Added value of spectral computed tomography quantitative parameters for differentiating tuberculosis-associated fibrosing mediastinitis from endobronchial lung cancer: initial results

OBJECTIVE

The objective of this study was to explore the added value of spectral computed tomography (CT) parameters to conventional CT features for differentiating tuberculosis-associated fibrosing mediastinitis (TB-associated FM) from endobronchial lung cancer (EBLC).

METHODS

Chest spectral CT enhancement images from 109 patients with atelectasis were analyzed retrospectively. These patients were divided into two distinct categories: the TB-associated FM group (n = 77) and the EBLC group (n = 32), based on bronchoscopy and/or pathological findings. The selection of spectrum parameters was optimized with the least absolute shrinkage and selection operator regression analysis. The relationship between the spectrum parameters and conventional parameters was explored using Pearson's correlation. Multivariate logistic regression analysis was used to build spectrum model. The spectrum parameters in the spectrum model were replaced with their corresponding conventional parameters to build the conventional model. Diagnostic performances were evaluated using receiver operating characteristic curve analyses.

RESULTS

There was a moderate correlation between the parameters ㏒(L-AEFNIC) - ㏒(L-AEFC) (r= 0.419; p< 0.0001), ㏒(O-AEF40KeV) - ㏒(O-AEFC) (r= 0.475; p< 0.0001), [L-A-hydroxyapatite {HAP}(I)] - (L-U-CT) (r= 0.604; p< 0.0001), {arterial enhancement fraction (AEF) derived from normalized iodine concentration (NIC) of lymph node (L-AEFNIC), AEF derived from CT40KeV of bronchial obstruction (O-AEF40KeV), arterial-phase Hydroxyapatite (Iodine) concentration of lymph node [L-A-HAP(I)], AEF derived from conventional CT (AEFC), unenhanced CT value (U-CT)}. Spectrum model could improve diagnostic performances compared to conventional model (area under curve: 0.965 vs 0.916, p= 0.038).

CONCLUSION

There was a moderate correlation between spectrum parameters and conventional parameters. Integrating conventional CT features with spectrum parameters could further improve the ability in differentiating TB-associated FM from EBLC.

Correlation of pericoronary adipose tissue CT attenuation values of plaques and periplaques with plaque characteristics

AIM

To investigate the relationship between different plaque characteristics and pericoronary adipose tissue (PCAT) computed tomography (CT) attenuation values for plaques and periplaques.

MATERIALS AND METHODS

The data from 188 eligible patients with stable coronary heart disease (280 lesions) who underwent coronary CT angiography between March 2021 and November 2021 were collected retrospectively. All PCAT CT attenuation values of plaques and periplaques (the area within 5 and 10 mm proximal and distal to the plaque) were calculated, and multiple linear regression was used to assess their correlation with different plaque characteristics.

RESULTS

PCAT CT attenuation of plaques and periplaques was higher in non-calcified plaques (-73.38 ± 10.41 HU, -76.77 ± 10.86 HU, 79.33 ± 11.13 HU, -75.67 ± 11.24 HU, -78.63 ± 12.09 HU) and mixed plaques (-76.83 ± 8.11 HU, -79 [-85, -68.5] HU, -78.55 ± 11 HU, -78.76 ± 9.9 HU, -78.79 ± 11.06 HU) than in calcified plaques (-86.96 ± 10 HU, -84 [-92, -76] HU, -84.14 ± 11.08 HU, -84.91 ± 11.41 HU, -84.59 ± 11.69 HU; all p<0.05) and higher in distal segment plaques than in proximal segment plaques (all p<0.05). Plaque PCAT CT attenuation was lower in plaques with minimal stenosis than in plaques with mild or moderate stenosis (p<0.05). The significant determinants of PCAT CT attenuation values of plaques and periplaques were non-calcified plaques, mixed plaques, and plaques located in the distal segment (all p<0.05).

CONCLUSIONS

PCAT CT attenuation values in both plaques and periplaques were related to plaque type and location.

[Establishment and validation of a nomogram for predicting prognosis of gastric neuroendocrine neoplasms based on data from 490 cases in a single center]

OBJECTIVE

To develop and validate a nomogram for predicting outcomes of patients with gastric neuroendocrine neoplasms (G-NENs).

METHODS

We retrospectively collected the clinical data from 490 patients with the diagnosis of G-NEN at our medical center from 2000 to 2021. Log-rank test was used to analyze the overall survival (OS) of the patients. The independent risk factors affecting the prognosis of G-NEN were identified by Cox regression analysis to construct the prognostic nomogram, whose performance was evaluated using the C-index, receiver-operating characteristic (ROC) curve, area under the ROC curve (AUC), calibration curve, DCA, and AUDC.

RESULTS

Among the 490 G-NEN patients (mean age of 58.6±10.92 years, including 346 male and 144 female patients), 130 (26.5%) had NET G1, 54 (11.0%) had NET G2, 206 (42.0%) had NEC, and 100 (20.5%) had MiNEN. None of the patients had NET G3. The numbers of patients in stage Ⅰ-Ⅳ were 222 (45.3%), 75 (15.3%), 130 (26.5%), and 63 (12.9%), respectively. Univariate and multivariate analyses identified age, pathological grade, tumor location, depth of invasion, lymph node metastasis, distant metastasis, and F-NLR as independent risk factors affecting the survival of the patients (P < 0.05). The C-index of the prognostic nomogram was 0.829 (95% CI: 0.800-0.858), and its AUC for predicting 1-, 3- and 5-year OS were 0.883, 0.895 and 0.944, respectively. The calibration curve confirmed a good consistency between the model prediction results and the actual observations. For predicting 1-year, 3-year and 5-year OS, the TNM staging system and the nomogram had AUC of 0.033 vs 0.0218, 0.191 vs 0.148, and 0.248 vs 0.197, respectively, suggesting higher net benefit and better clinical utility of the nomogram.

CONCLUSION

The prognostic nomogram established in this study has good predictive performance and clinical value to facilitate prognostic evaluation of individual patients with G-NEN.

The complete chloroplast genome of Utricularia tenuicaulis Miki (Lentibulariaceae) isolated in Korea

Utricularia tenuicaulis Miki 1935 is an aquatic carnivorous plant species found in East Asia including Korea and Japan. In this study, the chloroplast genome of U. tenuicaulis was successfully sequenced. The assembled genome (153,976 bp; GC ratio, 37.0%) contains four subregions, with the large single copy (LSC; 84,596 bp; 34.9%) and small single copy (SSC; 17,946 bp; 30.5%) regions separated by 25,718 bp of inverted repeat regions (42.7%), and includes 126 genes (81 protein-coding genes, 8 rRNAs, and 37 tRNAs). Phylogenetic analyses based on the whole-chloroplast genomes of 18 species, including 17 Lentibulariaceae species and one outgroup species, suggest a close relationship between U. tenuicaulis and Utricularia macrorhiza Leconte 1824. A comparison of genomic variation between U. tenuicaulis and U. macrorhiza confirmed the validity of the specific discrimination of U. tenuicaulis.

The complete chloroplast genome of Castanopsis sieboldii (Makino) Hatus (Fagaceae)

Castanopsis sieboldii (Makino) Hatus is an evergreen tree that distributes in Eastern Asia including Islands of Korea and Japan. The chloroplast genome of C. sieboldii was successfully sequenced. Its length is 160,705 bp long (GC ratio is 36.8%) and has four subregions: 90,821 bp of large single copy (34.6%) and 19,014 bp of small single copy (30.8%) regions are separated by 25,075 bp of inverted repeat (42.8%) regions including 134 genes (89 protein-coding genes, eight rRNAs, and 37 tRNAs). Interspecific variations of Castanopsis are at a moderate level in comparison to those of the other genera. Phylogenetic trees show that C. sieboldii chloroplast genome was clustered with the other two Castanopsis species.

Genome-wide comparative analyses of GATA transcription factors among seven Populus genomes

GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a basic region. We identified 262 GATA genes (389 GATA TFs) from seven Populus genomes using the pipeline of GATA-TFDB. Alternative splicing forms of Populus GATA genes exhibit dynamics of GATA gene structures including partial or full loss of GATA domain and additional domains. Subfamily III of Populus GATA genes display lack CCT and/or TIFY domains. 21 Populus GATA gene clusters (PCs) were defined in the phylogenetic tree of GATA domains, suggesting the possibility of subfunctionalization and neofunctionalization. Expression analysis of Populus GATA genes identified the five PCs displaying tissue-specific expression, providing the clues of their biological functions. Amino acid patterns of Populus GATA motifs display well conserved manner of Populus GATA genes. The five Populus GATA genes were predicted as membrane-bound GATA TFs. Biased chromosomal distributions of GATA genes of three Populus species. Our comparative analysis approaches of the Populus GATA genes will be a cornerstone to understand various plant TF characteristics including evolutionary insights.

P–138 When is low quality really low? Should we transfer low-grade blastocysts?

Study question

What is the live birth rate after single, low-grade blastocyst (LGB) transfer?

Summary answer

The live birth rate for LGBs is 28%, ranging between 15–31% for the different inner cell mass (ICM) and trophectoderm (TE) subgroups of LGBs.

What is known already

Live birth rates following LGB transfer are varied and have been reported to be in the range of 5–39%. However, these estimates are inaccurate as studies investigating live birth rates following LGB transfer are inherently limited by sample size (n = 10–440 for LGB transfers) due to LGBs being ranked last for transfer. Further, these studies are heterogenous with varied LGB definitions and design. Collating LGB live birth data from multiple clinics is warranted to obtain sufficient numbers of LGB transfers to establish reliable live birth rates, and to allow for delineation of different LGB subgroups, including blastocyst age and female age.

Study design, size, duration

We performed a multicentre, multinational retrospective cohort study in 9 IVF centres in China and New Zealand from 2012 to 2019. We studied the outcome of 6966 single blastocyst transfer cycles on days 5–7 (fresh and frozen) according to blastocyst grade, including 875 transfers from LGBs (&lt;3bb, this being the threshold typically applied to LGB studies). Blastocysts with expansion stage 1 or 2 (early blastocysts) were excluded.

Participants/materials, setting, methods

The main outcome measured was live birth rate. Blastocysts were grouped according to quality grade: good-grade blastocysts (GGBs; n = 3849, aa, ab and ba), moderate-grade blastocysts (MGBs; n = 2242, bb) and LGBs (n = 875, ac, ca, bc, cb and cc) and live birth rates compared using the Pearson Chi-squared test. A logistic regression analysis explored the relationship between blastocyst grade and live birth after adjustment for the confounders: clinic, female age, expansion stage, and blastocyst age.

Main results and the role of chance

The live birth rates for GGBs, MGBs and LGBs were 45%, 36% and 28% respectively (p &lt; 0.0001). Within the LGB group, the highest live birth rates were for grade c TE (30%) and the lowest were for grade c ICM (19%). The lowest combined grade (cc) maintained a 15% live birth rate (n = 7/48). After accounting for confounding factors, including female age and blastocyst characteristics, the odds of live birth were 2.33 (95% CI = 1.88–2.89) for GGBs compared to LGBs and 1.56 (95% CI = 1.28–1.92) for MGBs compared to LGBs following fresh and frozen blastocyst transfers (p &lt; 0.0001, odds ratios confirmed in exclusively frozen blastocyst transfer cycles). When stratified by individual ICM and TE grade, the odds of live birth according to ICM grade were 1.31 (a versus b; 95% CI = 1.15–1.48), 2.82 (a versus c; 95% CI = 1.91–4.18) and 2.16 (b versus c; 95% CI = 1.48–3.16; all p &lt; 0.0001). The odds of live birth according to TE grade were 1.33 (a versus b; 95% CI = 1.17–1.50, p &lt; 0.0001), 1.85 (a versus c; 95% CI = 1.45–2.34, p &lt; 0.0001) and 1.39 (b versus c; 95% CI = 1.12–1.73, p = 0.0024).

Limitations, reasons for caution

Despite the large multicentre design of the study, analyses of transfers occurring within the smallest subsets of the LGB group were limited by sample size. The study was not randomised and had a retrospective character.

Wider implications of the findings: LGBs maintain satisfactory live birth rates (averaging 28%) in the general IVF population. Even those in the lowest grading tier maintain modest live birth rates (15%; cc). It is recommended that LGBs not be universally discarded, and instead considered for subsequent frozen embryo transfer to maximize cumulative live birth rates.

Trial registration number

Not applicable

[Holistic view of surgery based on membrane anatomy for gastrointestinal tumor]

The mesentery is a continuous unity and the operation of digestive carcinoma is the process of mesenteric resection. This paper attempts to simplify the formation process of all kinds of fusion fascia in the process of digestive tract embryogenesis, and to illuminate the continuity of fusion fascia with a holistic concept. This is helpful for beginners to reversely dissect the fusion fascia and maintain the correct surgical plane during operation, and to achieve the purpose of complete mesenteric resection.

The complete chloroplast genome sequence of new species candidate of Plantago depressa Willd. in Korea (Plantaginaceae)

We presented a complete chloroplast genome of a new species candidate of Plantago depressa, Willd. named as Plantago wonjuenesis sp. nov, which is 164,946 bp long (GC ratio is 38.0%) and has four subregions: 82,985 bp of large single copy and 4,647 bp of small single-copy regions are separated by 38,657 bp of inverted repeat regions including 94 protein-coding genes (PCGs), eight rRNAs, and 38 tRNAs. Number of variations between P. wonjuenesis and P. depressa can be considered as interspecific variations. Bootstrapped phylogenetic trees constructed with conserved 78 PCGs of eleven Plantaginaceae chloroplast genomes present that P. wonjuensis is clustered with P. depressa, P. fengdouensis, and P. media.

Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors

GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a basic region. Due to the low cost of genome sequencing, multiple strains of specific species have been sequenced: e.g., number of plant genomes in the Plant Genome Database (http://www.plantgenome.info/) is 2,174 originated from 713 plant species. Thus, we investigated GATA TFs of 19 Arabidopsis thaliana genome-widely to understand intraspecific features of Arabidopsis GATA TFs with the pipeline of GATA database (http://gata.genefamily.info/). Numbers of GATA genes and GATA TFs of each A. thaliana genome range from 29 to 30 and from 39 to 42, respectively. Four cases of different pattern of alternative splicing forms of GATA genes among 19 A. thaliana genomes are identified. 22 of 2,195 amino acids (1.002%) from the alignment of GATA domain amino acid sequences display variations across 19 ecotype genomes. In addition, maximally four different amino acid sequences per each GATA domain identified in this study indicate that these position-specific amino acid variations may invoke intraspecific functional variations. Among 15 functionally characterized GATA genes, only five GATA genes display variations of amino acids across ecotypes of A. thaliana, implying variations of their biological roles across natural isolates of A. thaliana. PCA results from 28 characteristics of GATA genes display the four groups, same to those defined by the number of GATA genes. Topologies of bootstrapped phylogenetic trees of Arabidopsis chloroplasts and common GATA genes are mostly incongruent. Moreover, no relationship between geographical distribution and their phylogenetic relationships was found. Our results present that intraspecific variations of GATA TFs in A. thaliana are conserved and evolutionarily neutral along with 19 ecotypes, which is congruent to the fact that GATA TFs are one of the main regulators for controlling essential mechanisms, such as seed germination and hypocotyl elongation.

Complete Genome Sequence of a Blochmannia Endosymbiont of Colobopsis nipponica

Blochmannia endosymbionts (Gammaproteobacteria) live in bacteriocytes, which are specialized cells found in the genus Camponotus and its neighbor genera. In this announcement, we describe the complete genome sequence of the Blochmannia endosymbiont of Colobopsis nipponica, which originated from a colony collected in the Republic of Korea.

Complete mitochondrial genome of the acrobat ant Crematogaster teranishii Santschi, 1930 (Formicidae; Hymenoptera)

The genus Crematogaster is a diverse group of ants found around the world. We have completed the mitochondrial genome of Crematogaster teranishii, which is the first mitochondrial genome of the genus. The mitochondrial genome is 17,442 bp long and 20.3% in GC ratio, which is similar to those of other ants. It contains 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and a control region with same gene order to other myrmicine species. The intergenic region between nad3 and trnA was unusually long compared to other ant species. Phylogenetic analysis showed that C. teranishii was closely related to other members of tribe Crematogastrini.

The complete mitochondrial genome of Myzus persicae (Sulzer, 1776; Hemiptera: Aphididae) isolated in Korea

We de novo assembled the complete mitochondrial genome of the green peach aphid, Myzus persicae, using its genomic DNA isolated from the bell pepper in Korea. The circular mitogenome of M. persicae is 16,936 bp long and contains the standard 37 genes: 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, as well as a single control region of 798 bp. Given the high AT ratio (84.1%) of the M. persicae mitogenome, we found, through the comparison of the Chinese M. persicae mitogenomes, that approximately 1.6% of the mitogenome is polymorphic, including 30 single nucleotide polymorphisms (SNPs), 12 insertions and deletions (INDELs), and large sequence variations in the control region. To resolve the phylogenetic position of M. persicae, we analyzed all mitochondrial protein-coding genes from 38 species within the Aphidoidea superfamily, with Adelges laricis as an outgroup. Our M. persicae sample was significantly grouped with three existing M. persicae samples, and the species belonging to the family Aphididae formed a monophyletic clade.

The complete mitochondrial genome of the millipede Epanerchodus koreanus Verhoeff, 1937 collected in limestone cave of Korea (Polydesmidae: Polydesmida)

We have determined the second mitochondrial genome of Epanerchodus koreanus Verhoeff, 1937 collected in limestone cave of Korea. The circular mitochondrial genome of E. koreanus is 15,581 bp long. It includes 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. Its gene order was different from the rest three Polydesmida mitochondrial genomes, resulted from relocation of tRNAs, rRNAs, and ND1. The base composition was AT-biased (75.1%). Phylogenetic trees displayed phylogenetic relationship, which is congruent to previous study, except Sphaerotheriidae sp. clustering with Helminthomorpha.

The complete mitochondrial genome of Ricania speculum (Walker, 1851) (Hemiptera: Ricaniidae): investigation of intraspecific variations on mitochondrial genome

We have determined a mitochondrial genome of Ricania speculum (Walker, 1851) collected in Jeollabuk-do, Republic of Korea. The circular mitogenome of R. speculum is 15,530 bp long which is shorter than that of the previous mitogenome of R. speculum by 199 bp. It includes 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNAs. Intraspecific variation between two mitogenome of R. speculum was investigated: 171 SNPs and 18 INDELs were identified, presenting a high level of intraspecific variations on mitochondrial genome.

The complete mitochondrial genome of new species candidate of Rosa rugosa (Rosaceae)

Completed mitochondrial genome of a new species candidate of Rosa rugosa, named as Rosa angusta, is 303,484 bp long. The overall GC content of this mitochondrial genome is 45.2%. It contains 52 genes covering 31 protein-coding genes, 17 tRNAs, and 3 rRNAs. In comparison to R. rugosa mitochondrial genome assembled from the public NGS raw reads, 124 SNPs and 769 INDELs were identified. Phylogenetic trees suggest that more Rosa mitochondrial genomes will be needed to understand phylogenetic relationship of the two Rosa species.

The Complete Chloroplast Genome of Arabidopsis thaliana Isolated in Korea (Brassicaceae): An Investigation of Intraspecific Variations of the Chloroplast Genome of Korean A. thaliana

Arabidopsis thaliana (L.) Heynh. is a model organism of plant molecular biology. More than 1,700 whole genome sequences have been sequenced, but no Korean isolate genomes have been sequenced thus far despite the fact that many A. thaliana isolated in Japan and China have been sequenced. To understand the genetic background of Korean natural A. thaliana (named as 180404IB4), we presented its complete chloroplast genome, which is 154,464 bp long and has four subregions: 85,164 bp of large single copy (LSC) and 17,781 bp of small single copy (SSC) regions are separated by 26,257 bp of inverted repeat (IRs) regions including 130 genes (85 protein-coding genes, eight rRNAs, and 37 tRNAs). Fifty single nucleotide polymorphisms (SNPs) and 14 insertion and deletions (INDELs) are identified between 180404IB4 and Col0. In addition, 101 SSRs and 42 extendedSSRs were identified on the Korean A. thaliana chloroplast genome, indicating a similar number of SSRs on the rest five chloroplast genomes with a preference of sequence variations toward the SSR region. A nucleotide diversity analysis revealed two highly variable regions on A. thaliana chloroplast genomes. Phylogenetic trees with three more chloroplast genomes of East Asian natural isolates show that Korean and Chinese natural isolates are clustered together, whereas two Japanese isolates are not clustered, suggesting the need for additional investigations of the chloroplast genomes of East Asian isolates.

Comprehensive Analyses of the Complete Mitochondrial Genome of Figulus binodulus (Coleoptera: Lucanidae)

Figulus binodulus Waterhouse is a small stag beetle distributed in East Asia. We determined the first mitochondrial genome of F. binodulus of which is 16,261-bp long including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large noncoding region of 1,717 bp. Gene order of F. binodulus is identical to the ancestral insect mitochondrial gene order as in most other stag beetle species. All of 22 tRNAs could be shaped into typical clover-leaf structure except trnSer1. Comparative analyses of 21 Lucanidae mitochondrial genomes was conducted in aspect of their length and AT-GC ratio. Nucleotide diversities analyses provide that cox1 and cox2 in Lucanidae are less diverse than those of Scarabaeoidea. Fifty simple sequence repeats (SSRs) were identified on F. binodulus mitochondrial genome. Comparative analysis of SSRs among five mitochondrial genomes displayed similar trend along with SSR types. Figulus binodulus was sister to all other available family Lucanidae species in the phylogenetic tree.

The complete chloroplast genome of Agrimonia pilosa Ledeb. isolated in Korea (Rosaceae): investigation of intraspecific variations on its chloroplast genomes

The complete chloroplast genome of Agrimonia pilosa Ledeb. isolated in Korea is 155,125 bp long (GC ratio is 36.9%) and has four subregions: 84,458 bp of large single copy (34.9%) and 18,737 bp of small single copy (30.4%) regions are separated by 25,965 bp of inverted repeat (42.6%) regions including 129 genes (84 protein-coding genes, eight rRNAs, and 37 tRNAs). 258 SNPs and 542 INDELs were identified as intraspecific variations against the partial genome (KY419942). Phylogenetic trees show that our chloroplast genome was clustered with the previous A. pilosa chloroplast genome.

The complete mitochondrial genome of Riccia fluitans L. (Ricciaceae, Marchantiophyta): investigation of intraspecific variations on mitochondrial genomes of R. fluitans

Riccia fluitans L. is the most common species in Riccia genus. To investigate intraspecific variations on mitochondrial genomes of R. fluitans, we completed mitochondrial genome of R. fluitans. Its length is 185,640 bp, longer than that of NC_043906 by 19 bp and it contains 74 genes (42 protein-coding genes, 3 rRNAs, 28 tRNAs, and 1 pseudogene). 18 single nucleotide polymorphisms (SNPs) and 19 insertions and deletions are identified, higher than that of Marchantia polymorpha subsp. ruderalis. One non-synonymous SNP is found in ccmFN. Phylogenetic trees show that R. fluitans is clustered with Dumortiera hirsuta, requiring additional mitogenome to clarify the phylogenetic relationship.

The complete mitochondrial genome of Aphaenogaster famelica (Smith, 1874) (Hymenoptera: Formicidae)

Aphaenogaster famelica (Smith, 1874) is a slender ant found in Korea. We have completed the mitochondrial genome of A. famelica of which length is 19,464 bp, the third longest ant mitogenome so far. It was AT-biased (GC ratio is 18.0%) and includes 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region. The extra bases of A. famelica are placed in intergenic regions each between trnV-trnM and trnI-trnQ. Gene order of A. famelica is identical to other Myrmicinae ants. Phylogenetic trees show that tribe Stenammini and tribe Myrmicini are closely related.

The complete mitochondrial genome of Nylanderia flavipes (Smith, 1874) (Hymenoptera: Formicidae)

Nylanderia flavipes (Smith, 1874) is a Formicine ant found in East Asia. We have completed mitochondrial genome of N. flavipes of which length is 16,687 bp including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs, and a control region. The base composition was AT-biased (GC ratio is 18.9%). Gene order of N. flavipes presents a unique inversion of trnP in comparison to Camponotus species. Our phylogenetic trees together with phylogenomic analysis suggest that the gene order rearrangements occurred independently in Camponotus and N. flavipes.

The complete mitochondrial genome of Rotunda rotundapex (Miyata & Kishida, 1990) (Lepidoptera: Bombycidae)

Rotunda rotundapex (Miyata & Kishida, 1990) is a silk moth identified in Korea. We completed its mitochondrial genome which is 15,298 bp long and the shortest mitogenome of Bombycidae s.str. It includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs, and a control region. Comparison with COI sequence of Taiwan isolate suggests the Korean population of this species can be a novel species. Gene order of R. rotundapex mitogenome is conserved as in other Bombycidae species. Phylogenetic trees show that R. rotundapex is closely related to genus Rondotia.

The second complete chloroplast genome sequence of the Viburnum erosum (Adoxaceae) showed a low level of intra-species variations

We presented the second complete chloroplast genome of the plant. The length of chloroplast genome is 158,587 bp, consisting of four subregions: 87,050 bp of LSC and 18,503 bp of SSC regions separated by a pair of 26,517 bp IR regions. It includes 129 genes (84 protein-coding genes, 8 rRNAs, and 37 tRNAs). A low-level of molecular variation within Viburnum erosum was found with 16 SNPs and 49 indels. The phylogenetic tree shows that the two accessions of V. erosum are clustered with Viburnum japonicum with no resolution between the species, suggesting that chloroplast genome in these species evolve slowly.

The complete mitochondrial genome of Ochetellus glaber (Mayr, 1862) (Hymenoptera:Formicidae)

Ochetellus glaber (Mayr, 1867) is a dolichoderine ant found in the warm regions of Asia and Australia. We have determined the mitochondrial genome of O. glaber whose length is 16,259 bp including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs, and a single large control region. The base composition was AT-biased (GC ratio is 17.8%). Gene order of O. glaber is identical to other species of the subfamily Dolichoderinae. Phylogenetic trees show that O. glaber is nested in other mitochondrial genomes of tribe Leptomyrmecini, implying the neotropical genera are ancestral to Australian genera such as Ochetellus.

The complete mitochondrial genome of the fall armyworm, Spodoptera frugiperda Smith, 1797 (Lepidoptera; Noctuidae), firstly collected in Korea

The fall armyworm, Spodoptera frugiperda, is a serious pest in large numbers on more than 350 plant species in the world. We have determined a 15,388 bp mitogenome of S. frugiperda which includes 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNAs. The base composition was AT-biased (81.3%). Phylogenetic trees present that Korean S. frugiperda placed in basal position of S. frugiperda clade. S. frugiperda mitochondrial genome can be used for understanding recent active migration of S. frugiperda.

The complete chloroplast genome of a new candidate cultivar, Sang Jae, of Abeliophyllum distichum Nakai (Oleaceae): initial step of A. distichum intraspecies variations atlas

Chloroplast genome of Sang Jae, new candidate cultivar of Abeliophyllum distichum Nakai, has been sequenced to reveal infraspecific relationship of wildtypes and cultivars. Its length is 156,008 bp long (GC ratio is 37.8%) and has four subregions: 86,773 bp of large single copy (35.8%) and 17,827 bp of small single copy (31.9%) regions are separated by 25,704 bp of inverted repeat (43.2%) regions including 133 genes (87 protein-coding genes, eight rRNAs, and 37 tRNAs). Phylogenetic trees show that A. distichum is clustered with twelve Forsythia species and intraspecies variations level is similar to Olea europaea.

The complete chloroplast genome of a new candidate cultivar, Dae Ryun, of Abeliophyllum distichum Nakai (Oleaceae)

To understand genetic features of new candidate cultivar, Dae Ryun of A. distichum, chloroplast genome was sequenced. Its length is 156,019 bp and has four subregions: 86,783 bp of large single-copy (LSC) and 17,828 bp of small single-copy (SSC) regions are separated by 25,704 bp of inverted repeat (IR) regions including 133 genes (87 protein-coding genes, 8 rRNAs, and 37 tRNAs). Overall GC content is 35.8%. Intraspecies sequence variations among four A. distichum chloroplast genomes present various numbers. Phylogenetic trees show that A. distichum is clustered with 12 Forsythia species.

The complete chloroplast genome of Aconitum coreanum (H. Lév.) Rapaics (Ranunculaceae)

Aconitum coreanum (H. Lév.) Rapaics listed in the Korean Red List is a medicinal herb. We presented complete chloroplast genome, which is 157,024 bp long and has four subregions: 87,637 bp of large single-copy and 16,901 bp of small single-copy regions, which are separated by two 26,243 bp inverted repeat regions including 132 genes (86 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content of the chloroplast is 38.0%. Phylogenetic trees show that A. coreanum occupied a basal position at subgenus Aconitum clade and two A. coreanum isolated from midwestern and eastern regions of Korea are clustered together.

The complete chloroplast genome sequence of Viburnum erosum (Adoxaceae)

Viburnum erosum is a deciduous shrub distributed in eastern Asia. As part of the systematic study to understand the phylogenetic relationship of V. erosum, we present the complete chloroplast genome of V. erosum. Its length is 158,624 bp and it has four subregions: 87,060 bp of large single-copy and 18,530 bp of small single-copy regions separated by a pair of inverted repeat regions of 26,517 bp each, including 129 genes (84 protein-coding genes, 8 rRNAs, and 37 tRNAs). Phylogenetic analyses show that V. erosum is sister to Viburnum japonicum, supporting morphological affinity of the two species.

The complete mitochondrial genome of Aphis gossypii Glover, 1877 (Hemiptera: Aphididae) collected in Korean peninsula

Aphid gosypii Glover, 1877 is a widely recognized economically important aphid species in the world. We have determined mitochondrial genome of A. gossypii collected in Korean peninsula. The circular mitogenome of A. gossypii is 15,872 bp including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs, and a single control region of 627 bp. The base composition was AT-biased (83.8%). In comparison of Chinese A. gossypii mitochondrial genomes with that of Korean sample, 61 single nucleotide polymorphisms and 3 insertions and deletions were identified, presenting lower level of those of Nilaparvata lugens, Laodelphax striatellus, and Chilo suppresallis.

The complete chloroplast genome of Leucobryum juniperoideum (brid.) C. Müll. (Leucobryaceae, Bryophyta)

We presented complete chloroplast genome of Leucobryum juniperoideum which is 124,649 bp long and has four subregions: 86,309 bp of large single copy (LSC) and 18,696 bp of small single copy (SSC) regions are separated by 9,882 bp of inverted repeat (IR) regions including 127 genes (82 protein-coding genes, eight rRNAs, and 37 tRNAs). The overall GC content is 30.5% and those in the LSC, SSC, and IR regions are 28.1%, 26.8%, and 44.5%, respectively. Phylogenetic trees show that phylogenetic position of L. juniperoideum is congruent with the previous phylogenetic study of moss species.

Long-term decomposed straw return positively affects the soil microbial community

AIMS

In order to understand the response of soil microbial communities to the long-term of decomposed straw return, the modifications of soil microbial community structure and composition induced by more than 10 years of fresh and decomposed straw return was investigated and the key environmental factors were analysed.

METHODS AND RESULTS

Phospholipid fatty acid analysis and high-through sequencing technique were applied to analyse the structure and composition of the soil microbial communities. Compared with fresh straw, returning decomposed straw increased the relative abundance of bacteria and fungi by 1·9 and 7·7% at a rate of ~3750 kg ha^-1 , and increased by 23·1 and 5·7%, at a rate of ~7500 kg ha^-1 respectively. The relative abundance of the bacteria related to soil nitrification increased, but the ones related to soil denitrification decreased with decomposed straw return, which led to higher total nitrogen contents in soils. Moreover, returning decomposed straw reduced pathogenic fungal populations (genus of Alternara), which had significantly positive correlation with soil electric conductivity. It indicated that the long-term of decomposed straw return might have lower risk of soil-borne disease mainly for the reasonable soil salinity.

CONCLUSIONS

Long-term of decomposed straw return could provide suitable nutrient and salinity for healthier development of soil microbial community, both in abundance and structure, compared with fresh straw return.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results of the study helps to better understand how the microbial community modifications induced by decomposed straw return benefit on soil health. The obtained key factors impacting soil microbial community variations is meaningful in soil health management under conditions of straw return.

The complete chloroplast genome of coffee tree, Coffea arabica L. 'Blue Mountain' (Rubiaceae)

We presented complete chloroplast genome of Coffea arabica BM1 which is 155,189 bp long and has four subregions: 85,159 bp of large single copy (LSC), and 18,135 bp of small single copy (SSC) regions are separated by 25,946 bp of inverted repeat (IR) regions including 131 genes (86 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 37.4% and those in the LSC, SSC, and IR regions are 35.4, 31.3, and 43.0%, respectively. Low level of cultivar specific sequence variations was found among seven coffee chloroplast genomes.

The complete chloroplast genome of tulip tree, Liriodendron tulifipera L. (Magnoliaceae): investigation of intra-species chloroplast variations

Liriodendron tulifipera L. belongs to Magnoliaceae which is one of the basal angiosperm families. To understand intra-species variations on chloroplast genome in Liriodendron genus, we presented complete chloroplast genome of L. tulifipera, which is 156,387 bp long and has four subregions: 85,606 bp of large single copy (LSC) and 18,778 bp of small single copy (SSC) regions are separated by 26,002 bp of inverted repeat (IR) regions including 129 genes (84 coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 37.0% and those in the LSC, SSC, and IR regions are 34.9%, 30.5%, and 42.8%, respectively. Twelve single nucleotide polymorphisms (SNPs) located in one region and one insertion and deletion are found between two L. tulifipera genomes. INDEL Phylogenetic trees show that two L. tulifipera chloroplasts are clustered together and are sister to Magnolia species.

The complete chloroplast genome of Korean endemic species, Cirsium rhinoceros (H.Lév. & vaniot) Nakai (Asteraceae)

Cirsium rhinoceros (H.Lév. & Vaniot) Nakai has been used a traditional medicine. Complete chloroplast genome of C. rhinoceros is 152,576 bp long and has four subregions: 87,262 bp of large single copy (LSC) and 21,486 bp of small single copy (SSC) regions that are separated by 18,742 bp of inverted repeat (IR) regions including 133 genes (88 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content of this chloroplast genome is 37.7% and in the LSC, SSC, and IR regions are 36.0%, 31.4%, and 43.8%, respectively. Phylogenetic trees show that Cirsium species are clustered along with their distribution.

The complete chloroplast genome of candidate new species from Rosa rugosa in Korea (Rosaceae)

Complete chloroplast genome of candidate new species from Rosa rugosa, named as Rosa angusta, is 156,989 bp long and has four subregions: 86,227 bp of large single copy (LSC) and 18,816 bp of small single copy (SSC) regions are separated by 25,793 bp of inverted repeat (IR) regions including 130 genes (85 protein-coding genes, eight rRNAs, and 37 tRNAs). The overall GC content of this chloroplast genome is 37.2% and in the LSC, SSC, and IR regions are 35.2%, 31.1%, and 42.8%, respectively. Phylogenetic trees show that R. angusta is close to R. rugosa with enough number of sequence variations.

The complete chloroplast and mitochondrial genomes of Hyunsasi tree, Populus alba x Populus glandulosa (Salicaceae)

Populus alba x Populus glandulosa is a hybrid species made by Dr. Hyun. It is called as Hyunsasi tree in Korea. It has been used as a good resource for genetic engineering because it is sterile. Here, we presented its complete chloroplast and mitochondrial genomes: chloroplast genome is identical to that of P. alba (156,505 bp and 129 genes covering 84 protein-coding genes, 37 tRNAs, and eight rRNAs) and mitochondrial genome is 813,261 bp long and GC ratio is 44.9%. It contains 59 genes containing 32 protein-coding genes, 22 tRNAs, and three rRNAs. Based on alignment with P. tremula x P. alba mitochondrial genome, 1,752 single nucleotide polymorphisms (SNPs; 0.22%) and 41,506 insertion and deletions (INDELs; 5.10%) are found. Phylogenetic trees based on chloroplast and mitochondrial genomes show different topology in four Populus species, indicating that both genomes may be evolved in different ways after common ancestors of Populus genus.

The complete mitochondrial genome of Neocaridina heteropoda koreana Kubo, 1938 (Decapoda: Atyidae)

Neocaridina heteropoda koreana Kubo, 1938 is a freshwater shrimp native to the Korean peninsula. We have determined the mitogenome of N. heteropoda koreana, which's length is 15,558 bp long including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 674 bp. Its GC ratio is 33.0%. Gene order of N. heteropoda koreana is identical to those of other known Atyidae species. Phylogenetic trees show that N. heteropoda koreana is sister to N. davidi and placed within genus Caridina. Our mitogenome will be a useful resource for understanding molecular phylogeny of genus Neocradina.

The complete chloroplast genome of coffee tree, Coffea arabica L. 'Typica' (Rubiaceae)

We presented complete chloroplast genome of Coffea arabica L. 'Typica' which is 155,187 bp long and has four subregions: 85,159 bp of large single copy (LSC) and 18,135 bp of small single copy (SSC) regions are separated by 25,946 bp of inverted repeat (IR) regions including 131 genes (86 protein-coding genes, eight rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 37.4% and those in the LSC, SSC, and IR regions are 35.4%, 31.3%, and 43.0%, respectively. Interestingly, almost most of sequence variations identified against five coffee chloroplast genomes are insertions and deletions.

The complete chloroplast genome of Prince Ginseng, Pseudostellaria heterophylla (Miq.) Pax (Caryophyllaceae)

We presented complete chloroplast genome of Prince Ginseng, Pseudostellaria heterophylla which is 149,795 bp long and has four subregions: 81,460 bp of large single copy (LSC) and 16,983 bp of small single copy (SSC) regions are separated by 25,676 bp of inverted repeat (IR) regions including 126 genes (81 CDS, 8 rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 36.5% and those in the LSC, SSC, and IR regions are 34.3%, 29.4%, and 42.3%, respectively. Phylogenetic trees of 25 Caryophyllaceae species present phylogenetic position of P. heterophylla among available Pseudostellaria species.

The complete chloroplast genome of Fissidens nobilis Griff. (Fissidentaceae, Bryophyta)

We presented a complete chloroplast genome of Fissidens nobilis which is 124,962 bp long and has four subregions: 86,122 bp of large single-copy (LSC) and 18,708 bp of small single-copy (SSC) regions are separated by 10,066 bp of inverted repeat (IR) regions including 127 genes (82 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content is 29.2% and those in the LSC, SSC, and IR regions are 26.6%, 26.0%, and 43.5%, respectively. Phylogenetic trees show that the phylogenetic position of F. nobilis is congruent with the previous phylogenetic study of moss species.

The complete chloroplast genome sequence of rose-gold pussy willow, Salix gracilistyla Miq. (Salicaceae)

To understand genetic background of Salix gracilistyla Miq., we presented its complete chloroplast genome which is 155,557 bp and has four sub regions: 84,530 bp of large single copy (LSC) and 16,218 bp of small single copy (SSC) regions are separated by 27,405 bp of inverted repeat (IR) regions including 130 genes (84 protein-coding gene, eight rRNAs, and 38 tRNAs). The overall GC content of the chloroplast genome is 36.7% and those in the LSC, SSC, and IR regions are 34.5%, 31.0%, and 41.9%, respectively. Phylogenetic trees show phylogenetic position of S. gracilistyla with low level of inter-species sequence variations.