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.