scholarly journals Complete Genome Sequence and Comparative Analysis of Synechococcus sp. CS-601 (SynAce01), a Cold-Adapted Cyanobacterium from an Oligotrophic Antarctic Habitat

2019 ◽  
Vol 20 (1) ◽  
pp. 152 ◽  
Author(s):  
Jie Tang ◽  
Lian-Ming Du ◽  
Yuan-Mei Liang ◽  
Maurycy Daroch
Keyword(s):  
Marine Environment ◽  
Gene Prediction ◽  
Gc Content ◽  
Adaptation Strategy ◽  
Salt Adaptation ◽  
Trna Genes ◽  
Protein Coding ◽  
Single Chromosome ◽  
Cold Adapted ◽  
Synechococcus Sp

Marine picocyanobacteria belonging to Synechococcus are major contributors to the global carbon cycle, however the genomic information of its cold-adapted members has been lacking to date. To fill this void the genome of a cold-adapted planktonic cyanobacterium Synechococcus sp. CS-601 (SynAce01) has been sequenced. The genome of the strain contains a single chromosome of approximately 2.75 MBp and GC content of 63.92%. Gene prediction yielded 2984 protein coding sequences and 44 tRNA genes. The genome contained evidence of horizontal gene transfer events during its evolution. CS-601 appears as a transport generalist with some specific adaptation to an oligotrophic marine environment. It has a broad repertoire of transporters of both inorganic and organic nutrients to survive in inhospitable environments. The cold adaptation of the strain exhibited characteristics of a psychrotroph rather than psychrophile. Its salt adaptation strategy is likely to rely on the uptake and synthesis of osmolytes, like glycerol or glycine betaine. Overall, the genome reveals two distinct patterns of adaptation to the inhospitable environment of Antarctica. Adaptation to an oligotrophic marine environment is likely due to an abundance of genes, probably acquired horizontally, that are associated with increased transport of nutrients, osmolytes, and light harvesting. On the other hand, adaptations to low temperatures are likely due to prolonged evolutionary changes.

scholarly journals Complete Chloroplast Genomes from Sanguisorba: Identity and Variation Among Four Species

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2137 ◽  
Author(s):  
Xiang-Xiao Meng ◽  
Yan-Fang Xian ◽  
Li Xiang ◽  
Dong Zhang ◽  
Yu-Hua Shi ◽  
...  
Keyword(s):  
Gc Content ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Future Studies ◽  
Chloroplast Genomes ◽  
Close Relationship ◽  
Cp Genome ◽  
Sanguisorba Officinalis

The genus Sanguisorba, which contains about 30 species around the world and seven species in China, is the source of the medicinal plant Sanguisorba officinalis, which is commonly used as a hemostatic agent as well as to treat burns and scalds. Here we report the complete chloroplast (cp) genome sequences of four Sanguisorba species (S. officinalis, S. filiformis, S. stipulata, and S. tenuifolia var. alba). These four Sanguisorba cp genomes exhibit typical quadripartite and circular structures, and are 154,282 to 155,479 bp in length, consisting of large single-copy regions (LSC; 84,405–85,557 bp), small single-copy regions (SSC; 18,550–18,768 bp), and a pair of inverted repeats (IRs; 25,576–25,615 bp). The average GC content was ~37.24%. The four Sanguisorba cp genomes harbored 112 different genes arranged in the same order; these identical sections include 78 protein-coding genes, 30 tRNA genes, and four rRNA genes, if duplicated genes in IR regions are counted only once. A total of 39–53 long repeats and 79–91 simple sequence repeats (SSRs) were identified in the four Sanguisorba cp genomes, which provides opportunities for future studies of the population genetics of Sanguisorba medicinal plants. A phylogenetic analysis using the maximum parsimony (MP) method strongly supports a close relationship between S. officinalis and S. tenuifolia var. alba, followed by S. stipulata, and finally S. filiformis. The availability of these cp genomes provides valuable genetic information for future studies of Sanguisorba identification and provides insights into the evolution of the genus Sanguisorba.

scholarly journals The complete mitochondrial genome sequence of Scolopendra mutilans L. Koch, 1878 (Scolopendromorpha, Scolopendridae), with a comparative analysis of other centipede genomes

ZooKeys ◽  
2020 ◽  
Vol 925 ◽  
pp. 73-88
Author(s):  
Chaoyi Hu ◽  
Shuaibin Wang ◽  
Bisheng Huang ◽  
Hegang Liu ◽  
Lei Xu ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Gc Content ◽  
Sister Group ◽  
Rrna Genes ◽  
Sister Group Relationship ◽  
Trna Genes ◽  
Protein Coding ◽  
Generation Sequencing ◽  
Simple Sequence

Scolopendra mutilans L. Koch, 1878 is an important Chinese animal with thousands of years of medicinal history. However, the genomic information of this species is limited, which hinders its further application. Here, the complete mitochondrial genome (mitogenome) of S. mutilans was sequenced and assembled by next-generation sequencing. The genome is 15,011 bp in length, consisting of 13 protein-coding genes (PCGs), 14 tRNA genes, and two rRNA genes. Most PCGs start with the ATN initiation codon, and all PCGs have the conventional stop codons TAA and TAG. The S. mutilans mitogenome revealed nine simple sequence repeats (SSRs), and an obviously lower GC content compared with other seven centipede mitogenomes previously sequenced. After analysis of homologous regions between the eight centipede mitogenomes, the S. mutilans mitogenome further showed clear genomic rearrangements. The phylogenetic analysis of eight centipedes using 13 conserved PCG genes was finally performed. The phylogenetic reconstructions showed Scutigeromorpha as a separate group, and Scolopendromorpha in a sister-group relationship with Lithobiomorpha and Geophilomorpha. Collectively, the S. mutilans mitogenome provided new genomic resources, which will improve its medicinal research and applications in the future.

scholarly journals Draft Genome Sequence of Bacillus pacificus KVCMST-8A-12, Isolated from a Marine Sediment Sample from the Kanyakumari Coast, India

2021 ◽  
Vol 10 (50) ◽  
Author(s):  
Asha Santhi ◽  
Venkatesh Subramanian ◽  
Krishnaveni Muthan
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Content Type ◽  
Marine Sediment Sample

A DNase-producing Bacillus pacificus strain was isolated, and the whole-genome sequence is reported in this paper. The draft genome sequence of Bacillus pacificus KVCMST-8A-12 constitutes 2.4 Gbp of raw reads, with a GC content of 35.24%. In total, 5,661 protein-coding genes, 64 tRNA genes, and 4 rRNA genes were predicted.

scholarly journals The Complete Chloroplast Genome of Critically Endangered Chimonobambusa hirtinoda (Poaceae: Chimonobambusa) and Phylogenetic Analysis

2021 ◽  
Author(s):  
yanjiang liu ◽  
Xiao Zhu ◽  
Mingli Wu ◽  
Xue Xu ◽  
Zhaoxia Dai ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gc Content ◽  
Trna Genes ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Usage Frequency ◽  
Cp Genome ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Simple Sequence

Abstract Chimonobambusa hirtinoda is a threatened species and only naturally distributed in Doupeng Mountain, Duyun, Guizhou, China. Next-generation sequencing (NGS) is used obtained the complete chloroplast (cp) genome sequence of C. hirtinoda, and then the sequence was assembled and analyze for phylogenetic and evolutionary. We also analyzed comparing the cp genome among Chimonobambusa species with previously published. The complete cp genome of C. hirtinoda has the total length of 139, 561 bp, 38.90% GC content was detected. A total of 130 genes were founded in the cp genome, including 85 protein coding genes, 37 tRNA genes, 8 rRNA. Some genes are missing and the introns occur lost in the cp genome of C. hirtinoda. A total of 48 simple sequence repeat (SSR) were detected and by measuring the codon usage frequency of amino acids, the A/U preference of the third nucleotide in the cp genome of C. hirtinoda was obtained. Furthermore, phylogenetic analysis using complete cp sequences, matk gene exhibited genetic relationship within the Chimonobambusa genus.

scholarly journals Characterization of Haemophilus parasuis Serovar 2 CL120103, a Moderately Virulent Strain in China

2018 ◽  
Vol 13 (1) ◽  
pp. 217-226
Author(s):  
Yongliang Che ◽  
Longbai Wang ◽  
Xuemin Wu ◽  
Rujing Chen ◽  
Chenyan Wang ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Genomic Sequence ◽  
Virulent Strain ◽  
Sequence Similarity ◽  
Gc Content ◽  
Trna Genes ◽  
Haemophilus Parasuis ◽  
Protein Coding ◽  
Query Cover ◽  
Genes Encoding

AbstractHaemophilus parasuisis an important bacterium affecting pigs, causing Glässer’s disease. To further characterize this species, we determined the complete genomic sequence ofH. parasuisCL120103, which was isolated from diseased pigs. The strainH. parasuisCL120103 was identified as serovar 2. The size of the largest scaffold is 2,326,318 bp and contains 145 large contigs, with the N50 contig being 20,573 bp in length. The complete genome ofH. parasuisCL120103 is 2,305,354 bp in length with 39.97% GC content and contains 2227 protein-coding genes, 19 ribosomal rRNA operons and 60 tRNA genes. Sequence similarity of the genome ofH. parasuisCL120103 to the previously sequenced genome ofH. parasuiswas up to 96% and query cover to 86%. Annotation of the genome ofH. parasuisCL120103 identified a number of genes encoding potential virulence factors. These virulence factors are involved in metabolism, adhesion, secretion and LPS biosynthesis. These related genes pave the way to better understand mechanisms underlying metabolic capabilities. The comprehensive genetic and phylogenetic analysis shows thatH. parasuisis closely related toActinobacillus pleuropneumoniaeand provides a foundation for future experimental confirmation of the virulence and pathogen-host interactions inH. parasuis.

scholarly journals The Complete Plastid Genome of Rhododendron pulchrum and Comparative Genetic Analysis of Ericaceae Species

Forests ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 158
Author(s):  
Jianshuang Shen ◽  
Xueqin Li ◽  
Xiangtao Zhu ◽  
Xiaoling Huang ◽  
Songheng Jin
Keyword(s):  
Western Europe ◽  
Size Structure ◽  
Gc Content ◽  
Purifying Selection ◽  
Rrna Genes ◽  
Biological Research ◽  
Genome Comparison ◽  
Trna Genes ◽  
Protein Coding ◽  
Cp Genome

Background and Objectives: Rhododendron pulchrum Sweet (R. pulchrum) belongs to the genus Rhododendron (Ericaceae), a valuable horticultural and medicinal plant species widely used in Western Europe and the US. Despite its importance, this is the first member to have its cpGenome sequenced. Materials and Methods: In this study, the complete cp genome of R. pulchrum was sequenced with NGS Illumina HiSeq2500, analyzed, and compared to eight species in the Ericaceae family. Results: Our study reveals that the cp genome of R. pulchrum is 136,249 bp in length, with an overall GC content of 35.98% and no inverted repeat regions. The R. pulchrum chloroplast genome encodes 73 genes, including 42 protein-coding genes, 29 tRNA genes, and two rRNA genes. The synonymous (Ks) and nonsynonymous (Ka) substitution rates were estimated and the Ka/Ks ratio of R. pulchrum plastid genes were categorized; the results indicated that most of the genes have undergone purifying selection. A total of 382 forward and 259 inverted long repeats, as well as 221 simple-sequence repeat loci (SSR) were detected in the R. pulchrum cp genome. Comparison between different Ericaceae cp genomes revealed significant differences in genome size, structure, and GC content. Conclusions: The phylogenetic relationships among eight Ericaceae species suggested that R. pulchrum is closely related to Vaccinium oldhamii Miq. and Vaccinium macrocarpon Aiton. This study provides a theoretical basis for species identification and future biological research of Rhododendron resources.

scholarly journals Draft Genome Sequence of Limosilactobacillus fermentum Strain NKN-51, Isolated from Fermented Yak Milk in the Western Himalayas of India

2021 ◽  
Vol 10 (16) ◽  
Author(s):  
Arun Beniwal ◽  
Amit Gaurav ◽  
Rekha Sharma ◽  
Tamoghna Ghosh ◽  
Piyush Kumar ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Trna Genes ◽  
Western Himalayas ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Yak Milk

Here, we report the draft genome sequence of Limosilactobacillus fermentum strain NKN-51, which was isolated from naturally processed yak cheese from the western Himalayas of India. The genome was assembled in 101 contigs with a total length of 1,879,705 bp and a GC content of 53.5%. Genome annotation predicted 1,730 protein-coding genes and 50 tRNA genes.

Characterization of the Complete Chloroplast Genome of Buddleja Lindleyana

2021 ◽  
Author(s):  
Shanshan Liu ◽  
Shiyin Feng ◽  
Yuying Huang ◽  
Wenli An ◽  
Zerui Yang ◽  
...  
Keyword(s):  
Gc Content ◽  
Single Copy ◽  
Rrna Genes ◽  
Future Research ◽  
Trna Genes ◽  
Similar Species ◽  
Protein Coding ◽  
Genome Data ◽  
Cp Genome ◽  
Genomic Resource

Abstract Background Buddleja lindleyana Fort., which belongs to the Loganiaceae with a distribution throughout the tropics, is widely used as an ornamental plant in China. Buddleja contains several morphologically similar species, which need to be identified by molecular identification. But there is little molecular research on the genus Buddleja. Objective Using molecular biology techniques to sequence and analyze the complete chloroplast (cp) genome of B. lindleyana Methods According to next-generation sequencing to sequence the genome data, a series of bioinformatics software were used to assembly and analysis the molecular structure of cp genome of B. lindleyana. Results The complete cp genome of B. lindleyana is a circular 154,487-bp-long molecule with a GC content of 38.1%. It has a familiar quadripartite structure, including a large single-copy region (LSC; 85,489 bp), a small single-copy region (SSC; 17,898bp) and a pair of inverted repeats (IRs; 25,550 bp). A total of 133 genes were identified in the genome, including 86 protein-coding genes, 37 tRNA genes, 8 rRNA genes and 2 pseudogenes. Conclusions These results suggested that B. lindelyana cp genome could be used as a potential genomic resource to resolve the phylogenetic positions and relationships of Loganiaceae, and will offer valuable information for future research in the identification of Buddleja species and will conduce to genomic investigations of these species.

scholarly journals Complete Genome of the Broad-Host-Range Erwinia amylovora Phage ΦEa21-4 and Its Relationship to Salmonella Phage Felix O1

2009 ◽  
Vol 75 (7) ◽  
pp. 2139-2147 ◽  
Author(s):  
Susan M. Lehman ◽  
Andrew M. Kropinski ◽  
Alan J. Castle ◽  
Antonet M. Svircev
Keyword(s):  
Complete Genome ◽  
Erwinia Amylovora ◽  
Phage Genome ◽  
Gc Content ◽  
Trna Genes ◽  
Broad Host Range ◽  
Protein Coding ◽  
Ionization Time ◽  
Terminase Subunit ◽  
Salmonella Phage

ABSTRACT The first complete genome sequence for a myoviridal bacteriophage, ΦEa21-4, infecting Erwinia amylovora, Erwinia pyrifoliae, and Pantoea agglomerans strains has been determined. The unique sequence of this terminally redundant, circularly permuted genome is 84,576 bp. The ΦEa21-4 genome has a GC content of 43.8% and contains 117 putative protein-coding genes and 26 tRNA genes. ΦEa21-4 is the first phage in which a precisely conserved rho-independent terminator has been found dispersed throughout the genome, with 24 copies in all. Also notable in the ΦEa21-4 genome are the presence of tRNAs with six- and nine-base anticodon loops, the absence of a small packaging terminase subunit, and the presence of nadV, a principle component of the NAD+ salvage pathway, which has been found in only a few phage genomes to date. ΦEa21-4 is the first reported Felix O1-like phage genome; 56% of the predicted ΦEa21-4 proteins share homology with those of the Salmonella phage. Apart from this similarity to Felix O1, the ΦEa21-4 genome appears to be substantially different, both globally and locally, from previously reported sequences. A total of 43 of the 117 genes are unique to ΦEa21-4, and 32 of the Felix O1-like genes do not appear in any phage genome sequences other than ΦEa21-4 and Felix O1. N-terminal sequencing and matrix-assisted laser desorption ionization-time of flight analysis resulted in the identification of five ΦEa21-4 genes coding for virion structural proteins, including the major capsid protein.

scholarly journals Complete Genome Sequence of Megamonas funiformis Strain 1CBH44, Isolated from Human Feces

2021 ◽  
Vol 10 (48) ◽  
Author(s):  
Yusuke Ogata ◽  
Mitsuo Sakamoto ◽  
Naveen Kumar ◽  
Moriya Ohkuma ◽  
Masahira Hattori ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gc Content ◽  
Rrna Genes ◽  
Trna Genes ◽  
Human Feces ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Content Type

Here, we report the complete genome sequence of Megamonas funiformis strain 1CBH44, which was isolated from the feces of a healthy Japanese person. The genome consists of a circular chromosome (2,310,709 bp, with a GC content of 31.5%) and possesses 2,170 putative protein-coding genes, 18 rRNA genes, and 54 tRNA genes.

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