LSC Regions Research Articles

Theoretical Study of Oxygen Vacancy Formation at LSC/GDC Interface

One of the important factors to improve the cathode activity is the electronic structure of cathode materials in solid oxide fuel cell. In this study, we analyzed the formation energy of oxygen vacancy (VO) near the La1-xSrxCoO3- d (LSC) surface in CeO2 or gadolinium-doped CeO2 (GDC)-LSC interface model by using the density functional theory. We found the electron transfer from CeO2 to LSC region due to the difference of density of states. Stable formation energy of VO from LSC surface in CeO2-LSC interface model was obtained. The formation energy of VO in LSC near GDC interface was more stable than CeO2 interface. We clearly found that the different electronic structure in CeO2/GDC-LSC interface affects the difference of VO formation in LSC.

Characterization of the complete chloroplast genome of seabuckthorn (Hippophae rhamnoides L.)

Hippophae rhamnoides is an ecologically and economically important tree in arid areas, but its natural distribution is now very fragmented and contracted. Here we assembled and characterized its whole chloroplast (cp) genome based on Illumina pair-end sequencing data. The H. rhamnoides cp genome was 156,132 bp in size, containing a large single copy region (LSC) of 83,970 bp and a small single copy region (SSC) of 18,831 bp separated by a pair of inverted repeats (IRs) of 26,658 bp. The genome had 132 genes, including 86 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Most of genes occurred as single-copy, while 18 gene species had two copies. The overall GC content of this genome was 36.7%, with the corresponding values of LSC, SSC and IR regions being 34.5, 30.3 and 42.4%, respectively. Further, the phylogenomic analysis strongly supported the sister relationship of H. rhamnoides and Elaeagnus in Elaeagnaceae.

Characterization of the complete chloroplast genome of Xanthoceras sorbifolium, an endangered oil tree

Xanthoceras sorbifolium is an important biodiesel tree in northern China, but its natural population is now very fragmented and in decline. Here we assembled and characterized the complete chloroplast (cp) genome of X. sorbifolium using Illumina pair-end sequencing data. The X. sorbifolium cp genome was 161,231 bp in size, containing a large single copy region (LSC) of 85,299 bp and a small single copy region (SSC) of 18,692 bp separated by a pair of inverted repeats (IRs) of 28,620 bp. The genome had 132 genes, including 86 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The overall GC content of the X. sorbifolium cp genome was 37.7%, with the corresponding values of LSC, SSC and IR regions being 36.0, 31.7 and 42.3%, respectively. The phylogenomic analysis strongly supported that X. sorbifolium diverged firstly in Sapindaceae. This complete cp genome will be useful for further studies of this endangered plant.

Characterization of the complete chloroplast genome of the golden crane butterfly, Euonymus schensianus (Celastraceae)

The golden crane butterfly, Euonymus schensianus, is an important forest tree species with dramatically fragmented and declined populations. Here we characterized the complete chloroplast (cp) genome of this plant using Illumina pair-end sequencing data. The E. schensianus cp genome was 157,702 bp in length, containing a pair of inverted repeats (IRs) of 26,574 bp which separated a large single copy region (LSC) of 86,026 bp and a small single copy region (SSC) of 18,528 bp. The genome contained 131 genes, including 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. Most of genes occurred as single-copy in the LSC or SSC, while 18 gene species had two copies in the IRs. The GC content of E. schensianus cp genome, LSC, SSC and IR regions were 37.2, 35.0, 31.8 and 42.5%, respectively. Further, phylogenomic analysis strongly supported the close relationship of E. schensianus and E. japonicus in Celastrales.

Characterization of the complete chloroplast genome of the endangered Przewalskia tangutica Maxim

Przewalskia tangutica Maxim., an endangered medicinal species, is endemic to the Qinghai-Tibetan Plateau of China. In this study, we sequenced and characterized the chloroplast genome of P. tangutica for the first time. The P. tangutica chloroplast genome is 155,569 bp in length, exhibits a typical quadripartite structural organization, consisting of a LSC region of 86,707 bp, two IR regions of 25,287 bp and a SSC region of 18,288 bp. The genome contains 138 complete genes, including 85 protein-coding genes (85 PCG species), 44 tRNA genes (21 tRNA species) and eight rRNA genes (four rRNA species, rrn16S, rrn23S, rrn4.5 S, rrn5S). The most of gene species occur as a single copy, while 18 gene species occur in double copies including eight PCG species, six tRNA species (trnN, trnR, trnA, trnI, trnV, trnL) and all of rRNA species. Further, phylogenetic analysis indicated that P. tangutica clustered together with Scopolia parviflora, and formed a clade with Hyoscyamus niger in the Solanaceae. The whole chloroplast genome of P. tangutica not only provides important insight into conservation and restoration efforts for P. tangutica, but also plays a critical role in phylogenetic and evolution studies of the Solanaceae family. More importantly, it will contribute to the ongoing efforts for maintenance of existing genetic resource in the Qinghai-Tibet Plateau.

Plastid phylogenomics and adaptive evolution of Gaultheria series Trichophyllae (Ericaceae), a clade from sky islands of the Himalaya-Hengduan Mountains

Gaultheria series Trichophyllae Airy Shaw is an angiosperm clade of high-alpine shrublets endemic to the Himalaya-Hengduan Mountains and characterized by recent species divergence and convergent character evolution that has until recently caused much confusion in species circumscription. Although multiple DNA sequence regions have been employed previously, phylogenetic relationships among species in the group have remained largely unresolved. Here we examined the effectiveness of the plastid genome for improving phylogenetic resolution within the G. series Trichophyllae clade. Plastid genomes of 31 samples representing all 19 recognized species of the series and three outgroup species were sequenced with Illumina Sequencing technology. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) phylogenetic analyses were performed with various datasets, i.e., that from the whole plastid genome, coding regions, noncoding regions, large single-copy region (LSC) and inverted-repeat region a (IRa). The partitioned whole plastid genome with inverted-repeat region b (IRb) excluded was also analyzed with ML and BI. Tree topologies based on the whole plastid genome, noncoding regions, and LSC region datasets across all analyses, and that based on the partitioned dataset with ML and BI analyses, are identical and generally strongly supported. Gaultheria series Trichophyllae form a clade with three species and one variety that is sister to a clade of the remaining 16 species; the latter comprises seven main subclades. Interspecific relationships within the series are strongly supported except for those based on the coding-region and IRa-region datasets. Eight divergence hotspot regions, each possessing >5% percent variable sites, were screened across the whole plastid genome of the 28 individuals sampled in the series. Results of morphological character evolution reconstruction diagnose several clades, and a hypothesis of adaptive evolution for plant habit is postulated.

Characterization of the complete chloroplast genome of Elaeagnus mollis, a rare and endangered oil plant

Elaeagnus mollis is a rare and endangered oil tree species endemic to China. Here we assembled and characterized its whole chloroplast (cp) genome using Illumina pair-end sequencing data. The E. mollis cp genome was 151,428 bp in length, containing a large single copy region (LSC) of 81,003 bp and a small single copy region (SSC) of 18,561 bp separated by a pair of inverted repeats (IRs) of 25,932 bp. The genome possessed 131 genes, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Most of genes occurred as single-copy, while 18 gene species had two copies. The overall GC content of the E. mollis cp genome was 37.0%, and the corresponding values of LSC, SSC and IR regions were 35.0, 30.3 and 42.2%, respectively. The phylogenomic analysis revealed that E. mollis clustered with E. macrophylla in Elaeagnaceae, which was closely related to Moraceae and Cannabaceae belonging to Rosales.

Complete chloroplast genomes from apomictic Taraxacum (Asteraceae): Identity and variation between three microspecies.

Chloroplast DNA sequences show substantial variation between higher plant species, and less variation within species, so are typically excellent markers to investigate evolutionary, population and genetic relationships and phylogenies. We sequenced the plastomes of Taraxacum obtusifrons Markl. (O978); T. stridulum Trávniček ined. (S3); and T. amplum Markl. (A978), three apomictic triploid (2n = 3x = 24) dandelions from the T. officinale agg. We aimed to characterize the variation in plastomes, define relationships and correlations with the apomictic microspecies status, and refine placement of the microspecies in the evolutionary or phylogenetic context of the Asteraceae. The chloroplast genomes of accessions O978 and S3 were identical and 151,322 bp long (where the nuclear genes are known to show variation), while A978 was 151,349 bp long. All three genomes contained 135 unique genes, with an additional copy of the trnF-GGA gene in the LSC region and 20 duplicated genes in the IR region, along with short repeats, the typical major Inverted Repeats (IR1 and IR2, 24,431bp long), and Large and Small Single Copy regions (LSC 83,889bp and SSC 18,571bp in O978). Between the two Taraxacum plastomes types, we identified 28 SNPs. The distribution of polymorphisms suggests some parts of the Taraxacum plastome are evolving at a slower rate. There was a hemi-nested inversion in the LSC region that is common to Asteraceae, and an SSC inversion from ndhF to rps15 found only in some Asteraceae lineages. A comparative repeat analysis showed variation between Taraxacum and the phylogenetically close genus Lactuca, with many more direct repeats of 40bp or more in Lactuca (1% larger plastome than Taraxacum). When individual genes and non-coding regions were for Asteraceae phylogeny reconstruction, not all showed the same evolutionary scenario suggesting care is needed for interpretation of relationships if a limited number of markers are used. Studying genotypic diversity in plastomes is important to characterize the nature of evolutionary processes in nuclear and cytoplasmic genomes with the different selection pressures, population structures and breeding systems.

Complete Chloroplast Genome of Medicinal Plant Lonicera japonica: Genome Rearrangement, Intron Gain and Loss, and Implications for Phylogenetic Studies.

The complete chloroplast (cp) genome of Lonicera japonica, a common ornamental and medicinal plant in North America and East Asia, was sequenced and analyzed. The length of the L. japonica cp genome is 155,078 bp, contains a pair of inverted repeat regions (IRa and IRb), of 23,774 bp each, as well as large (LSC, 88,858 bp) and small (SSC, 18,672 bp) single-copy regions. A total of 129 genes were identified in the cp genome, 16 of which were duplicated within the IR regions. Relative to other plant cp genomes, the L. japonica cp genome had a unique rearrangement between trnI-CAU and trnN-GUU. In L. japonica cpDNA, rps19, rpl2, and rpl23 move to the LSC region, from the IR region. The ycf1 pesudogene in the IR region is lost, and only one copy locates in the SSC region. Comparative cp DNA sequence analyses of L. japonica with other cp genomes reveal that the gene order, and the gene and intron contents, are slightly different. The introns in ycf2 and rps18 genes are found for the first time. Four genes (clpP, petB, petD, and rpl16) lost introns. However, its genome structure, GC content, and codon usage were similar to those of typical angiosperm cp genomes. All preferred synonymous codons were found to use codons ending with A/T. The AT-rich sequences were less abundant in the coding regions than in the non-coding ones. A phylogenetic analysis based on 71 protein-coding genes supported the idea that L. japonica is a sister of the Araliaceae species. This study identified unique characteristics of the L. japonica cp genome that contribute to our understanding of the cpDNA evolution. It offers valuable information for the phylogenetic and specific barcoding of this medicinal plant.

Characterization of the complete chloroplast genome of Carpinus tientaiensis

The complete chloroplast (cp) genome sequence of a rare xylophyta species, Carpinus tientaiensis, was determined by Illumina pair-end sequencing in this study. The whole cp genome was 160,104 bp in length, containing a large single copy region (LSC) of 91,509 bp and small single copy region (SSC) of 18,974 bp, which were separated by a pair of 26,033 bp and 26,143 bp inverted repeat regions (IRs). The genome contained 114 genes, including 71 protein-coding genes, 36 tRNA genes and 6 ribosomal RNA genes. The majority of these gene species occurred as a single copy and 15 gene species occurred in two copies. The overall AT content of C. tientaiensis chloroplast genome was 63.6%, while the corresponding values of the LSC, SSC and IR regions were 60.7%, 69.8% and 57.5%, respectively. A phylogenetic analysis demonstrated a close relationship between C. tientaiensis and Ostrya rehderiana.

Characterization of the complete chloroplast genome of Camptotheca acuminata

The whole chloroplast (cp) genome sequence of Camptotheca acuminata has been characterized from Illumina pair-end sequencing. The complete cp genome was 162,382 bp in length, containing a large single copy region (LSC) of 89,493 bp and a small single copy region (SSC) of 16,540 bp, which were separated by two inverted repeat (IR) regions of 56,648 bp. The genome contained 129 genes, including 83 protein-coding genes, 38 tRNA genes and 8 ribosomal RNA genes (4 rRNA species). The most of gene species occur as a single copy, while 18 gene species occur in double copies. The overall GC content of C. acuminata cp genome is 38%, while the corresponding values of the LSC, SSC and IR regions are 36.2, 32.7 and 42.3%, respectively. Further, phylogenetic analysis suggested that C. acuminata is closely related to the species of Davidia involucrata.

Characterization of the complete chloroplast genome of alfalfa (Medicago sativa) (Leguminosae)

Alfalfa is the most widely cultivated forage legume and one of the most economically valuable crops throughout the world. We sequenced the complete chloroplast genome of alfalfa, which is 128,574bp in size and contains only one copy of the inverted repeat (IR) in the results from the second generation of high-throughput sequencing platform, Illumina HiSeq 2000. The genome encodes 109 genes, including 4 ribosomal RNA genes, 30 tRNAs, and 75 protein-coding genes. The genes rps16, ycf4, and infA are absent in the alfalfa chloroplast genome, and ndhB has an internal stop codon in the 5′ exon, which is similar to what is observed in other legumes. The rps12 gene, minus its intron, is a trans-spliced gene with the 5′ end located in the LSC region, and the duplicated 3′ end is located in the IR regions. Relative to other legume chloroplast genomes, the alfalfa genome differs in total length, IR length, GC content, the number of total genes and the number of functional genes (including protein genes, pseudogenes, rRNA genes, and tRNA genes). Phylogenetic analysis based on 5 chloroplast genes demonstrates a close relationship between alfalfa and Medicago hybrida and provides strong support for the IRLC group. These results provide a solid foundation for chloroplast molecular biology and genetic breeding and molecular evolution of alfalfa.

Chloroplast Genome Sequence of Pigeonpea (Cajanus cajan (L.) Millspaugh) and Cajanus scarabaeoides (L.) Thouars: Genome Organization and Comparison with Other Legumes.

Pigeonpea (Cajanus cajan (L.) Millspaugh), a diploid (2n = 22) legume crop with a genome size of 852 Mbp, serves as an important source of human dietary protein especially in South East Asian and African regions. In this study, the draft chloroplast genomes of Cajanus cajan and Cajanus scarabaeoides (L.) Thouars were generated. Cajanus scarabaeoides is an important species of the Cajanus gene pool and has also been used for developing promising CMS system by different groups. A male sterile genotype harboring the C. scarabaeoides cytoplasm was used for sequencing the plastid genome. The cp genome of C. cajan is 152,242bp long, having a quadripartite structure with LSC of 83,455 bp and SSC of 17,871 bp separated by IRs of 25,398 bp. Similarly, the cp genome of C. scarabaeoides is 152,201bp long, having a quadripartite structure in which IRs of 25,402 bp length separates 83,423 bp of LSC and 17,854 bp of SSC. The pigeonpea cp genome contains 116 unique genes, including 30 tRNA, 4 rRNA, 78 predicted protein coding genes and 5 pseudogenes. A 50 kb inversion was observed in the LSC region of pigeonpea cp genome, consistent with other legumes. Comparison of cp genome with other legumes revealed the contraction of IR boundaries due to the absence of rps19 gene in the IR region. Chloroplast SSRs were mined and a total of 280 and 292 cpSSRs were identified in C. scarabaeoides and C. cajan respectively. RNA editing was observed at 37 sites in both C. scarabaeoides and C. cajan, with maximum occurrence in the ndh genes. The pigeonpea cp genome sequence would be beneficial in providing informative molecular markers which can be utilized for genetic diversity analysis and aid in understanding the plant systematics studies among major grain legumes.

The complete chloroplast genome of a rare candelabra primrose Primula stenodonta (Primulaceae)

The whole chloroplast genome (cp genome) of Primula stenodonta was sequenced using an Illumina platform. The cp genome is 150,785 bp in size, and exhibits a typical bicyclic and quadripartite structure, including a pair of inverted repeat regions (IRs) of 25,182 bp that are separated by large and small single copy regions of 82,682 and 17,739 bp, respectively. A total of 131 genes were identified, including 86 protein-coding genes (PCG), 37 tRNA genes, and eight ribosomal RNA (rRNA) genes. Among them, 18 genes occur in IRs, containing seven PCG, seven tRNA genes and four rRNA genes. The overall AT content of P. stenodonta cp genome is 62.9%, and the corresponding values of the LSC, SSC and IR regions are 65, 69.8 and 57%, respectively. The phylogenetic analysis suggested that the sampled Primula species formed a monophyletic clade, and P. stenodonta is closely related to Primula poissonii.

Characterization of the complete chloroplast genome of Platycarya strobilacea (Juglandaceae)

The whole chloroplast genome (cp genome) sequence of Platycarya strobilacea was characterized from Illumina pair-end sequencing data. The complete cp genome was 160,994 bp in length and contained a large single copy region (LSC) of 90,225 bp and a small single copy region (SSC) of 18,371 bp, which were separated by a pair of inverted repeat regions (IRs, 26,199 bp). The genome contained 130 genes, including 85 protein-coding genes (80 PCG species), 36 tRNA genes (29 tRNA species) and 8 ribosomal RNA genes (4 rRNA species). Most genes occur as a single copy, but 15 genes are duplicated. The overall AT content of the cp genome is 64 %, and the corresponding values of the LSC, SSC and IR regions are 66.4, 70.1 and 57.5 %, respectively. Phylogenetic analysis confirmed the placement of P. strobilacea near to Juglans.

Characterization of the whole chloroplast genome of an endangered species Primula kwangtungensis (Primulaceae)

The complete chloroplast genome (plastome) of Primula kwangtungensis was characterized through Illumina paired-end sequencing. The plastome is circular and 153,757 bp in length, comprising a pair of 25,855 bp inverted repeat regions (IRs) which are separated by a large single copy region (LSC) of 84,479 bp and a small single copy region (SSC) of 17,568 bp. The plastome contains 130 genes, including 85 protein-coding genes (PCGs), 37 tRNA genes and eight ribosomal RNA genes. Of these, seven PCGs, seven tRNA genes and four rRNA genes occur in double copies. The overall AT content of the P. kwangtungensis plastome is 62.9 %, while the corresponding values of the LSC, SSC and IR regions are 65, 69.6 and 57.3 %, respectively. The phylogenetic analysis suggested that the sampled Primula species formed a monophyletic clade, and P. kwangtungensis is closely related to P. sinensis.

Characterization of the complete chloroplast genome of Cycas panzhihuaensis

The whole chloroplast (cp) genome sequence of Cycas panzhihuaensis has been characterized from Illumina pair-end sequencing. The complete cp genome was 162,470 bp in length, containing a large single copy region (LSC) of 88,932 bp and a small single copy region (SSC) of 23,448 bp, which were separated by a pair of 25,045 bp inverted repeat regions (IRs). The genome contained 156 genes, including 109 protein-coding genes (98 PCG species), 39 tRNA genes (32 tRNA species) and eight ribosomal RNA genes (four rRNA species). The most of gene species occur as a single copy, while 22 gene species occur in double copies. The overall AT content of C. panzhihuaensis cp genome is 60.6 %, while the corresponding values of the LSC, SSC and IR regions are 61.3, 63.5 and 58.0 %, respectively. Further, phylogenetic analysis suggested that C. panzhihuaensis is closely related to the species of C. revoluta.

Characterization of the complete chloroplast genome of the endangered species Carya sinensis (Juglandaceae)

Carya sinensis (Chinese Hickory, beaked walnut, or beaked hickory) is an endangered species that needs urgent conservation action. Here, we reported the complete chloroplast (cp) genome sequence and the genomic features of the C. sinensis cp, which is the first complete cp genome of any member of Carya. The C. sinensis cp genome was 160,195 bp, containing a large single copy region (LSC) of 89,541 bp and a small single copy region (SSC) of 18,538 bp separated by a pair of 26,058 bp inverted repeat regions (IRs). The genome contained 135 genes, including 87 protein-coding genes (79 species), 40tRNA genes (30tRNA species) and eight ribosomal RNA genes (four rRNA species). Most genes occurred as a single copy; 22 were duplicated. The overall GC content of the C. sinensis cp genome was 36.3 %; the corresponding GC content values of the LSC, SSC and IR regions were 33.9, 30.0 and 42.5 %, respectively. A maximum likelihood (ML) phylogenetic analysis showed that C. sinensis is closely related to Juglans, as expected based on taxonomic affinity. The complete cp genome of C. sinensis will be useful for further investigations of genetic diversity and conservation of this endemic relict woody plant.

Plastid Genome of Seseli montanum: Complete Sequence and Comparison with Plastomes of Other Members of the Apiaceae Family.

This work reports the complete plastid (pt) DNA sequence of Seseli montanum L. of the Apiaceae family, determined using next-generation sequencing technology. The complete genome sequence has been deposited in GenBank with accession No. KM035851. The S. montanum plastome is 147,823bp in length. The plastid genome has a typical structure for angiosperms and contains a large single-copy region (LSC) of 92,620bp and a small single-copy region (SSC) of 17,481bp separated by a pair of 18,861bp inverted repeats (IRa and IRb). The composition, gene order, and AT-content in the S. montanum plastome are similar to that of a typical flowering plant pt DNA. One hundred fourteen unique genes have been identified, including 30 tRNA genes, four rRNA genes, and 80 protein genes. Of 18 intron-containing genes found, 16 genes have one intron, and two genes (ycf3, clpP) have two introns. Comparative analysis of Apiaceae plastomes reveals in the S. montanum plastome a LSC/IRb junction shift, so that the part of the ycf2 (4980bp) gene is located in the LSC, but the other part of ycf2 (1301bp) is within the inverted repeat. Thus, structural rearrangements in the plastid genome of S. montanum result in an enlargement of the LSC region by means of capture of a large part of ycf2, in contrast to eight Apiaceae plastomes where the complete ycf2 gene sequence is located in the inverted repeat.

Characterization of the complete chloroplast genome of Populus ilicifolia

The whole chloroplast (cp) genome sequence of Populus ilicifolia has been characterized from Illumina pair-end sequencing. The complete cp genome was 158,017 bp in length, containing a large single copy region (LSC) of 85,926 bp and a small single copy region (SSC) of 16,533 bp, which were separated by a pair of 27,780 and 27,778 bp inverted repeat regions (IRs). The genome contained 126 genes, including 82 protein-coding genes (75 PCG species), 36 tRNA genes (29 tRNA species) and 8 ribosomal RNA genes (4 rRNA species). The most of gene species occur as a single copy, while 18 gene species occur in double copies. The overall AT content of P. ilicifolia cp genome is 63.5 %, while the corresponding values of the LSC, SSC and IR regions are 65.7, 69.4 and 58.2 %, respectively. Further, phylogenetic analysis suggested that P. ilicifolia is closely related to P. euphratica.