Is there any intron sliding in mammals?

Abstract Background Eukaryotic protein-coding genes consist of exons and introns. Exon–intron borders are conserved between species and thus their changes might be observed only on quite long evolutionary distances. One of the rarest types of change, in which intron relocates over a short distance, is called "intron sliding", but the reality of this event has been debated for a long time. The main idea of a search for intron sliding is to use the most accurate genome annotation and genome sequence, as well as high-quality transcriptome data. We applied them in a search for sliding introns in mammals in order to widen knowledge about the presence or absence of such phenomena in this group. Results We didn’t find any significant evidence of intron sliding in the primate group (human, chimpanzee, rhesus macaque, crab-eating macaque, green monkey, marmoset). Only one possible intron sliding event supported by a set of high quality transcriptomes was observed between EIF1AX human and sheep gene orthologs. Also, we checked a list of previously observed intron sliding events in mammals and showed that most likely they are artifacts of genome annotations and are not shown in subsequent annotation versions as well as are not supported by transcriptomic data. Conclusions We assume that intron sliding is indeed a very rare evolutionary event if it exists at all. Every case of intron sliding needs a lot of supportive data for detection and confirmation.

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Chromosome-level genome assembly of Scapharca kagoshimensis reveals the expanded molecular basis of heme biosynthesis in ark shell

10.22541/au.162155566.67560449/v1 ◽

2021 ◽

Author(s):

Teng Weiming ◽

Xie Xi ◽

Hongtao Nie ◽

Yamin Sun ◽

Liu Xiangfeng ◽

...

Keyword(s):

Genome Assembly ◽

Molecular Basis ◽

Molecular Mechanisms ◽

Heme Biosynthesis ◽

High Quality ◽

Protein Coding ◽

Conserved Genes ◽

Long Time ◽

Muddy Sediments ◽

Chromosome Level

Ark shells are commercially important clam species that inhabit in muddy sediments of shallow coasts in East Asia. For a long time, the lack of genome resources has hindered scientific research of ark shells. Here, we reported a high-quality chromosome-level genome assembly of Scapharca kagoshimensis, with an aim to unravel the molecular basis of heme biosynthesis, and develop genomic resources for genetic breeding and population genetics in ark shells. Nineteen scaffolds corresponding to 19 chromosomes were constructed from 938 contigs (contig N50=2.01 Mb) to produce a final high-quality assembly with a total length of 1.11 Gb and scaffold N50 around 60.64 Mb. The genome assembly represents 93.4% completeness via matching 303 eukaryota core conserved genes. A total of 24,908 protein-coding genes were predicted and 24,551 genes (98.56%) of which were functionally annotated. The enrichment analyses suggested that genes in heme biosynthesis pathways were expanded and positive selection of the hemoglobin genes was also found in the genome of S. kagoshimensis, which gives important insights into the molecular mechanisms and evolution of the heme biosynthesis in mollusca. The valuable genome assembly of S. kagoshimensis would provide a solid foundation for investigating the molecular mechanisms that underlie the diverse biological functions and evolutionary adaptations of S. kagoshimensis.

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Update on hypnotherapy for psychiatrists

BJPsych Advances ◽

10.1192/bja.2021.54 ◽

2021 ◽

pp. 1-7

Author(s):

Natalie A. Chan ◽

Zhisong Zhang ◽

Guoxing Yin ◽

Zhimeng Li ◽

Roger C. Ho

Keyword(s):

Psychiatric Disorders ◽

Practice Guidelines ◽

Review Article ◽

Outcome Studies ◽

Evidence Based ◽

High Quality ◽

Long Time ◽

Meta Analyses ◽

Evidence Based Therapy

SUMMARY Although hypnosis has played a part in psychotherapy for a long time, it is not yet seen as an evidence-based therapy and is absent from many practice guidelines when it comes to the treatment of psychiatric disorders. At present, the applications and methods of hypnotherapy are poorly understood and other methods of psychotherapy tend to be favoured. This review article aims to introduce the role of hypnotherapy and its application for certain common psychiatric presentations, as well as examine its efficacy by summarising recent evidence from high-quality outcome studies and meta-analyses.

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Whole-Genome Sequencing of Chinese Yellow Catfish Provides a Valuable Genetic Resource for High-Throughput Identification of Toxin Genes

Toxins ◽

10.3390/toxins10120488 ◽

2018 ◽

Vol 10 (12) ◽

pp. 488 ◽

Cited By ~ 5

Author(s):

Shiyong Zhang ◽

Jia Li ◽

Qin Qin ◽

Wei Liu ◽

Chao Bian ◽

...

Keyword(s):

High Throughput ◽

Genome Assembly ◽

Raw Materials ◽

Pelteobagrus Fulvidraco ◽

Yellow Catfish ◽

High Quality ◽

Protein Coding ◽

Toxin Genes ◽

Sequencing Platforms ◽

High Quality Genome

Naturally derived toxins from animals are good raw materials for drug development. As a representative venomous teleost, Chinese yellow catfish (Pelteobagrus fulvidraco) can provide valuable resources for studies on toxin genes. Its venom glands are located in the pectoral and dorsal fins. Although with such interesting biologic traits and great value in economy, Chinese yellow catfish is still lacking a sequenced genome. Here, we report a high-quality genome assembly of Chinese yellow catfish using a combination of next-generation Illumina and third-generation PacBio sequencing platforms. The final assembly reached 714 Mb, with a contig N50 of 970 kb and a scaffold N50 of 3.65 Mb, respectively. We also annotated 21,562 protein-coding genes, in which 97.59% were assigned at least one functional annotation. Based on the genome sequence, we analyzed toxin genes in Chinese yellow catfish. Finally, we identified 207 toxin genes and classified them into three major groups. Interestingly, we also expanded a previously reported sex-related region (to ≈6 Mb) in the achieved genome assembly, and localized two important toxin genes within this region. In summary, we assembled a high-quality genome of Chinese yellow catfish and performed high-throughput identification of toxin genes from a genomic view. Therefore, the limited number of toxin sequences in public databases will be remarkably improved once we integrate multi-omics data from more and more sequenced species.

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Three Complete Mitochondrial Genomes of Orestes guangxiensis, Peruphasma schultei, and Phryganistria guangxiensis (Insecta: Phasmatodea) and Their Phylogeny

Insects ◽

10.3390/insects12090779 ◽

2021 ◽

Vol 12 (9) ◽

pp. 779 ◽

Cited By ~ 1

Author(s):

Ke-Ke Xu ◽

Qing-Ping Chen ◽

Sam Pedro Galilee Ayivi ◽

Jia-Yin Guan ◽

Kenneth B. Storey ◽

...

Keyword(s):

Sister Group ◽

Recent Common Ancestor ◽

Mitochondrial Genomes ◽

Sister Group Relationship ◽

Protein Coding ◽

Most Recent Common Ancestor ◽

Stick Insects ◽

Long Time ◽

Relationship Of ◽

Complete Mitochondrial Genomes

Insects of the order Phasmatodea are mainly distributed in the tropics and subtropics and are best known for their remarkable camouflage as plants. In this study, we sequenced three complete mitochondrial genomes from three different families: Orestes guangxiensis, Peruphasma schultei, and Phryganistria guangxiensis. The lengths of the three mitochondrial genomes were 15,896 bp, 16,869 bp, and 17,005 bp, respectively, and the gene composition and structure of the three stick insects were identical to those of the most recent common ancestor of insects. The phylogenetic relationships among stick insects have been chaotic for a long time. In order to discuss the intra- and inter-ordinal relationship of Phasmatodea, we used the 13 protein-coding genes (PCGs) of 85 species for maximum likelihood (ML) and Bayesian inference (BI) analyses. Results showed that the internal topological structure of Phasmatodea had a few differences in both ML and BI trees and long-branch attraction (LBA) appeared between Embioptera and Zoraptera, which led to a non-monophyletic Phasmatodea. Consequently, after removal of the Embioptera and Zoraptera species, we re-performed ML and BI analyses with the remaining 81 species, which showed identical topology except for the position of Tectarchus ovobessus (Phasmatodea). We recovered the monophyly of Phasmatodea and the sister-group relationship between Phasmatodea and Mantophasmatodea. Our analyses also recovered the monophyly of Heteropterygidae and the paraphyly of Diapheromeridae, Phasmatidae, Lonchodidae, Lonchodinae, and Clitumninae. In this study, Peruphasma schultei (Pseudophasmatidae), Phraortes sp. YW-2014 (Lonchodidae), and species of Diapheromeridae clustered into the clade of Phasmatidae. Within Heteropterygidae, O. guangxiensis was the sister clade to O. mouhotii belonging to Dataminae, and the relationship of (Heteropteryginae + (Dataminae + Obriminae)) was recovered.

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From a smokehouse to a vacuum dehydrator

Journal of Agricultural Sciences Belgrade ◽

10.2298/jas0401131z ◽

2004 ◽

Vol 49 (1) ◽

pp. 131-139

Author(s):

Branislav Zlatkovic ◽

Todor Vulic

Keyword(s):

Product Quality ◽

Food Industry ◽

Liquid Fuel ◽

Machine Building ◽

High Quality ◽

Great Honor ◽

Fruit Processing ◽

Long Time ◽

Vacuum Condensation ◽

Vacuum Dehydration

The tradition of fruit dehydration in Serbia has been long and anviable. It seems that Serbian machine-building in the area of fruit processing technology has given its greatest contribution in this field. It has been one 100 years since the smoking house of Mr Stokovic, PhD was announced to be the best and the most promising plum dehydrator at the open competition organized in Topcider by the Ministry of Agriculture. It was the first real almost continual fruit dehydrator where plums were moved at certain intervals closer and closer to the source of heat. Such a concept of plum dehydration from lower to higher temperatures was held on even later in perhaps our most famous dehydrator CER. Even the smoky smell was retained but liquid fuel was used for technical purposes. For a long time, it has been a well- known fact that vacuum dehydration has many advantages. In our country there have been many attempts to make fruit dehydrator of greater capacities in which vacuum would be used. Of course, there have been many problems, both technical and technological, but today a hundred years after accepting Stojkovic?s smokehouse, it is our great honor to present to you the results of plum dehydration in a home-made vacuum condensation dehydrator. We hope that now path is widely open to high quality dehydration, and not only for that plum, but for fruit susceptible to oxidation which is the reason our food industry has not produced it so far. This is probably a farewell to the most dangerous, but for the product quality, the most necessary operation - sulphuration.

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A Chromosome-Scale Genome Assembly Resource for Myriosclerotinia sulcatula Infecting Sedge Grass (Carex sp.)

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-03-20-0060-a ◽

2020 ◽

Vol 33 (7) ◽

pp. 880-883

Author(s):

Stefan Kusch ◽

Heba M. M. Ibrahim ◽

Catherine Zanchetta ◽

Celine Lopez-Roques ◽

Cecile Donnadieu ◽

...

Keyword(s):

Host Range ◽

Sclerotinia Sclerotiorum ◽

Genome Assembly ◽

Plant Pathogens ◽

Reference Genome ◽

Close Relative ◽

High Quality ◽

Protein Coding ◽

Protein Coding Genes ◽

Reference Genome Assembly

The fungus Myriosclerotinia sulcatula is a close relative of the notorious polyphagous plant pathogens Botrytis cinerea and Sclerotinia sclerotiorum but exhibits a host range restricted to plants from the Carex genus (Cyperaceae family). To date, there are no genomic resources available for fungi in the Myriosclerotinia genus. Here, we present a chromosome-scale reference genome assembly for M. sulcatula. The assembly contains 24 contigs with a total length of 43.53 Mbp, with scaffold N50 of 2,649.7 kbp and N90 of 1,133.1 kbp. BRAKER-predicted gene models were manually curated using WebApollo, resulting in 11,275 protein-coding genes that we functionally annotated. We provide a high-quality reference genome assembly and annotation for M. sulcatula as a resource for studying evolution and pathogenicity in fungi from the Sclerotiniaceae family.

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De Novo Assembly of a High-Quality Reference Genome for the Horned Lark (Eremophila alpestris)

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400846 ◽

2019 ◽

Vol 10 (2) ◽

pp. 475-478 ◽

Cited By ~ 3

Author(s):

Nicholas A. Mason ◽

Paulo Pulgarin ◽

Carlos Daniel Cadena ◽

Irby J. Lovette

Keyword(s):

Genome Assembly ◽

De Novo ◽

Single Copy ◽

Single Copy Gene ◽

High Quality ◽

Data Set ◽

Copy Gene ◽

Assembly Pipeline ◽

Horned Lark ◽

Gene Orthologs

The Horned Lark (Eremophila alpestris) is a small songbird that exhibits remarkable geographic variation in appearance and habitat across an expansive distribution. While E. alpestris has been the focus of many ecological and evolutionary studies, we still lack a highly contiguous genome assembly for the Horned Lark and related taxa (Alaudidae). Here, we present CLO_EAlp_1.0, a highly contiguous assembly for E. alpestris generated from a blood sample of a wild, male bird captured in the Altiplano Cundiboyacense of Colombia. By combining short-insert and mate-pair libraries with the ALLPATHS-LG genome assembly pipeline, we generated a 1.04 Gb assembly comprised of 2713 scaffolds, with a largest scaffold size of 31.81 Mb, a scaffold N50 of 9.42 Mb, and a scaffold L50 of 30. These scaffolds were assembled from 23685 contigs, with a largest contig size of 1.69 Mb, a contig N50 of 193.81 kb, and a contig L50 of 1429. Our assembly pipeline also produced a single mitochondrial DNA contig of 14.00 kb. After polishing the genome, we identified 94.5% of single-copy gene orthologs from an Aves data set and 97.7% of single-copy gene orthologs from a vertebrata data set, which further demonstrates the high quality of our assembly. We anticipate that this genomic resource will be useful to the broader ornithological community and those interested in studying the evolutionary history and ecological interactions of larks, which comprise a widespread, yet understudied lineage of songbirds.

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Genome sequence of the model rice variety KitaakeX

BMC Genomics ◽

10.1186/s12864-019-6262-4 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 6

Author(s):

Rashmi Jain ◽

Jerry Jenkins ◽

Shengqiang Shu ◽

Mawsheng Chern ◽

Joel A. Martin ◽

...

Keyword(s):

Functional Genomics ◽

De Novo ◽

Rice Variety ◽

Rice Genome ◽

Life Cycles ◽

Model Organisms ◽

High Quality ◽

Rice Varieties ◽

Protein Coding ◽

High Quality Genome

Abstract Background The availability of thousands of complete rice genome sequences from diverse varieties and accessions has laid the foundation for in-depth exploration of the rice genome. One drawback to these collections is that most of these rice varieties have long life cycles, and/or low transformation efficiencies, which limits their usefulness as model organisms for functional genomics studies. In contrast, the rice variety Kitaake has a rapid life cycle (9 weeks seed to seed) and is easy to transform and propagate. For these reasons, Kitaake has emerged as a model for studies of diverse monocotyledonous species. Results Here, we report the de novo genome sequencing and analysis of Oryza sativa ssp. japonica variety KitaakeX, a Kitaake plant carrying the rice XA21 immune receptor. Our KitaakeX sequence assembly contains 377.6 Mb, consisting of 33 scaffolds (476 contigs) with a contig N50 of 1.4 Mb. Complementing the assembly are detailed gene annotations of 35,594 protein coding genes. We identified 331,335 genomic variations between KitaakeX and Nipponbare (ssp. japonica), and 2,785,991 variations between KitaakeX and Zhenshan97 (ssp. indica). We also compared Kitaake resequencing reads to the KitaakeX assembly and identified 219 small variations. The high-quality genome of the model rice plant KitaakeX will accelerate rice functional genomics. Conclusions The high quality, de novo assembly of the KitaakeX genome will serve as a useful reference genome for rice and will accelerate functional genomics studies of rice and other species.

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Labelling Training Samples Using Crowdsourcing Annotation for Recommendation

Complexity ◽

10.1155/2020/1670483 ◽

2020 ◽

Vol 2020 ◽

pp. 1-10

Author(s):

Qingren Wang ◽

Min Zhang ◽

Tao Tao ◽

Victor S. Sheng

Keyword(s):

Supervised Learning ◽

Random Order ◽

Ground Truth ◽

Training Sample ◽

Machine Intelligence ◽

High Quality ◽

Inference Algorithms ◽

Training Samples ◽

Expert Annotation ◽

Long Time

The supervised learning-based recommendation models, whose infrastructures are sufficient training samples with high quality, have been widely applied in many domains. In the era of big data with the explosive growth of data volume, training samples should be labelled timely and accurately to guarantee the excellent recommendation performance of supervised learning-based models. Machine annotation cannot complete the tasks of labelling training samples with high quality because of limited machine intelligence. Although expert annotation can achieve a high accuracy, it requires a long time as well as more resources. As a new way of human intelligence to participate in machine computing, crowdsourcing annotation makes up for shortages of machine annotation and expert annotation. Therefore, in this paper, we utilize crowdsourcing annotation to label training samples. First, a suitable crowdsourcing mechanism is designed to create crowdsourcing annotation-based tasks for training sample labelling, and then two entropy-based ground truth inference algorithms (i.e., HILED and HILI) are proposed to achieve quality improvement of noise labels provided by the crowd. In addition, the descending and random order manners in crowdsourcing annotation-based tasks are also explored. The experimental results demonstrate that crowdsourcing annotation significantly improves the performance of machine annotation. Among the ground truth inference algorithms, both HILED and HILI improve the performance of baselines; meanwhile, HILED performs better than HILI.

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High-Quality Draft Genome Sequence of Burkholderia contaminans CH-1, a Gram-Negative Bacterium That Metabolizes 2-Azahypoxanthine, a Plant Growth-Regulating Compound

Genome Announcements ◽

10.1128/genomea.01148-17 ◽

2017 ◽

Vol 5 (41) ◽

Cited By ~ 1

Author(s):

Jae-Hoon Choi ◽

Hikaru Sugiura ◽

Ryota Moriuchi ◽

Hirokazu Kawagishi ◽

Hideo Dohra

Keyword(s):

Plant Growth ◽

Genome Sequence ◽

Draft Genome ◽

Draft Genome Sequence ◽

Negative Bacterium ◽

High Quality ◽

Protein Coding ◽

Coding Sequences ◽

Content Type ◽

Burkholderia Contaminans

ABSTRACT Burkholderia contaminans strain CH-1 converts 2-azahypoxnathine to 2-aza-8-oxohypoxanthine, plant growth-regulating compounds, by oxidation. We report here the high-quality draft genome sequence of B. contaminans CH-1. The genome contains 8,065 protein-coding sequences, including several genes possibly involved in metabolizing 2-azahypoxanthine.

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