Notes

Genomic features of Listeria monocytogenes separated through mushroom (Agaricus bisporus) manufacturing and also digesting.
The complete chloroplast genome of Stephania tetrandra was sequenced and assembled for the first time. read more The chloroplast genome is 159,974 bp in length, containing a large single-copy (LSC) region of 90,539 bp and a small single-copy region (SSC) of 20,735 bp, separated by a pair of inverted repeats (IRs) of 24,350 bp. The genome contains 113 unique genes, including 79 protein-coding genes (PCGs), 30 tRNA genes, and four rRNA genes. Among them, 15 genes have one intron each and three genes contain two introns. The overall GC content is 37.8%, while the corresponding values of LSC, SSC, and IR regions are 35.8, 32.4, and 43.7%, respectively. Phylogenetic analysis showed that S. tetrandra is more closely related to the clade of two species within Stephania, providing new insight into the evolution of Menispermaceae.We applied next-generation sequencing (NGS) method to construct the complete mitochondrial genome of Glossogobius aureus. The obtained mitogenome of G. aureus (16,590 bp) exhibited a typical structure harboring 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control regions (D-loop). Most of mitochondrial genes are encoded on the heavy (H) strand, except for eight tRNAs and ND6. Unusual start codons were identified in COX1 (GTG) and ATP6 (TTG). Six genes (ND2, COX2, COX3, ND3, ND4, and CytB) were terminated by an incomplete stop codon (TA-/T-). A phylogenetic study showed that Glossogobius formed a clade distinct from other species in the subfamily Gobiinae. G. aureus was most closely related to G. giuris with 87.04% sequence identity among the four species in the genus Glossogobius.The complete mitochondrial genome of Sirembo imberbis was determined by the bioinformatic assembly of the next generation sequencing (NGS) reads. Total length of the mitogenome was 16,717 bp, which harbors the conserved 13 protein-coding genes (PCGs), 2 ribosomal RNAs (12S and 16S), 22 tRNAs, and two non-coding region (the control region and the origin of light-strand replication). Among 13 protein-coding genes, unusual start codon (GTG) was exclusively identified in COX1, while the incomplete stop codons (TA- or T-) were detected in COX2, COX3, ND2, ND3, ND4 and CytB. As a result of phylogenetic tree, S. imberbis formed a cluster of the family Ophidiidae together with Bassozetus zenkevitchi and Lamprogrammus niger.In this study, we have sequenced and annotated the complete mitochondrial genome of Ricania shantungensis (Hemiptera Ricaniidae) for the first time. The circular mitogenome of R. shantungensis was 15,789 bp, including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single control region of 1,363 bp. Its AT ratio was 74.6%. According to the phylogenetic tree, R. shantungensis was clustered with the genus Ricania.Alstroemeria, a member of the Alstroemeriaceae family, is a species from South America. The chloroplast genome of Alstroemeria spp. was completed by de novo assembly using a small amount of whole genome sequencing data. The chloroplast genome of Alstroemeria spp. was 155,672 bp in length consisting of 84,379 bp of large single copy, 17,815 bp of small single copy, and 26,739 bp of a pair of inverted repeat regions. A total of 157 genes were annotated including 103 protein-coding genes (PCGs), 46 tRNA genes, and eight rRNA genes. Maximum likelihood phylogenetic analysis with seven species belonging to the Alstroemeriaceae or Liliaceae family revealed that Alstroemeria spp. is grouped with the species in the Alstroemeriaceae family.In this study, the complete mitochondrial genome of Dermestes dimidiatus ab. rosea was characterized using next-generation sequencing, and the phylogenetic relationships of superfamily Bostrichoidea were established. The results showed that the mitochondrial genome of D. dimidiatus ab. rosea was 16,073 bp in size, and it contained thirteen protein-coding genes (PCGs), twenty-two transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a control region. The composition of the whole mitochondrial genome of this species was 41.3% A, 13.5% C, 9.3% G, and 35.9% T, which had high A + T content (77.2%). Phylogenetic relationships of the superfamily Bostrichoidea showed that D. dimidiatus ab. rosea and Dermestes tessellatocollis formed in a clade that was a sister group to (Dermestes maculatus + Dermestes frischii), indicating that Dermestidae was a monophyletic group. This is the first report of a complete mitochondrial genome of D. dimidiatus ab. rosea and preliminary study of Bostrichoidea mitochondrial genome, which is of great significance for the molecular identification of this species and the enrichment of mitochondrial genome database.Magnolia ofeliae A. Vázquez & Cuevas, a plant species endemic to south Jalisco, Mexico, is a critically endangered (CR) species based on the IUCN Red List. In this study, we assembled its complete chloroplast (cp) genome. The total genome size of M. ofeliae was 159,839 bp including four subregions a large single-copy (LSC) region of 88,027 bp and a small single-copy (SSC) region of 18,752 bp separated by a pair of identical inverted repeat regions (IRs) of 26,530 bp each. The GC content of the cp genome of M. ofeliae is 39.3%. The cp genome encoded a set of 113 genes, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis results that M. ofeliae is a sister to all other magnolias in the subfamily Magnolioideae.Pholidota Lindl. ex Hook. was placed in tribe Arethuseae Lindl. (Epidendroideae, Orchidaceae), while its generic relationship has been unclear. Since the plastid genome could play a key role in plant systematics, the complete chloroplast (cp) genome of P. link2 articulata was reported in this paper. The cp genome was 160,114 bp in length with four typical quadripartite structures, which was consisted of a large single copy (LSC) region of 87,756 bp, a small single copy (SSC) region of 18,872 bp, and two inverted repeats (IR) of 26,734 bp. In addition, the cp genome encoded 132 genes in total, of which were 113 unique genes, including 79 protein-coding genes, 30 tRNAs, and 4 rRNAs. The phylogenetic analysis indicated that P. articulata was closely clustered with other two species of Pholidota and that they appeared to be related to Pleione in Arethuseae Lindl.The complete mitochondrial genome sequence of Desis martensi (L. Koch, 1872) was reported. In this study, we sequenced, assembled and annotated the mitochondrial genome of Desis martensi using next-generation sequencing (NGS). The sequence was 14,662 base pairs (bp) in length and consisted of 37 mitochondrial genes (13 protein-coding genes, 22 transfer RNAs, two ribosomal RNA genes). The overall base composition of the genome showed slightly A + T bias, AT content (77.2%) higher than GC content (22.9%). The phylogenetic analyses based on 13 protein-coding genes indicated that the family Desidae belonged to the Retrolateral Tibial Apophysis (RTA) clade in Araneae.Ilex micrococca Maxim. is a widely distributed species of Aquifoliaceae in Eastern Asia. In this study, the complete chloroplast (cp) genome sequence of I. micrococca was assembled and characterized by high-throughput sequencing data. The entire cp genome was 157,782 bp in length, containing a large single-copy region (LSC) of 87,200 bp, and a small single-copy region (SSC) of 18,434 bp, which were separated by a pair of 26,074 bp inverted repeat (IR) regions. The cp genome contained 134 genes, including 89 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. Eighteen genes occur in double copies. The overall GC content is 37.6%. The phylogenetic tree reconstructed by 13 chloroplast genomes reveals that I. link3 micrococca is most related with Ilex wilsonii. The complete cp genome provides valuable information for further phylogenetic and cp genetic engineering studies of this important Ilex species I. micrococca.Ilex viridis Champ. ex Benth. is domestic to southern China. In the present work, the complete chloroplast (cp) genome sequence of Ilex viridis was assembled and characterized by high-throughput sequencing analyses. The chloroplast genome was 157,701 bp in length, consisting of large single-copy (LSC) and small single-copy (SSC) regions of 87,177 bp and 18,394 bp, respectively, which were separated by a pair of 26,065 bp inverted repeat (IR) regions. The genome was predicted to contain 134 genes, including 89 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of the genome is 37.7%. The phylogenetic tree reconstructed using 13 chloroplast genomes reveals that I. viridis is mostly related to Ilex szechwanensis.Hormaphis betulae (Hemiptera Hormaphidinae) is a common aphid of birch plants. Here, the complete mitochondrial genome sequence of a representative of this aphid from China was determined using next generation sequencing platform. The genome was 15,129 bp in length and encoded 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. The phylogeny revealed that two Chinese isolates of H. betulae clustered together and formed a monophyletic relationship with Pseudoregma bambucicola in the subfamily Hormaphidinae, supporting their species validity in Aphididae. The cumulative mitochondrial DNA data provides a better understanding of the phylogenetic relationship of this species in plant aphids.In this study, we provide the first report of the complete mitochondrial genomic sequencing of a yellow-bellied sea snake (Hydrophis platurus) that has the broadest distribution range of all Squamata species. The mitogenome length was 18,101 bp and consisted of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 3 non-coding regions. The sequence presented could be very useful for further phylogenetic and evolutionary studies.We describe the complete mitochondrial genome sequence of Cyriopagopus hainanus, a spider in the family of Theraphosidae and endemic to Hainan Island, China. Phylogenetic analyses using mitogenomes of 32 spider species from 20 families strongly supported our sample is sister to Cyriopagopus schmidti. This is also the largest mitogenomic phylogeny of spiders to date. The mitogenomic length of C. hainanus is 13,874 bp, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. The complete mitochondrial genome of C. hainanus will contribute to studies of mitogenomic evolution and trait evolution in spiders.Murrah buffalo (Bubalus bubalis Linnaeus, 1758 breed Murrah, MB) is a most productive water buffalo breed. It is the first time that the complete mitochondrial genome sequence of the MB was reported. The total length of the mtDNA is 16,359 bp, It contains the typical structure, including 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and 1 non-coding control region (D-loop region). The overall composition of the mtDNA was estimated to be 33.00% for A, 26.32% for T, 26.71% for C and 13.97% for G. Phylogenetic analyses using N-J computational algorithms showed that the analyzed 18 Ruminantia species are divided into four major clades Bovidae, Cervidae, Giraffidae and Atilocapridae. In addition, our work confirmed that MB and Bubalus bubalis isolate India 4 have a close genetic relationship.
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