A Gram-stain negative, rod-shaped, facultatively aerobic, pale-beige-coloured bacterial strain, designated F7233
, was isolated from coastal sediment sampled at Jingzi Bay, Weihai, PR China. Cells of ...strain F7233
were 0.3-0.4 µm wide, 1.2-1.4 µm wide long, non-spore-forming and motile with one flagellum. Optimum growth occurred at 30 °C, with 1.0 % (w/v) NaCl and at pH 6.5-7.0. Positive for nitrate reduction, hydrolysis of Tweens and oxidase activity. The sole respiratory quinone of strain F7233
was ubiquinone-10 and the predominant cellular fatty acid was summed feature 8 (C
7
/C
6
). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and one unidentified aminophospholipid. The G+C content of the chromosomal DNA was 63.3 mol%. Phylogenetic analysis of the 16S rRNA gene sequence revealed that the newly isolate belonged to the genus
, with 96.8 % sequence similarity to
MCCC 1A01226
, 96.1 % similarity to
JCM 20692
and 95.5% similarity to
CC-SPIO-10-1
. On the basis of phylogenetic, phenotypic and chemotaxonomic data, it is considered that strain F7233
should represent a novel species within the genus
, for which the name
sp. nov. is proposed. The type strain is F7233
(=MCCC 1H00419
=KCTC 72859
).
Abstract
Plentiful bast fiber, a high crude protein content, and vigorous vegetative growth make ramie a popular fiber and forage crop. Here, we report the draft genome of ramie, along with a genomic ...comparison and evolutionary analysis. The draft genome contained a sequence of approximately 335.6 Mb with 42,463 predicted genes. A high-density genetic map with 4,338 single nucleotide polymorphisms (SNPs) was developed and used to anchor the genome sequence, thus, creating an integrated genetic and physical map containing a 58.2-Mb genome sequence and 4,304 molecular markers. A genomic comparison identified 1,075 unique gene families in ramie, containing 4,082 genes. Among these unique genes, five were cellulose synthase genes that were specifically expressed in stem bark, and 3 encoded a WAT1-related protein, suggesting that they are probably related to high bast fiber yield. An evolutionary analysis detected 106 positively selected genes, 22 of which were related to nitrogen metabolism, indicating that they are probably responsible for the crude protein content and vegetative growth of domesticated varieties. This study is the first to characterize the genome and develop a high-density genetic map of ramie and provides a basis for the genetic and molecular study of this crop.
A Gram-stain-negative, aerobic and non-motile strain, designated 18x22-1
, was isolated from a forest soil sample collected from Limushan Nature Reserve in Hainan Province, PR China. Growth occurred ...at 15-37 °C and pH 6.0-8.0 without NaCl. The 16S rRNA gene sequence analyses showed that strain 18x22-1
was closely related to
DSM 14655
(98.5 %), followed by
DSM 14656
(97.9 %) and other
species and formed a stable cluster with
DSM 14655
,
DSM 14656
,
JCM 19319
and
s CCTCC AB 2015357
. Results of chemotaxonomic analyses showed that ubiquinone-8 (Q-8) was the major respiratory quinone, and the major fatty acids (>10 % of the total amounts) were C
and C
cyclo. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified aminopholipids and four unidentified phospholipids. The draft genome sequence was 4.47 Mb long with a G+C content of 68.9 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain 18x22-1
and four closely related type strains were in the range of 79.3-82.3 % and 21.9-25.1 %, respectively. The results of phenotypic, phylogenetic and chemotaxonomic analyses supported that strain 18x22-1
represents a novel species of the genus
, for which the name
sp. nov. is proposed. The type strain is 18x22-1
(=GDMCC 1.1584
=KCTC 52922
).
Shiga toxin-producing Escherichia coli (STEC) is one of the most frequent bacterial agents associated with food-borne outbreaks in Europe. In humans, the infection can lead to life-threatening ...diseases. Domestic and wild animals can harbor STEC, and ruminants are the main STEC reservoirs, although asymptomatic. In the present study we have characterized STEC from wildlife (wild boar (n = 56), red deer (n = 101), red fox (n = 37) and otter (n = 92)). Cultivable STEC (n = 52) were isolated from 17% (n = 49) of the faecal samples. All the isolates were non-O157 STEC encoding stx1 (n = 2; 4%) and/or stx2 genes (n = 51; 98%). Only one strain (2%) isolated from red fox had an antibiotic resistant phenotype. However, when the normalized resistance interpretation of epidemiological cutoffs (NRI ECOFFs) were used, 23% (n = 12) of the strains were non-wildtype to at least one of the antibiotics tested. After analysis by pulsed-field gel electrophoresis (PFGE), 20 strains were selected for whole genome sequencing and belonged to the following serotypes: O27:H30 (n = 15), O146:H28 (n = 2), O146:H21 (n = 1), O178:H19 (n = 1), and O103:H2 (n = 1). In addition to stx, all strains encode several virulence factors such as toxins, adhesins, fimbriae and secretion systems, among others. All sequenced genomes carried several mobile genetic elements (MGEs), such as prophages and/or plasmids. The core genome and the phylogenetic analysis showed close evolutionary relationships between some of the STEC recovered from wildlife and strains of clinical origin, highlighting their pathogenic potential. Overall, our results show the zoonotic potential of STEC strains originating from wildlife, highlighting the importance of monitoring their genomic characteristics following a One Health perspective, in which the health of humans is related to the health of animals, and the environment.
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•Cultivable STEC were isolated from 17% of the wild animals.•All the isolates were non-O157, encoding stx1 (4%) and/or stx2 genes (98%).•Serotypes O27:H30, O146:H28, O146:H21, O178:H19 and O103:H2 were identified.•Besides Shiga toxin, all genomes encode, at least, 10 additional virulence factors.•Some wild animals STEC have close evolutionary relationships with human-derived STEC.
Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, ...uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth-death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.
Bitter gourd (Momordica charantia) is an important vegetable and medicinal plant in tropical and subtropical regions globally. In this study, the draft genome sequence of a monoecious bitter gourd ...inbred line, OHB3-1, was analyzed. Through Illumina sequencing and de novo assembly, scaffolds of 285.5 Mb in length were generated, corresponding to ∼84% of the estimated genome size of bitter gourd (339 Mb). In this draft genome sequence, 45,859 protein-coding gene loci were identified, and transposable elements accounted for 15.3% of the whole genome. According to synteny mapping and phylogenetic analysis of conserved genes, bitter gourd was more related to watermelon (Citrullus lanatus) than to cucumber (Cucumis sativus) or melon (C. melo). Using RAD-seq analysis, 1507 marker loci were genotyped in an F2 progeny of two bitter gourd lines, resulting in an improved linkage map, comprising 11 linkage groups. By anchoring RAD tag markers, 255 scaffolds were assigned to the linkage map. Comparative analysis of genome sequences and predicted genes determined that putative trypsin-inhibitor and ribosome-inactivating genes were distinctive in the bitter gourd genome. These genes could characterize the bitter gourd as a medicinal plant.
Modern high-throughput DNA sequencing has made it possible to inexpensively produce genome sequences, but in practice many of these draft genomes are fragmented and incomplete. Genetic linkage maps ...based on recombination rates between physical markers have been used in biology for over 100 years and a linkage map, when paired with a de novo sequencing project, can resolve mis-assemblies and anchor chromosome-scale sequences. Here, I summarize the methodology behind integrating de novo assemblies and genetic linkage maps, outline the current challenges, review the available software tools, and discuss new mapping technologies.
An aerobic and Gram-stain-negative bacterial strain, designated UKS-15
, was isolated from lake water in the Republic of Korea. Results of 16S rRNA gene sequence and phylogenetic analyses indicated ...that the novel isolate belongs to the genus
and was most closely related to
RCML-52
(98.0 %),
9 NM-14
(97.4 %) and
FJY8
(97.2 %). The DNA G+C content was 69.1 mol%. Strain UKS-15
possessed ubiquinone-8 (Q-8) as the sole respiratory quinone and the fatty acid profile comprised iso-C
, iso-C
and summed feature 9 (iso-C
ω9
and/or C
10-methyl) as its major components. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one unidentified aminophospholipid. Moreover, the physiological and biochemical results and low level of DNA-DNA relatedness (<22.0 %) allowed the phenotypic and genotypic differentiation of strain UKS-15
from other
species. Therefore, on the basis of the data from this polyphasic taxonomic study, strain UKS-15
should represent a novel species of the genus
, for which the name
sp. nov. is proposed. The type strain is UKS-15
(=JCM 30983
=KACC 18719
).
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