Ranunculaceae is a large family of angiosperms comprising 2500 known species-a few with medicinal and ornamental values. Despite this, only two mitochondrial genomes (mitogenomes) of the family have ...been released in GenBank. Isopyrum anemonoides is a medicinal plant belonging to the family Ranunculaceae, and its chloroplast genome has recently been reported; however, its mitogenome remains unexplored. In this study, we assembled and analyzed the complete mitochondrial genome of I. anemonoides and performed a comparative analysis against different Ranunculaceae species, reconstructing the phylogenetic framework of Isopyrum. The circular mitogenome of I. anemonoides has a length of 206,722 bp, with a nucleotide composition of A (26.4%), T (26.4%), C (23.6%), and G (23.6%), and contains 62 genes, comprising 37 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and three ribosomal RNA (rRNA) genes. Abundantly interspersed repetitive and simple sequence repeat (SSR) loci were detected in the I. anemonoides mitogenome, with tetranucleotide repeats accounting for the highest proportion of SSRs. By detecting gene migration, we observed gene exchange between the chloroplast and mitogenome in I. anemonoides, including six intact tRNA genes, six PCG fragments, and fragments from two rRNA genes. Comparative mitogenome analysis of three Ranunculaceae species indicated that the PCG contents were conserved and the GC contents were similar. Selective pressure analysis revealed that only two genes (nad1 and rpl5) were under positive selection during their evolution in Ranunculales, and two specific RNA editing sites (atp6 and mttB) were detected in the I. anemonoides mitogenome. Moreover, a phylogenetic analysis based on the mitogenomes of I. anemonoides and the other 15 taxa accurately reflected the evolutionary and taxonomic status of I. anemonoides. Overall, this study provides new insights into the genetics, systematics, and evolution of mitochondrial evolution in Ranunculaceae, particularly I. anemonoides.
Data Parallel C++ Reinders, James; Ashbaugh, Ben; Brodman, James ...
2020, 2020-11-02T00:00:00, 2020-11-02, 2021.
eBook
Learn how to accelerate C++ programs using data parallelism. This open access book enables C++ programmers to be at the forefront of this exciting and important new development that is helping to ...push computing to new levels. It is full of practical advice, detailed explanations, and code examples to illustrate key topics. Data parallelism in C++ enables access to parallel resources in a modern heterogeneous system, freeing you from being locked into any particular computing device. Now a single C++ application can use any combination of devices—including GPUs, CPUs, FPGAs and AI ASICs—that are suitable to the problems at hand.This book begins by introducing data parallelism and foundational topics for effective use of the SYCL standard from the Khronos Group and Data Parallel C++ (DPC++), the open source compiler used in this book. Later chapters cover advanced topics including error handling, hardware-specific programming, communication and synchronization, and memory model considerations.Data Parallel C++ provides you with everything needed to use SYCL for programming heterogeneous systems.What You'll LearnAccelerate C++ programs using data-parallel programmingTarget multiple device types (e.g. CPU, GPU, FPGA)Use SYCL and SYCL compilers Connect with computing’s heterogeneous future via Intel’s oneAPI initiativeWho This Book Is ForThose new data-parallel programming and computer programmers interested in data-parallel programming using C++.
Fuji is a vital apple cultivar, and has been propagated clonally for nearly a century. The chloroplast genome variation of Fuji apples in China has not been investigated.
This study used ...next-generation high-throughput sequencing and bioinformatics to compare and analyze the chloroplast genome of 24 Red Fuji varieties from nine regions in China.
The results showed that the 24 chloroplast genomes were highly conserved in genome size, structure, and organization. The length of the genomes ranged from 160,063 to 160,070 bp, and the GC content was 36.6%. Each of the 24 chloroplast genomes encoded 131 genes, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The results of repeat sequence detection were consistent; the most common sequence was forward repeats (53.1%), and the least common sequence was complementary repeats (4.1%). The chloroplast genome sequence of Red Fuji was highly conserved. Two indels were detected, but the PI value was 0, and there were no SNP loci. The chloroplast genome variation rate of Red Fuji was low.
Apple is one of the most important temperate deciduous fruit trees worldwide, with a wide range of cultivation. In this study, we assessed the variations and phylogenetic relationships between the ...complete chloroplast genomes of wild and cultivated apples (
spp.).
We obtained the complete chloroplast genomes of 24 apple varieties using next-generation sequencing technology and compared them with genomes of (downloaded from NCBI) the wild species.
The chloroplast genome of
is highly conserved, with a genome length of 160,067-160,290 bp, and all have a double-stranded circular tetrad structure. The gene content and sequences of genomes of wild species and cultivated apple were almost the same, but several mutation hotspot regions (
I-
A,
M-
D, and
C-
E) were detected in these genomes. These regions can provide valuable information for solving specific molecular markers in taxonomic research. Phylogenetic analysis revealed that
formed a new clade and four cultivated varieties clustered into a branch with
and
, which indicated that
and
were the ancestor species of the cultivated apple.
Data Parallel C++ Reinders, James; Ashbaugh, Ben; Brodman, James ...
2023
eBook
Open access
"This book, now in is second edition, is the premier resource to learn SYCL 2020 and is the ONLY book you need to become part of this community." Erik Lindahl, GROMACS and Stockholm University Learn ...how to accelerate C++ programs using data parallelism and SYCL. This open access book enables C++ programmers to be at the forefront of this exciting and important development that is helping to push computing to new levels. This updated second edition is full of practical advice, detailed explanations, and code examples to illustrate key topics. SYCL enables access to parallel resources in modern accelerated heterogeneous systems. Now, a single C++ application can use any combination of devices–including GPUs, CPUs, FPGAs, and ASICs–that are suitable to the problems at hand. This book teaches data-parallel programming using C++ with SYCL and walks through everything needed to program accelerated systems. The book begins by introducing data parallelism and foundational topics for effective use of SYCL. Later chapters cover advanced topics, including error handling, hardware-specific programming, communication and synchronization, and memory model considerations. All source code for the examples used in this book is freely available on GitHub. The examples are written in modern SYCL and are regularly updated to ensure compatibility with multiple compilers. What You Will Learn Accelerate C++ programs using data-parallel programming Use SYCL and C++ compilers that support SYCL Write portable code for accelerators that is vendor and device agnostic Optimize code to improve performance for specific accelerators Be poised to benefit as new accelerators appear from many vendors Who This Book Is For New data-parallel programming and computer programmers interested in data-parallel programming using C++ This is an open access book.
Insufficient prey density is a major factor hindering the recovery of the Amur tiger (
Panthera tigris altaica
), and to effectively restore the Amur tiger, red deer (
Cervus elaphus
) was released ...into the Huangnihe National Nature Reserve of Northeast China as the main reinforcement. Differences in feeding and synergistic changes caused by the intestinal microbial communities could impact the adaptation of wildlife following reintroductions into field environments. We analyzed the foraging changes in shaping the intestinal microbial community of the red deer after being released to the Huangnihe National Nature Reserve and screened the key microbial flora of the red deer when processing complex food resources. The feeding and intestinal microbial communities of the red deer were analyzed by plant Deoxyribonucleic acid (DNA) barcoding sequencing and 16S rRNA high-throughput sequencing, respectively. The results showed that there were significant differences in food composition between wild and released groups released in 2019 (R2):
n
= 5; released in 2021 (R0):
n
= 6; the wild group fed mainly on
Acer
(31.8%) and
Abies
(25.6%), R2 fed mainly on
Betula
(44.6%), R0 had not formed a clear preferred feeding pattern but had certain abilities to process and adapt to natural foods. Firmicutes (77.47%) and Bacteroides (14.16%) constituted the main bacterial phylum of red deer, of which, the phylum Firmicutes was the key species of the introduced red deer for processing complex food resources (
p
< 0.05). The wild release process significantly changed the intestinal microbial structure of the red deer, making it integrate into the wild red deer. The period since release into the wild may be a key factor in reshaping the structure of the microbial community. This study suggested that the intestinal microbial structure of red deer was significantly different depending on how long since captive deer has been translocated. Individuals that have lived in similar environments for a long time will have similar gut microbes. This is the adaption process of the wildlife to natural environment after wild release, taking into account the gut microbes, and the feeding changes in shaping microbial communities can help introduced red deer match complex food resources and novel field environments.
is an endangered species endemic to the tropical Hainan Island in southern China and of historical importance for Chinese medicine. It is currently the only unplaced species of the genus
...(Euphorbiaceae) due to its isolated island distribution and debated placement by a previous molecular phylogenetic study. We sequenced nuclear ITS and chloroplast
and
for newly collected accessions of
and additional
species found in Hainan, and analyzed the sequences in the context of the entire genus together with published data. All gene regions highly supported that
occupied an isolated phylogenetic position, showing no close affinity with any known
sections suggesting it was a new section. ITS placed
sister to sect.
(subgenus
) from Brazil with an estimated divergence time of 9.3-30.6 Mya while the chloroplast markers placed
at a position sister to the entire New World clade of
subgenus
. In addition, our karyological results suggested a close affinity between
and the New World species of
subg.
, with which shared the same chromosome number 2n = 28 and basic chromosome number x = 7. Phenotypically,
is unique with no close resemblance to other species in
subg.
. Based on its isolated biogeographical, karyological, and phenotypical position, we propose a new section
. subgenus
section
that might origin from long distance dispersal events because collective evidences showed a close affinity between the species from the Old World with those from the New World.
During the growth cycle, complex and variable environmental conditions, such as salinity, moisture, nutrients, and plant-plant interactions, may prompt plants to modulate ecological strategies. As a ...typical halophyte, the response mechanism and adaptation strategy of Suaeda salsa to various abiotic stress-by-competition interactions are still unclear. In this study, we aimed to explore the responses of S. salsa to combined abiotic stress and competition conditions to gain further insights into the ecological adaptation of halophytes to stress conditions. In this study, we aimed to explore the responses of S. salsa to combined abiotic stress and competition conditions to gain further insights into the ecological adaptation of halophytes to stress conditions. In a pot experiment, we set five density gradients of 1, 3, 6, 9, and 12 plants and conducted salt and drought stress experiments to explore the ecological adaptation strategies under abiotic stress-by-competition and the direct and/or indirect effects of key endogenous hormones and nutrients on plant growth. The results demonstrated that drought and planting density were the main environmental factors that restricted growth. Drought decreased biomass accumulation and competition intensity and delayed reproductive phenology and senescence. Competition promoted early anthesis and fructescence and reduced the vegetative organ to reproductive organ ratio to improve fitness. Changes in hormone and nutrient levels driven by the environment directly and/or indirectly affected growth independently and/or jointly. Total leaf phosphorus content and the endogenous hormone strigolactones directly affected biomass in different interaction modes and had positive and negative effects, respectively. This study improves our understanding of the importance of hormones and nutrients in plant ecological adaptation strategies and provides an effective reference for explaining the physiological mechanisms of plant ecological adaptation.
Collagens from marine animals are an important component of marine organic nitrogen. Collagenase-producing bacteria and their collagenases play important roles in collagen degradation and organic ...nitrogen recycling in the ocean. However, only a few collagenase-producing marine bacteria have been so far discovered. Here, we reported the isolation and characterization of a collagenase-secreting bacterium, designated strain SM1988
, isolated from a green alga
sample. Strain SM1988
is a Gram-negative, aerobic, oxidase-, and catalase-positive, unipolar flagellated, and rod-shaped bacterium capable of hydrolyzing casein, gelatin and collagens. Phylogenetic analysis revealed that strain SM1988
formed a distinct phylogenetic lineage along with known genera within the family
, with 16S rRNA gene sequence similarity being less than 93.3% to all known species in the family. Based on the phylogenetic, genomic, chemotaxonomic and phenotypic data, strain SM1988
was considered to represent a novel species in a novel genus in the family
, for which the name
gen. nov., sp. nov. is proposed, with the type strain being SM1988
(= MCCC 1K04279
= KCTC 72761
). Strain SM1988
showed a high production of extracellular collagenases, which had high activity against both bovine collagen and codfish collagen. Biochemical tests combined with genome and secretome analyses indicated that the collagenases secreted by strain SM1988
are serine proteases from the MEROPS S8 family. These data suggest that strain SM1988
acts as an important player in marine collagen degradation and recycling and may have a promising potential in collagen resource utilization.
Malus sieversii (Rosaceae), a wild apple tree occurred in China's Xinjiang province, is considered to be the ancestor of the modern cultivated apple. However, information on the chloroplast (cp) ...genome of this species is limited. With this study, we produced the first cp genome of M. sieversii using genome skimming. The whole cp genome was 163,230 bp long and comprised 128 genes, including 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The M. sieversii cp genome had a GC content of 35.6%. Phylogenetic analysis showed that M. sieversii was deeply nested within the Malus clade. This study will be useful for future studies on conservation genetics and potential applications in apple breeding.
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