloroplast genome of the traditional Chinese herb, Uncaria rhynchophylla (Rubiaceae).

Uncaria rhynchophylla is a vine plant belonging to the family Rubiaceae and has been used as medicine for a long time in China. In this study, the complete chloroplast (cp) genome sequence of U. rhynchophylla was first reported and characterized. The cp genome was 154,605 bp in length and contains a pair of inverted repeats (IRs, 34,165 bp each) separated by a large (84,327 bp) and small (12,966 bp) single-copy regions. A total of 113 unique genes were predicted, including 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The phylogenetic analysis suggested that U. rhynchophylla was closer to Neolamarckia cadamba.

Characterization of the complete chloroplast genome and phylogenetic analysis of Silene jenisseensis (Caryophyllaceae).

The first complete chloroplast genome (cp) sequences of Silene jenisseensis were reported in this study. The S. jenisseensis cp genome was 150,299 bp in size, with two inverted repeat (IR) regions of 25,384 bp, the large single-copy (LSC) region of 82,153 bp, and the small single-copy (SSC) region of 17,378 bp. The cp genome of this species contained 111 genes, including 77 protein-coding genes, 4 ribosomal RNA, and 30 transfer RNA genes. The overall GC content was 36.4%. Phylogenetic analysis of the cp genomes within the Caryophyllaceae family suggests that S. jenisseensis is closer to the clade formed by S. capitata and S. aprica.

The complete chloroplast genome of Hovenia dulcis (Rhamnaceae).

The first complete chloroplast (cp) genome of Hovenia dulcis was reported in this study. The H. dulcis cp genome was 161,636 bp long with two inverted repeat (IR) regions of 26,574 bp, the large single-copy (LSC) region of 89,574 bp, and the small single-copy (SSC) region of 18,914 bp. The cp genome of this species contained 113 genes, including 79 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. The overall GC content was 36.6%. Phylogenetic analysis based on the complete cp genomes within the Rhamnaceae family suggests that H. dulcis is closer to the genus of Ziziphus.

The complete chloroplast genome and phylogenetic analysis of Indofevillea khasiana (Cucurbitaceae).

The first complete chloroplast (cp) genome of Indofevillea khasiana was reported in this study. The I. khasiana cp genome was 159,238 bp in size, with two inverted repeat (IR) regions of 26,275 bp separated by a large single copy (LSC) region of 88,538 bp and a small single copy (SSC) region of 18,150 bp. The cp genome of this species contained 113 genes, including 79 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. The overall GC content was 36.9%. Phylogenetic analysis based on the cp genome sequences suggests that I. khasiana is sister to the rest species of subfam. Cucurbitoideae.

Characterization of the complete chloroplast genome of Gentiana rhodantha (Gentianaceae).

The first complete chloroplast genome (cp) sequences of Gentiana rhodantha were reported in this study. The cp genome of G. rhodantha was 148,967 bp in size, with two inverted repeat (IR) regions of 25,760 bp, the large single copy (LSC) region of 79,831 bp, and the small single copy (SSC) region of 17,616 bp. The cp genome contained 112 genes, including 78 protein-coding genes, 4 ribosomal RNA, and 30 transfer RNA genes. The overall GC content was 36.4%. Phylogenetic analysis of the cp genomes within the tribe Gentianeae suggests that G. rhodantha is in a sister clade of other subtribe Gentianinae.

The complete chloroplast genome and phylogenetic analysis of Paris delavayi (Melanthiaceae).

Paris delavayi Franchet is a perennial herb of the family Melanthiaceae. In this study, the complete chloroplast (cp) genome sequence of P. delavayi was characterized. The cp genome is 164,195 bp in length and contains a pair of inverted repeats (33,415 bp) separated by a large (84,400 bp) and small (12,965 bp) single-copy regions. A total of 112 unique genes were predicted, including 78 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The phylogenetic analysis suggested that P. delavayi is sister to P. mairei but with low support.

Characterization of the chloroplast genome of Calanthe henryi (Epidendroideae; Orchidaceae).

The first complete chloroplast (cp) genome sequences of an endemic and endangered species in China, Calanthe henryi, were reported in this study. The cp genome of C. henryi was 158,256 bp long, with two inverted repeat (IR) regions of 26,348 bp, a large single copy (LSC) region of 87,137 bp, and a small single copy (SSC) region of 18,423 bp. The cp genome of this species contained 113 genes, including 79 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. The overall GC content was 36.7%. Phylogenetic analysis of 60 cp genomes within the subfamily of Epidendroideae suggests that C. henryi is closely related to C. bicolor.

The complete chloroplast genome of Pinus squamata (Pinaceae), a critically endangered species in China.

The complete chloroplast (cp) genome of Pinus squamata, a critically endangered species in China, was reported in this study. The cp genome is 118,300 bp in length and has four regions: 65,298 bp of large single copy (LSC) region and 52,098 bp of small single copy (SSC) region separated by 452 bp of highly reduced inverted repeat (IR) regions. This cp genome with GC content of 38.8% contains 107 unique genes (73 protein-coding genes, 30 tRNA genes, and four rRNA genes). Phylogenetic analysis based on the complete cp genomes indicates that P. squamata is closer to P. gerardiana than P. bungeana.

The complete chloroplast genome of Humulus yunnanensis and phylogenetic analysis of the genus Humulus.

Humulus yunnanensis is an endemic species in Yunnan, China, which is used for beer and pharmacology industry. The phylogenetic position of this species in Humulus remains controversial. The complete chloroplast (cp) genome sequence of H. yunnanensis was reported and characterized in this study. The cp genome is 153,612 bp in length and contains a pair of inverted repeats (IRs, 29,824 bp) separated by a large (87,728 bp) and small (15,390 bp) single-copy regions. A total of 112 unique genes were predicted, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis revealed that H. yunnanensis is more closely related to H. scandens than H. lupulus.

Characterization of the complete chloroplast genome of Magnolia wilsonii (Magnoliaceae).

The complete chloroplast (cp) genome of Magnolia wilsonii, an endangered and endemic species in China, was first reported in this study. The M. wilsonii cp genome was 157,434 bp in length, including two inverted repeat (IR) regions of 26,868 bp, a large single copy (LSC) region of 85,387 bp, and a small single copy (SSC) region of 18,311 bp. A total of 113 unique genes, including 79 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes, were annotated. The overall GC content was 38.8%. Phylogenetic analysis of 34 representative cp genomes within the genus Magnolia suggests that M. wilsonii was sister to M. sieboldii.

The complete chloroplast genome of the multipurpose and traditional herb, Ruta graveolens L.

Ruta graveolens L. is a perennial plant belonging to the family Rutaceae and has been used for traditional medicines for a long time. In this study, the complete chloroplast (cp) genome sequence of R. graveolens was first reported and characterized. The cp genome is 157,434 bp in length and contains a pair of inverted repeats (IRs, 26,868 bp) separated by a large (85,387 bp) and small (18,311 bp) single-copy regions. A total of 132 genes were predicted, including 87 protein-coding genes, 37 tRNA genes and 8 rRNA genes. The phylogenetic analysis suggested that R. graveolens is more closely related to the monophyletic subfam. Aurantioideae.

Characterization of the complete chloroplast genome of Paederia scandens (Rubiaceae): a Chinese folk medicinal plant.

Paederia scandens has been used as a traditional medicine in Asian countries to treat jaundice, dysentery, and the pain of rheumatism. The complete chloroplast (cp) genome sequence of P. scandens was reported and characterized in this study. The cp genome is 153,626 bp in length, composed of a pair of 26,513 bp inverted repeat (IR) regions separated by a large single-copy (LSC) region of 83,712 bp and a small single-copy (SSC) region of 16,888 bp. There were 131 predicted genes (86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes) in the genome, and the overall GC content of the genome is 37.7%. Phylogenetic analysis based on the cp genome data showed that P. scandens was sister to the clade formed by Galium mollugo and G. aparine.

The complete chloroplast genome sequence of a traditional Chinese medicine: Achyranthes bidentata (Amaranthaceae).

Achyranthes bidentata (Amarathaceae) has been commonly used as a traditional Chinese medicine in the treatment of osteoporosis and bone nonunion. Here, the complete chloroplast genome of A. bidentata was assembled and characterized. The cp genome is 151,451 bp in length, composed of a pair of 25,150 bp inverted repeat (IR) regions separated by a large single-copy (LSC) region of 83,899 bp and a small single-copy (SSC) region of 17,252 bp. The whole cp genome of A. bidentata contains 130 genes(85 protein-coding genes, 37 tRNAs and eight rRNAs) and the overall GC content is 36.5%. Phylogenetic analysis based on the cp genome data showed that A. bidentata was close to Cyathula capitata.

The complete chloroplast genome of an endangered and endemic species, Acer yangbiense (Aceraceae).

Acer yangbiense Y.S. Chen & Q.E. Yang is a species of Aceraceae with a very restricted distribution in Yunnan, China. In this study, the complete chloroplast (cp) genome sequence of A. yangbiense was reported and characterized. The cp genome is 155,706 bp in length and contains a pair of inverted repeats (IRs, 25,858 bp) separated by a large (85,859 bp) and small (18,131 bp) single-copy regions. A total of 128 genes were predicted, including 83 protein-coding genes, 37 tRNA genes and 8 rRNA genes. The phylogenetic analysis suggested that A. yangbiense is sister of the clade formed by A. laevigatum, A. palmatum, A. wilsonii, and A. buergerianum.