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Anaplasma capra is an emerging tickborne human pathogen initially recognized in China in 2015; it has been reported in ticks and in a wide range of domestic and wild animals worldwide. We describe whole-genome sequences of 2 A. capra strains from metagenomic sequencing of purified erythrocytes from infected goats in China. The genome of A. capra was the smallest among members of the genus Anaplasma. The genomes of the 2 A. capra strains contained comparable G+C content and numbers of pseudogenes with intraerythrocytic Anaplasma species. The 2 A. capra strains had 54 unique genes. The prevalence of A. capra was high among goats in the 2 endemic areas. Phylogenetic analyses revealed that the A. capra strains detected in this study were basically classified into 2 subclusters with those previously detected in Asia. Our findings clarify details of the genomic characteristics of A. capra and shed light on its genetic diversity. [ABSTRACT FROM AUTHOR]

Background: Since the first report of carbapenem-resistant Klebsiella pneumoniae isolates in China in 2007, the prevalence of CRKP and CRE has increased significantly. However, the molecular characteristics of IMP-producing Klebsiella pneumoniae (IMPKp) are rarely reported. Methods: A total of 29 IMPKp isolates were collected from a Chinese tertiary hospital from 2011 to 2017. Clinical IMPKp were identified by VITEK®MS, and further analyzed by whole-genome DNA sequencing with HiSeq and PacBio RSII sequencer. Sequencing data were analyzed using CSI Phylogeny 1.4, Resfinder, PlasmidFinder and the MLST tool provided by the Centre for Genomic Epidemiology. The analysis results were visualized using iTOL editor v1_1. The open reading frames and pseudogenes were predicted using RAST 2.0 combined with BLASTP/BLASTN searches against the RefSeq database. The databases CARD, ResFinder, ISfinder, and INTEGRALL were performed for annotation of the resistance genes, mobile elements, and other features. The types of blaIMP in clinical isolates were determined by BIGSdb-Pasteur. Integrons were drawn by Snapgene, and the gene organization diagrams were drawn by Inkscape 0.48.1. Results: Four novel ST type, including ST5422, ST5423, ST5426 and ST5427 were identified. The IMP-4 and IMP-1 were the dominant IMP type. The majority of blaIMP-carrying plasmids belonged to IncN and IncHI5. Two novel blaIMP-carrying integrons (In2146 and In2147) were uncovered. A novel variant blaIMP-90 presented in novel integron In2147 has been identified. Conclusions: IMPKp showed low prevalence in China. Novel molecular characteristics of IMPKp have been identified. Continuous monitoring of IMPKp shall also be carried out in the future. [ABSTRACT FROM AUTHOR]

Background: Heteroplexis Chang is an endangered genus endemic to China with important ecological and medicinal value. However, due to the lack of genetic data, our conservation strategies have repeatedly been delayed by controversial phylogenetic (molecular) relationships within the genera. In this study, we reported three new Heteroplexis chloroplast (cp.) genomes (H. vernonioides, H. impressinervia and H. microcephala) to clarify phylogenetic relationships between species allocated in this genus and other related Compositae. Results: All three new cp. genomes were highly conserved, showing the classic four regions. Size ranged from 152,984 − 153,221 bp and contained 130 genes (85 protein-coding genes, 37 tRNA, eight rRNA) and two pseudogenes. By comparative genomic and phylogenetic analyses, we found a large-scale inversion of the entire large single-copy (LSC) region in H. vernonioides, H. impressinervia and H. microcephala, being experimentally verified by PCR. The inverted repeat (IR) regions showed high similarity within the five Heteroplexis plastomes, showing small-size contractions. Phylogenetic analyses did not support the monophyly of Heteroplexis genus, whereas clustered the five species within two differentiated clades within Aster genus. These phylogenetic analyses suggested that the five Heteroplexis species might be subsumed into the Aster genus. Conclusion: Our results enrich the data on the cp. genomes of the genus Heteroplexis, providing valuable genetic resources for future studies on the taxonomy, phylogeny, and evolution of Aster genus. [ABSTRACT FROM AUTHOR]

Burkholderia glumae is an important rice pathogen, thus the genomic and evolutionary history may be helpful to control this notorious pathogen. Here, we present two complete genomes of the B. glumae strains HN1 and HN2, which were isolated from diseased rice seed in China. Average nucleotide identity (ANI) analysis shows greater than 99% similarity of the strains HN1 and HN2 with other published B. glumae genomes. Genomic annotation revealed that the genome of strain HN1 consists of five replicons (6,680,415 bp) with an overall G + C content of 68.06%, whereas the genome of strain HN2 comprises of three replicons (6,560,085 bp) with an overall G + C content of 68.34%. The genome of HN1 contains 5434 protein-coding genes, 351 pseudogenes, and 1 CRISPR, whereas the genome of HN2 encodes 5278 protein-coding genes, 357 pseudogenes, and 2 CRISPR. Both strains encode many pathogenic-associated genes (143 genes in HN1 vs. 141 genes in HN2). Moreover, comparative genomic analysis shows the extreme plasticity of B. glumae, which may contribute to its pathogenicity. In total, 259 single-copy genes were affected by positive selection. These genes may contribute to the adaption to different environments. Notably, six genes were characterized as virulence factors which may be an additional way to assist the pathogenicity of B. glumae. [ABSTRACT FROM AUTHOR]

Three Gram-stain-positive, aerobic, motile actinobacterial strains designated as CPCC 205119T, CPCC 205215, and CPCC 205251 were isolated from different biological soil crust samples collected from Tengger Desert, China. The 16S rRNA gene sequence comparison of these three strains showed they had almost identical 16S rRNA genes, which were closely related to members of the family Geodermatophilaceae , with the highest similarities of 96.3–97.3% to the species of Modestobacter. In the phylogenetic tree based on 16S rRNA gene sequences, these isolates clustered into a subclade next to the branch containing the species of Modestobacter lapidis and Modestobacter multiseptatus , within the lineage of the genus Modestobacter. The comparative genomic characteristics (values of ANI, dDDH, AAI, and POCP) and the phenotypic properties (morphological, physiological, and chemotaxonomic characteristics) of these isolates readily supported to affiliate them to the genus Modestobacter as a single separate species. For which, we proposed that the isolates CPCC 205119T, CPCC 205215, and CPCC 205251 represent a novel species of the genus Modestobacter as Modestobacter deserti sp. nov. CPCC 205119T (=I12A-02624=NBRC 113528T=KCTC 49201T) is the type strain. The genome of strain CPCC 205119T consisted of one chromosome (4,843,235bp) containing 4,424 coding genes, 48 tRNA genes, five rRNA genes, three other ncRNA genes, and 101 pseudogenes, with G+C content of 74.7%. The whole-genome sequences analysis indicated that this species contained alkaline phosphatase genes (phoA / phoD), phosphate transport-related genes (phoU , phnC , phnD , phnE , phoB , phoH , phoP , phoR , pitH , ppk , pstA , pstB , pstC , and pstS), trehalose-phosphate synthase gene (otsA), trehalose 6-phosphate phosphatase gene (otsB) and other encoding genes for the properties that help the microorganisms to adapt to harsh environmental conditions prevalent in deserts. Strains of this species could solubilize tricalcium phosphate [Ca3(PO4)2] and phytin, assimilate pyrophosphate, thiophosphate, dithiophosphate, phosphoenol pyruvate, 2-deoxy-d-glucose-6-phosphate, and cysteamine-S-phosphate. [ABSTRACT FROM AUTHOR]

We report the complete chloroplast genome (plastome) sequences of Pedicularis cephalantha (147,087 bp) and P. nigra (145,726 bp), endemic to southwestern China. Both plastomes have typical quadripartite structures with one large-single copy region, one small-single copy region, and two inverted repeat regions. Both plastome sequences contained 37 tRNA genes and eight rRNA genes, but they differed in the numbers of protein-coding genes: P. cephalantha had 76 functional genes and 12 pseudogenes while P. nigra had 74 functional genes and 13 pseudogenes. Phylogenetic analysis shows that P. cephalantha and P. nigra are closely related, then sister to P. oederi in the family Orobanchaceae. [ABSTRACT FROM AUTHOR]

Background. Species in the genus Morus (Moraceae) are deciduous woody plants of great economic importance. The classification and phylogenetic relationships of Morus, especially the abundant mulberry resources in China, is still undetermined. Internal transcribed spacer (ITS) regions are among the most widely used molecular markers in phylogenetic analyses of angiosperms. However, according to the previous phylogenetic analyses of ITS sequences, most of the mulberry accessions collected in China were grouped into the largest clade lacking for phylogenetic resolution. Compared with functional ITS sequences, ITS pseudogenes show higher sequence diversity, so they can provide useful phylogenetic information. Methods. We sequenced the ITS regions and the chloroplast DNA regions TrnL-TrnF and TrnT-TrnL from 33 mulberry accessions, and performed phylogenetic analyses to explore the evolution of mulberry. Results We found ITS pseudogenes in 11 mulberry accessions. In the phylogenetic tree constructed from ITS sequences, clade B was separated into short-type sequence clades (clades 1 and 2), and a long-type sequence clade (clade 3). Pseudogene sequences were separately clustered into two pseudogroups, designated as pseudogroup 1 and pseudogroup 2. The phylogenetic tree generated from cpDNA sequences also separated clade B into two clades. Conclusions. Two species were separated in clade B. The existence of three connection patterns and incongruent distribution patterns between the phylogenetic trees generated from cpDNA and ITS sequences suggested that the ITS pseudogene sequences connect with genetic information from the female progenitor. Hybridization has played important roles in the evolution of mulberry, resulting in low resolution of the phylogenetic analysis based on ITS sequences. An evolutionary pattern illustrating the evolution history of mulberry is proposed. These findings have significance for the conservation of local mulberry resources. Polyploidy, hybridization, and concerted evolution have all played the roles in the evolution of ITS sequences in mulberry. This study will expand our understanding of mulberry evolution. [ABSTRACT FROM AUTHOR]

Passiflora caerulea is native to brazil. In recent years, the edible, medicinal, and ornamental value of P. caerulea has stimulated its wide cultivation in Southeast Asian countries, especially China. Because the chloroplast genome is rich with information about the species evolution as well as its genetic relationship to other species, the P. caerulea chloroplast genome was sequenced, assembled, and annotated in this study. The P. caerulea chloroplast genome is 151,362 bp in total with an overall GC content of 37.03%. It has a quadripartite structure, includes a large single-copy region (LSC, 85,623 bp), a small single-copy region (SSC, 13,397 bp), and two inverted repeat regions (IRa and IRb, 26,180 bp combined). There are 131 genes in the P. caerulea chloroplast genome, including 79 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 7 pseudogenes. Phylogenetic analysis of 29 Passiflora spp. showed that P. caerulea is most closely related to P. edulis. These results provide a considerable foundation for P. caerulea conservation genetics research. [ABSTRACT FROM AUTHOR]

Salix chienii W.C. Cheng (Salicaceae) is a dioecious small tree with high economic and medicinal value. In this study, we reported the complete chloroplast DNA (cpDNA) of S. chienii by employing HiSeq sequencing and de novo assembly. The chloroplast genome of S. chienii is 155,672 bp in length, with a 36.60% GC content; it contains one large single copy (LSC), one small single copy (SSC) and two inverted repeat (IR) regions with lengths of 84,494, 16,330, and 27,424 bp, respectively. A total of 132 genes were predicted, including 85 protein-coding genes, 37 tRNA genes, 8 rRNA genes and 2 pseudogenes. A maximum-likelihood phylogenetic tree showed that S. chienii is closely related to S. wilsonii and S. triandra. [ABSTRACT FROM AUTHOR]

Potentilla glabra Lodd is an important traditional Chinese medicine, which is widely distributed in many areas of China. It has a variety of pharmacological activities and has been drunk as a tea for a long time. Therefore, it has great economic, research, and social value. However, no plastid genome has been reported to date. Here, we report species of this genus complete chloroplast genome of Potentilla glabra Lodd. The chloroplast genome of Potentilla glabra Lodd is found to be 152,900 bp in length with 37.24% GC contents. The cp genome sequences contained 130 genes, including 84 mRNA genes, 37 tRNA, eight rRNA genes, and one pseudogenes, respectively. A phylogenetic tree reconstructed by 42 chloroplast genomes reveals that Potentilla glabra Lodd is most related with Potentilla parvifolia. The complete chloroplast genome of these plants will be benefit for studies on the general characteristics and evolution of the Potentilla family genome. [ABSTRACT FROM AUTHOR]

Lilium regale E.H.Wilson is a native lily species in western Sichuan of China and an important resource for lily breeding. In this study, the plastid genome of L. regale was assembled de novo using the next-generation sequencing data. The plastid genome of L. regale was 152,998 bp in length, with a typical quadripartite circle structure consisting of a small single-copy region of 17,529 bp, a large single-copy region of 82,375 bp, and a pair of inverted repeats of 26,547 bp each. A total of 137 different genes were predicted, including 84 protein-coding genes, 38 transfer RNA genes, 8 ribosomal RNA genes, and 7 pseudogenes. The overall GC content of the plastid genome was 36.98%. Phylogenetic analysis revealed that L. regale is most closely related to Lilium leucanthum. [ABSTRACT FROM AUTHOR]

The Castanea mollissima ‘Chuizhili’ is an important variety of C. mollissima in breeding for dwarf chestnut and ornamental trees due to the weeping characteristic in China. In this study, the complete chloroplast genome of C. mollissima ‘Chuizhili’ was identified and sequenced by using Illumina sequencing data. The genome size is 160,799 bp, with a large single-copy (LSC, 90,430 bp) region, a small single-copy (SSC, 18,997 bp) region, and separated by a pair of 25,686 bp inverted repeat (IR) regions. A total of 130 genes are successfully annotated, including 83 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 2 pseudo-genes. The phylogenetic relationships revealed that C. mollissima ‘Chuizhili’ is closely related to Castanea henryi in Fagaceae. [ABSTRACT FROM AUTHOR]

Hosta plantaginea is an important ornamental and horticultural plant endemic to China. In this study, we generated complete chloroplast genome of H. plantaginea using high-throughput sequencing. The complete chloroplast sequence is a circular molecule of 157,091 bp in size, consisting of a large single copy (LSC, 86,061 bp) and a small single copy (SSC; 18,282 bp) separated by a pair of inverted repeats (IRs; 26,374 bp), The total GC content is 37.8%, with 35.9, 31.7, and 43.0% in LSC, SSC, and IRs, respectively. A total of 132 genes are annotated, including 84 protein-coding genes, 38 tRNAs, 8 rRNAs, and 2 pseudogenes. The phylogenetic analysis revealed that H. plantaginea was formed to be the early diverging species within Hosta. [ABSTRACT FROM AUTHOR]

Study Question: How does ectopic endometrial stromal cell (Ecto-ESC)-derived extracellular vesicular Legumain pseudogene 1 (EV-LGMNP1), a newly identified pseudogene of Legumain (LGMN), contribute to M2-phenotype macrophage polarization, and does it predict recurrence in patients with ovarian endometriosis (EMs)?, Summary Answer: EV-LGMNP1, which is abundant in Ecto-ESCs and serum from ovarian EMs, can direct macrophages towards an M2 phenotype by upregulating LGMN expression and is a promising biomarker for predicting ovarian EMs recurrence., What Is Known Already: Extracellular vesicles (EVs) can mediate cell-to-cell crosstalk to promote disease progression via cargo molecule transport. Recently, LGMNP1, a newly identified pseudogene of LGMN, has been reported to promote cancer progression by upregulating LGMN. LGMN is a well-studied protein that can induce M2-like polarization., Study Design, Size, Duration: An in vitro study was conducted with Ecto-ESCs isolated from ectopic endometrial samples, collected from two patients with ovarian EMs (diagnosed by laparoscopy and histological analysis). A clinical retrospective cohort study of 52 ovarian EMs patients and 21 controls with available preoperative serum samples was carried out (2013-2017). The follow-up period ended either at the time of recurrence or on 31 December 2018., Participants/materials, Setting, Methods: Ecto-ESC-derived EVs (EV/Ecto-ESCs) were characterized by nanoparticle tracking analysis, transmission electron microscopy and western blotting. EV internalization by THP-1 cells, which are the most widely used primary human macrophages model, was detected by fluorescence labelling. After EV treatment, THP-1 cell polarization was detected by quantitative real-time PCR (qRT-PCR) and western blot analyses of CD86 (M1-related marker) and CD206 (M2-related marker). LGMNP1 mRNA expression level in EVs from both primary ectopic endometrioc stromal cells and serum was examined using qRT-PCR. Additionally, the expression of LGMN, the downstream target gene of LGMNP1, in THP-1 cells was evaluated using qRT-PCR and western blotting. Kaplan-Meier and multivariate Cox regression analyses were applied to evaluate the independent predictive factors of EMs recurrence-free survival. A novel nomogram model based on serum EV-LGMNP1 was then formulated to predict EMs recurrence., Main Results and the Role of Chance: In vitro assays demonstrated that EV/Ecto-ESCs drove macrophages towards an M2-like phenotype. Moreover, LGMNP1 contributed to EV/Ecto-ESC-induced M2 macrophage polarization by upregulating LGMN mRNA expression levels. Clinically, serum EV-LGMNP1 was more highly expressed in recurrent EMs patients than in controls and EMs patients without recurrence. Survival analysis and our novel nomogram reconfirmed that serum EV-LGMNP1 was a novel promising and meaningful non-invasive biomarker for predicting EMs recurrence., Large Scale Data: N/A., Limitations, Reasons for Caution: In vitro experiments were only performed on samples from two patients with ovarian endometriosis, and a larger sample size is needed. ESCs isolated from the eutopic endometrium of EMs and non-EMs patients should be studied in the future. Additionally, in vitro experiments should be performed using endometrial epithelium cells and further in vivo experiments, such as using mice endometriotic models to investigate whether EV/Ecto could induce M2 macrophage polarization, should be conducted. Moreover, multicentre, large-sample data are needed to validate our predictive nomogram model., Wider Implications of the Findings: Our study provides novel insights into the mechanism of M2 polarization involved in ovarian EMs progression mediated by an 'EV-shuttled pseudogene LGMNP1' mode. In addition, serum EV-LGMNP1 may serve as a novel non-invasive biomarker for predicting recurrence, providing a new therapeutic target for ovarian EMs., Study Funding/competing Interest(s): This project was supported by funding from the National Natural Science Foundation of China (81971361), the Natural Science Foundation of Shanghai Science and Technology (19ZR1406900), the Shanghai 'Rising Stars of Medical Talent' Youth Development Program (AB83030002019004), the Clinical Research Plan of SHDC (SHDC2020CR4087), the Shanghai Municipal Health Commission (202040498), the Research and Innovation Project of the Shanghai Municipal Education Commission (2019-01-07-00-07-E00050) and the Clinical Research Plan of SHDC (SHDC2020CR1045B). There are no competing interests to declare., (© The Author(s) 2021. Published by Oxford University Press on behalf of European Society of Human Reproduction and Embryology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Mosquitoes are insects of the Diptera, Nematocera, and Culicidae families, some species of which are important disease vectors. Identifying mosquito species based on morphological characteristics is difficult, particularly the identification of specimens collected in the field as part of disease surveillance programs. Because of this difficulty, we constructed DNA barcodes of the cytochrome c oxidase subunit 1, the COI gene, for the more common mosquito species in China, including the major disease vectors. A total of 404 mosquito specimens were collected and assigned to 15 genera and 122 species and subspecies on the basis of morphological characteristics. Individuals of the same species grouped closely together in a Neighborhood-Joining tree based on COI sequence similarity, regardless of collection site. COI gene sequence divergence was approximately 30 times higher for species in the same genus than for members of the same species. Divergence in over 98% of congeneric species ranged from 2.3% to 21.8%, whereas divergence in conspecific individuals ranged from 0% to 1.67%. Cryptic species may be common and a few pseudogenes were detected. [ABSTRACT FROM AUTHOR]

Clematis guniuensis is a new plant species in China, which distributes in both provinces of Zhejiang and Anhui with extremely small population. The whole chloroplast (CP) genome was assembled by NovoPlasty using high-throughput sequencing data generated by an Illumina Hiseq X Ten platform. The circular chloroplast genome is 159,682 bp in length, and comprises a large single copy of 79,461 bp, a small single copy of 49,156 bp, and two inverted repeats of 31,064 bp each. The CP genome contains 137 genes, including 89 protein-coding genes, eight rRNA genes, 36 tRNA genes, and four pseudogenes. All the pseudogenes were infA, rpl32, ycf1, and ndhK. Phylogenetic analysis results indicated that C. guniuensis was sister to C. trichotoma, with a support rate of 100%. [ABSTRACT FROM AUTHOR]

Stephania kwangsiensis (Menispermaceae) is a rare and critically endangered species endemic to China. Here, we first report and characterize its complete chloroplast genome sequence based on Illumina paired-end sequencing data. The complete plastid genome was 156,624 bp, which contained inverted repeats (IR) of 24,348 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 87,759 bp and 20,169 bp, respectively. The cpDNA contains 132 genes, comprising 85 protein-coding genes, 37 tRNA genes, eight rRNA genes, and two processed pseudogenes. The overall GC content of the plastome is 38.4%. The phylogenetic analysis of 18 selected chloroplast genomes demonstrated that S. kwangsiensis is related to the congeneric S. japonica. [ABSTRACT FROM AUTHOR]

Dysosma versipellis (Berberidaceae) is a rare and threatened medicinal herb endemic to subtropical China. Here, we first report and characterize its complete chloroplast genome based on Illumina paired-end sequencing data. The complete plastid genome was 156,735 bp, which contained inverted repeats (IR) of 25,925 bp separated by a large single copy (LSC) and a small single copy (SSC) of 86,514 bp and 18,371 bp, respectively. The cpDNA contains 133 genes, comprising 86 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 2 processed pseudogenes. The overall GC content of the plastome is 38.5%. The phylogenetic analysis of 17 selected chloroplast genomes demonstrated that D. versipellis is closely related to the congeneric D. pleiantha. [ABSTRACT FROM AUTHOR]

Hemsleya zhejiangensis is a rare and endangered plant species which is listed as a key protected wild plant in Zhejiang province, China. In our present study, we assembled the complete chloroplast (CP) genome of H. zhejiangensis using high-throughput sequencing data. The whole genome sequence of H. zhejiangensis is 157,289 bp in size, with a GC content of 37.1%. Sequencing analyses reveal that the CP genome encodes 133 genes, including 84 protein-coding genes, 8 rRNA genes, 37 tRNA genes, and four pseudogenes. Phylogenetic analysis results indicate that H. zhejiangensis is clustered with H. lijiangensis, with a support value of 100%, and they are sister to the three Gynostemma species. [ABSTRACT FROM AUTHOR]

Gynostemma pentaphyllum (Cucurbitaceae) is a perennial medicinal herb widely distributed in China. It's well known for its medicinal values due to contains important medicinal components gypenosides. Here, we first report and characterize its complete chloroplast genome based on Illumina paired-end sequencing data. The complete plastid genome was 154,457 bp, which contained inverted repeats (IR) of 25,603 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 84,998 bp and 18,253 bp, respectively. The cpDNA contains 132 genes, comprising 81 protein-coding genes, 37 tRNA genes, 8 rRNA genes and six processed pseudogenes. The overall GC content of the plastome is 37.1%. The phylogenetic analysis of 17 selected chloroplast genomes demonstrated that G. pentaphyllum is closely related to the congeneric G. compressum. [ABSTRACT FROM AUTHOR]

Taxillus chinensis (DC) Danser, which is a hemiparasitic shrub distributed in southern China and Southeast Asian countries, is wildly used in various traditional Chinese medicine prescriptions. In this study, the complete chloroplast genome of the T. chinensis was assembled from the whole genome Illumina sequencing data. The complete plastome is a typical quadripartite structure with a length of 121,305 bp, which contained two inverted repeats (IRs) of 22,460 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 70,295 bp and 6090 bp, respectively. The plastome contains 106 genes, comprising 66 protein-coding genes, 28 tRNA genes, eight rRNA genes, and four processed pseudogenes. The overall GC content of the plastome is 37.4%, which is unevenly distributed across the whole chloroplast genome. The phylogenetic analysis shows that T. chinensis was closely related to the congeneric species T. sutchuenensis. [ABSTRACT FROM AUTHOR]

Epimedium sagittatum is an important traditional medicinal plant in China. In this study, we assembled the complete chloroplast (cp) genome of E. sagittatum. The whole cp genome of E. sagittatum is 157,114 bp in length, comprising a pair of inverted repeat (IR) regions (25,775 bp) separated by a large single copy (LSC) region (88,507 bp) and a small single copy (SSC) region (17,057 bp). The E. sagittatum cp genome contains 133 genes, of which 82 protein-coding genes, 38 tRNA genes, 8 rRNA genes and 5 pseudogenes. Phylogenetic analysis shows that E. sagittatumis closely clustered with E. lishihchenii. This genome provides a wealth of information for distinguishing of Epimedium species. [ABSTRACT FROM AUTHOR]

Rheum rhabarbarum is widely used in China to treat gout and constipation. We assembled and annotated the complete chloroplast genome of R. rhabarbarum. The length of the chloroplast genome is 161,723 bp, including a large single-copy (LSC) region of 87,004 bp, a small single-copy (SSC) region of 12,761 bp, and a pair of inverted repeat (IR) regions of 30,979 bp. The chloroplast genome included 130 genes, consisting of 36 tRNA genes, 8 rRNA genes, 2 pseudogenes, and 84 protein-coding genes. Phylogenetic analysis confirmed the position of R. rhabarbarum within the family Polygonaceae. [ABSTRACT FROM AUTHOR]

Isoetes yunguiensis is a rare and endangered fern endemic to Yunnan–Guizhou Plateau, China. The complete chloroplast genome sequence of I. yunguiensis was generated by de novo assembly using whole genome next-generation sequencing. The cp genome of I. yunguiensis was a circular structure and 145,355 bp in length, comprising a pair of inverted repeat (IR) regions of 26,130 bp, a large single copy (LSC) of 91,923 bp, and a small single copy (SSC) of 27,302 bp. The genome encoded 124 unique genes consisting of 82 protein-coding genes, 32 transfer RNA, four ribosomal RNA genes, and six pseudogenes. A maximum-likelihood phylogenetic analysis revealed that I. yunguiensis was closely related to I. butleri, I. engelmannii, I. flaccida, I. melanospora, and I. valida, with strong support values. [ABSTRACT FROM AUTHOR]

Pteroceltis tatarinowii is an endangered Tertiary relict tree endemic to China with high ecological and economic value. Meanwhile, P. tatarinowii is the sole representative of the genus Pteroceltis Maxim., thus it is of great importance to the phylogenetic studies of Ulmaceae. Here, we first conducted the paired-end shotgun sequencing of P. tatarinowii on the Illumina HiSeq platform. Based on the resulting sequence, the complete chloroplast (cp) genome of P. tatarinowii was 158,635 bp long and displayed a typical quadripartite structure consisting of a pair of inverted repeats (IRs) with a length of 26,020 bp, separating by two single-copy regions (LSC, 87,627 bp and SSC, 18,968 bp). Besides, it encoded 119 genes, including 80 protein-coding genes, 29 transfer RNAs, eight ribosomal RNAs, and two pseudogenes. Moreover, a maximum likelihood (ML) phylogenetic analysis based on the 14 cp genomes revealed that P. tatarinowii was closely related to the genus Cannabis and the Ulmaceae species did not form a monophyletic clade. [ABSTRACT FROM AUTHOR]

Taxillus nigrans (Hance) Danser (Loranthaceae) is a widely distributed mistletoe species in low mountains, hills, and river basins in subtropical areas of southwestern China. The whole chloroplast (cp) genome sequence of T. nigrans has been characterized using Illumina pair-end sequencing. The complete cp genome was 121,419 bp in length, containing a large single copy (LSC) region of 70,181 bp and a small single copy (SSC) region of 6100 bp, which were separated by a pair of 22,569 bp inverted repeat (IRs) regions. The genome contained 106 genes, including 66 protein-coding genes, 28 tRNA genes, 8 ribosomal RNA genes, and 4 pseudogenes. The most of gene species occur as a single copy, while 15 gene species occur in double copies. The overall GC content of T. nigrans cp genome is 37.4%, while the corresponding values of the LSC, SSC, and IR regions are 34.8, 26.3, and 42.95%, respectively. Phylogenetic analysis revealed that T. nigrans is closely related to T. sutchuenensis, with strong support values. [ABSTRACT FROM AUTHOR]

Aim: To investigate DNA methylation changes in placenta tissues associated with small for gestational age (SGA). Materials & methods: A prospective cohort study consisting of 1292 pregnant women from China (including 39 SGA with placenta tissues) was performed, microarray and pyrosequencing were conducted. Results:  Total 2012 methylation variable positions stood out from all probes (p < 0.05; Δβ > 0.2). In SGA cases, a CpG site within ANKRD20B showed lower methylation level (p = 0.032) than appropriate for gestational age in validation cohort. Five sites within FAM198A (p = 0.047, 0.050, 0.039, 0.026 and 0.043, respectively) had a reduced methylation in male newborns whose mother had preconception folic acid supplementation. Conclusion: DNA methylation changes in placenta tissues may be associated with SGA, maternal preconception folic acid supplementation status and also be fetal sex-specific.

Background: A member of the TaHKT2;1 multigene family was previously identified as a Na(+) transporter with a possible role in root Na(+) uptake. In the present study, the existing full-length cDNA of this member was used as a basis to query the International Wheat Genome Survey Sequence to identify all members of the TaHKT2;1 family. Individual TaHKT2;1 genes were subsequently studied for gene and predicted protein structures, promoter variability, tissue expression and their role in Na(+) and K(+) status of wheat., Results: Six TaHKT2;1 genes were characterized which included four functional genes (TaHKT2;1 7AL-1, TaHKT2;1 7BL-1, TaHKT2;1 7BL-2 and TaHKT2;1 7DL-1) and two pseudogenes (TaHKT2;1 7AL-2 and TaHKT2;1 7AL-3), on chromosomes 7A, 7B and 7D of hexaploid wheat. Variability in protein domains for cation specificity and in cis-regulatory elements for salt response in gene promoters, were identified amongst the functional TaHKT2;1 members. The functional genes were expressed under low and high NaCl conditions in roots and leaf sheaths, but were down regulated in leaf blades. Alternative splicing events were evident in TaHKT2;1 7AL-1. Aneuploid lines null for each functional gene were grown in high NaCl nutrient solution culture to identify potential role of each TaHKT2;1 member. Aneuploid lines null for TaHKT2;1 7AL-1, TaHKT2;1 7BL-1 and TaHKT2;1 7BL-2 showed no difference in Na(+) concentration between Chinese Spring except for higher Na(+) in sheaths. The same aneuploid lines had lower K(+) in roots, sheath and youngest fully expanded leaf but only under high (200 mM) NaCl in the external solution. There was no difference in Na(+) or K(+) concentration for any treatment between aneuploid line null for the TaHKT2;1 7DL-1 gene and Chinese Spring., Conclusions: TaHKT2;1 is a complex family consisting of pseudogenes and functional members. TaHKT2;1 genes do not have an apparent role in controlling root Na(+) uptake in bread wheat seedlings under experimental conditions in this study, contrary to existing hypotheses. However, TaHKT2;1 genes or, indeed other genes in the same chromosome region on 7AL, are candidates that may control Na(+) transport from root to sheath and regulate K(+) levels in different plant tissues.

The tripartite motif protein (TRIM)5α/CypA fusion protein TRIMCyp in Old World monkeys is generally considered unable to restrict HIV-1 replication. Monkeys with TRIMCyp can serve as a unique animal model for studies of HIV-1 infection. The present study investigated the distribution and expression status of TRIMCyp in four species of macaques originating from China and its borderlands: pigtail macaques (Macaca nemestrina), rhesus macaques (Macaca mulatta), long-tailed macaques (Macaca fascicularis), and Tibetan macaques (Macaca thibetana). The results revealed that the frequencies of the TRIMCyp genotype were significantly different among different species and even within different populations of the same species. Interestingly, the TRIMCyp genotype was more prevalent among macaques originating from Yunnan and surrounding regions than those from other regions of China. Importantly, TRIMCyp individuals were first identified in Chinese M. mulatta originating from Yunnan, although multiple earlier studies failed to find CypA retrotransposition in this subspecies. Furthermore, TRIMe7-CypA, one of the splicing isoforms of the TRIMCyp transcript was expressed in M. nemestrina and M. mulatta but not M. fascicularis. The intra- and interspecies polymorphisms in the deduced TRIMCyp amino acid sequences of these macaques were also analyzed. Taken together, the data in this study provide important information about the genomic background of TRIMCyp among major species of Chinese macaques.

Developmental dysplasia of the hip is the most frequent inborn deformity of the locomotor apparatus. Genetic factors play a considerable role in pathogenesis of Developmental dysplasia of the hip. Recently, several DVWA SNPs were found to be consistent and most significantly associated in Japanese and Han Chinese knee OA studies. Its functions may be associated with cartilage. It may be involved in etiology and pathogenesis of Developmental dysplasia of the hip. Our objective is to evaluate whether the DVWA SNPs (rs7639618, rs9864422 and rs11718863) are associated with Developmental dysplasia of the hip in Han Chinese. Three SNPs rs7639618, rs9864422 and rs11718863 (in DVWA) were genotyped using a Taqman 5' allelic discrimination assay on an ABI 7500 real-time polymerase chain reaction (PCR) instrument in 368 children who suffered from Developmental dysplasia of the hip and 508 control subjects, and analyzed their associations. The genotype distribution and allele frequency were compared between Developmental dysplasia of the hip and healthy control. Neither genotype distributions nor allelic frequencies of the assayed single nucleotide polymorphisms were found to be significantly different between patients and controls. There was also no significant difference when the patients were stratified by sex or severity (all P > 0.05). Our results indicate that DVWA does not seem to be a risk factor for Developmental dysplasia of the hip etiology in Chinese Han population.

Plague is a natural focus-based disease, and for better understanding of this disease it is crucial to determine the molecular mechanisms of its pathogen, Yersinia pestis, for adapting to different foci. Gene inactivation, loss and acquisition are the main mechanisms that contribute to a pathogen's fitness. Determination of the whole-genome sequences of three Y. pestis strains, CO92, KIM and 91001, provided a good opportunity to probe into its genome in minute detail. Many genetic variations were found between the three strains. The present work focused on adaptive microevolutionary analysis of Y. pestis from different natural plague foci in China based on pseudogene profiles. Twenty-four mutations that led to inactivation in the corresponding genes were analysed, and a PCR-based screening method was employed to investigate the distribution of these mutations among Y. pestis isolates from different foci and also among seven strains of Yersinia pseudotuberculosis. It was found that Y. pestis isolates from the same focus had identical mutation profiles, and 260 isolates of Y. pestis were divided into eight genotypes, while Y. pseudotuberculosis harboured wild-type alleles for all the mutations. The isolates of three known biovars were grouped into distinct branches in the phylogenetic tree, which supports the proposition that biovars mediaevalis and orientalis directly arose from biovar antiqua individually. The constructed phylogenetic tree suggests that the isolates from focus B should be the oldest lineage of Y. pestis in China except for isolates from foci L and M, which might be a special lineage of Y. pestis and originated differently to the others.

A PCR-based screening method was used to study the genetic variations of the pgm locus among natural isolates of Yersinia pestis from China. Our results indicate that genetic variations in the pgm locus are well correlated with biovars of Y. pestis and plague foci, suggesting that the pgm locus plays a role in Y. pestis adaptation to its environment. The gene encoding two-component regulatory system sensor kinase became a pseudogene in all strains of biovar Orientalis due to a thymidine deletion, while it is intact in all the strains of the other biovars. Only strains from Foci H and L are the same as Yersinia pseudotuberculosis in that they have an intact transmembrane helix in the sensor kinase protein, which is lost in all the other strains because of the 18 bp in-frame deletion. The IS100 element that flanks the 39 terminus of the pgm locus was inserted into the chromosome during the within-species microevolution of Y. pestis, which is absent in strains from Foci G, H and L and also in Y. pseudotuberculosis. This fact indicates that the strains from these three foci are of an older lineage of Chinese Y. pestis. It is this IS100 element's absence that maintained high stability of the pgm locus in the Y. pestis strains from these three foci. The IS285 element insertion in the pigmentation segment and the IS100 element insertion in the downstream flanking region of the pgm locus are only present in strains from Foci H and L. The flanking region outside the 59 terminus of the upstream IS100 element is identical in the strains from these two foci, which is different in the other strains. All of these unique characteristics suggest that they are of a special lineage of Chinese Y. pestis.