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1. Genome-wide identification of RNA editing sites in chloroplast transcripts and multiple organellar RNA editing factors in tea plant (Camellia sinensis L.): Insights into the albinism mechanism of tea leaves

Author:
Yuxin Zhao; Ruoshi Gao; Zhen Zhao; Shunkai Hu; Rui Han; Anburaj Jeyaraj; Emmanuel Arkorful; Xinghui Li; Xuan Chen
Source:
Gene 2023 v.848 pp. 146898
ISSN:
0378-1119
Subject:
chloroplast genome,   etc   ; Camellia sinensis; RNA; albino; chloroplasts; chromosomes; cultivars; genes; models; tea;     Show all 10 Subjects
Abstract:
... RNA editing is a post-transcriptional modification process, the chloroplast genes of which are involved in the process of chloroplast development in plant. However, the RNA editing sites of chloroplast genes remains unknown. In this study, we identified 39 RNA editing sites in 18 chloroplast genes from chloroplast genome of C. sinensis. Furthermore, the feature, structures and specificity of RNA e ...
DOI:
10.1016/j.gene.2022.146898

2. The complete mitogenome of Echinoparyphium aconiatum (Digenea: Echinostomatidae) and a comparison with other digenean species

Author:
Janelle Laura J. Gacad; Shoko Tanabe-Hosoi; Natalia I. Yurlova; Misako Urabe
Source:
Parasitology international 2023 v.92 pp. 102682
ISSN:
1383-5769
Subject:
mitochondrial genome,   etc   ; Echinoparyphium; Echinostoma; genes; intestines; mitochondria; monophyly; parasites; parasitology; transfer RNA; Eurasia;     Show all 11 Subjects
Abstract:
... Echinoparyphium aconiatum (Digenea: Echinostomatidae) is an intestinal parasite of anatid and snail-eating birds. In Eurasia, it is also common in lymnaeid snails, which may serve as the first and second intermediate hosts. The systematics of its genus, Echinoparyphium, have long been inadequate, with poor descriptions and extensive synonymy. To provide a basis for developing new genetic markers f ...
DOI:
10.1016/j.parint.2022.102682

3. Characterization of invertase inhibitors (InvInhs) in tea plant, and their potential roles in participating in growth, development and cold response

Author:
Shan He; Bo Li; Huan Wang; Shicai Liang; Zhaotang Ding; Yu Wang; Kai Fan; Jianhui Hu; Xinchao Wang; Wenjun Qian
Source:
Scientia horticulturae 2023 v.308 pp. 111580
ISSN:
0304-4238
Subject:
genome,   etc   ; acclimation; beta-fructofuranosidase; bioinformatics; chromosomes; cold; cold stress; cultivars; tea; water stress;     Show all 10 Subjects
Abstract:
... Invertase inhibitor (InvInh) represses acid invertase (AI) activity though interacting with AI at post-translation level, which plays important roles in vegetative and reproductive processes and stress responses of plant. Our previous studies revealed that CsAI genes were involved in regulating cold response of tea plant, while the post-translation regulation mechanism of AI and the roles of InvIn ...
DOI:
10.1016/j.scienta.2022.111580

4. Evaluating cost-effective genotyping strategies for genomic selection in oysters

Author:
Thomas A. Delomas; Christopher M. Hollenbeck; Joseph L. Matt; Neil F. Thompson
Source:
Aquaculture 2023 v.562 pp. 738844
ISSN:
0044-8486
Subject:
genome,   etc   ; Crassostrea; aquaculture; breeding stock; cost effectiveness; genetic improvement; genotype; genotyping; marker-assisted selection; oysters; phenotype;     Show all 11 Subjects
Abstract:
... Genomic selection has the potential to increase the rate of genetic gain in aquaculture breeding programs by enabling selection between and within families without phenotyping selection candidates. Due to the wide range of environments in which oysters are cultured, an industry-wide approach of multiple regional breeding programs has been suggested for Crassostrea sp. This necessitates genotyping ...
DOI:
10.1016/j.aquaculture.2022.738844
CHORUS:
10.1016/j.aquaculture.2022.738844

5. Metabolic profiling reveals genotype-associated alterations in carotenoid content during banana postharvest ripening

Author:
Ou Sheng; Zhibin Yin; Wenjie Huang; Mengyu Chen; Mingyi Du; Qian Kong; Alisdair R. Fernie; Ganjun Yi; Shijuan Yan
Source:
Food chemistry 2023 v.403 pp. 134380
ISSN:
0308-8146
Subject:
genome,   etc   ; bananas; carotenoids; cultivars; food chemistry; genotype; glycolysis; health promotion; metabolites; metabolomics; pulp; tricarboxylic acid cycle;     Show all 12 Subjects
Abstract:
... Banana fruits have attracted considerable attention for health-promoting effects attributed to ubiquitous functional metabolites. However, genotype-dependent accumulation patterns of carotenoids in banana remain largely unclear. Here, we performed a systematic metabolomic investigation of 18 banana cultivars of the AAA, AAB, or ABB genome groups. Our results indicate that the levels of soluble sug ...
DOI:
10.1016/j.foodchem.2022.134380

6. β-ketoacyl-CoA synthase improves the drought tolerance of root restricted grown grapevines by regulating the cuticular wax biosynthesis

Author:
Boyang Liu; Yanli Sun; Xiangyi Li; Dinghan Guo; Liping Zhao; Chao Ma; Lei Wang; Shiping Wang
Source:
Scientia horticulturae 2023 v.307 pp. 111494
ISSN:
0304-4238
Subject:
genome,   etc   ; Arabidopsis; Vitis; biosynthesis; cultivars; drought; drought tolerance; endoplasmic reticulum; epicuticular wax; fruits; grapes; transcriptomics; water stress;     Show all 13 Subjects
Abstract:
... Drought stress limits fruit ripening and quality of grape cultivar, particularly with the use of root restriction. However, the mechanism involved in the molecular response to water deficit concomitant to agriculture adjustment remains poorly understood. In the present study, the regulation of two grape β-ketoacyl-CoA synthase (KCS) genes obtained with transcriptome analysis whose expression is si ...
DOI:
10.1016/j.scienta.2022.111494

7. New insights into lincomycin biodegradation by Conexibacter sp. LD01: Genomics characterization, biodegradation kinetics and pathways

Author:
Huaxin Lei; Jiayu Zhang; Jin Huang; Dengjin Shen; Yin Li; Rui Jiao; Renxin Zhao; Xiaoyan Li; Lin Lin; Bing Li
Source:
Journal of hazardous materials 2023 v.441 pp. 129824
ISSN:
0304-3894
Subject:
genome,   etc   ; Actinobacteria; activated sludge; ammonium nitrogen; biodegradation; carbon; energy; genomics; glucose; lincomycin; logit analysis; nitrogen; oxidation; sodium pyruvate;     Show all 14 Subjects
Abstract:
... The aerobic, lincomycin-degrading bacterial strain Conexibacter sp. LD01, belonging to the phylum Actinobacteria, was isolated from activated sludge. Both second- and third-generation sequencing technologies were applied to uncover the genomic characterization and high-quality genome with 99.2% completeness and 2.2% contamination was obtained. The biodegradation kinetics of lincomycin fit well wit ...
DOI:
10.1016/j.jhazmat.2022.129824

8. Mitochondrial genomes of the land hermit crab Coenobita clypeatus (Anomura: Paguroidea) and the mole crab Emerita talpoida (Anomura: Hippoidea) with insights into phylogenetic relationships in the Anomura (Crustacea: Decapoda)

Author:
Angélica Colín; Carolina Galván-Tirado; Laura Carreón-Palau; Heather D. Bracken-Grissom; J. Antonio Baeza
Source:
Gene 2023 v.849 pp. 146896
ISSN:
0378-1119
Subject:
mitochondrial genome,   etc   ; Coenobitidae; Diogenidae; Emerita talpoida; Lithodidae; Paguridae; codon usage; cytosine; ecology; mitochondria; monophyly; physiology; polyphyly; ribosomal RNA; thymine; transfer RNA;     Show all 16 Subjects
Abstract:
... The infraorder Anomura is a species-rich clade of decapod crustaceans recognized by its remarkable disparity in terms of morphology, anatomy, ecology, physiology, and behavior. This study assembled and characterized the complete mitochondrial genomes of two anomuran species, the hermit crab Coenobita clypeatus and the mole crab Emerita talpoida. The AT-rich mitochondrial genomes of C. clypeatus an ...
DOI:
10.1016/j.gene.2022.146896

9. Comprehensive analysis of bZIP gene family and function of RcbZIP17 on Botrytis resistance in rose (Rosa chinensis)

Author:
Dandan Li; Xiaomei Li; Xintong Liu; Zhao Zhang
Source:
Gene 2023 v.849 pp. 146867
ISSN:
0378-1119
Subject:
genome-wide association study,   etc   ; Botrytis cinerea; Rosa chinensis; chromosomes; gene duplication; gene expression; genes; gray mold; ornamental plants; phylogeny; plant pathogens;     Show all 11 Subjects
Abstract:
... Rose is an important ornamental plant and a commercial source of natural fragrances and essential oils. However, gray mold is the most serious disease of rose during cultivation and post-harvest. In plants, the bZIP gene family is one of the important families of transcription factors that regulate many biological processes, including pathogen defense, light response, and stress signaling. Althoug ...
DOI:
10.1016/j.gene.2022.146867

10. A sustainability assessment framework for genome-edited salmon

Author:
Torill B. Blix; Anne I. Myhr
Source:
Aquaculture 2023 v.562 pp. 738803
ISSN:
0044-8486
Subject:
genome,   etc   ; animal welfare; aquaculture; aquaculture industry; biosphere; case studies; crossing; environmental protection; ethics; gene editing; issues and policy; salmon; society; stakeholders;     Show all 14 Subjects
Abstract:
... In this paper we present a suggestion for a sustainability assessment framework using genome editing of salmon as a case study. The salmon farming industry is facing several challenges hindering sustainable production. Genome editing has entered as a tool that can improve selective breeding and feed ingredients in aquaculture, hence providing solutions such as resistance to salmon lice and other p ...
DOI:
10.1016/j.aquaculture.2022.738803

11. Integrated multi-omic analyses on yellow Flammulina filiformis cultivar reveal postharvest oxidative damage responses

Author:
Yu Fu; Hao Tan; Bo Wang; Weihong Peng; Qun Sun; Yang Yu
Source:
Postharvest biology and technology 2023 v.195 pp. 112111
ISSN:
0925-5214
Subject:
genome,   etc   ; DNA; Flammulina; biosynthesis; catechol oxidase; cell senescence; cultivars; laccase; melanin; mushrooms; oxidative phosphorylation; oxygen; proteolysis; proteome; proteomics; technology; transcriptome; transcriptomics; tyrosine;     Show all 19 Subjects
Abstract:
... Yellow cultivars of Flammulina filiformis are prone to browning, which causes significant yearly loss. This study investigated the critical factors involved and revealed that oxygen plays an essential role in the browning process. Integrated multi-omic analyses, including genome sequencing, transcriptome profiling, and 4D label-free proteome quantification, were incorporated to dissect essential g ...
DOI:
10.1016/j.postharvbio.2022.112111

12. Genome–wide association study and genomic prediction of growth traits in bighead catfish (Clarias macrocephalus Günther, 1864)

Author:
Prapaiphan Chaivichoo; Sila Sukhavachana; Rabuesak Khumthong; Prapansak Srisapoome; Satid Chatchaiphan; Uthairat Na-Nakorn
Source:
Aquaculture 2023 v.562 pp. 738748
ISSN:
0044-8486
Subject:
genome-wide association study,   etc   ; Clarias macrocephalus; DNA; aquaculture; body weight; catfish; cost effectiveness; genes; genetic improvement; genetic variance; genomics; genotyping; heritability; marker-assisted selection; parentage; phenotype; prediction; technology; variance; zinc finger motif;     Show all 20 Subjects
Abstract:
... Next-generation sequencing (NGS) enables cost-effective exploration of genome-wide single nucleotide polymorphisms (SNPs). This new technology has made enormous contributions in various fields including genetic improvement. This study was conducted to identify SNPs that associated with growth traits (body weight, standard length, and total length) of bighead catfish (Clarias macrocephalus Günther, ...
DOI:
10.1016/j.aquaculture.2022.738748

13. TT-Mars: structural variants assessment based on haplotype-resolved assemblies

Author:
Jianzhi Yang; Mark J.P. Chaisson
Source:
Genome biology 2022 v.23 no.1 pp. 110
ISSN:
1474-760X
Subject:
genome; genome assembly,   etc   ; testing;     Show all 3 Subject
Abstract:
... Variant benchmarking is often performed by comparing a test callset to a gold standard set of variants. In repetitive regions of the genome, it may be difficult to establish what is the truth for a call, for example, when different alignment scoring metrics provide equally supported but different variant calls on the same data. Here, we provide an alternative approach, TT-Mars, that takes advantag ...
DOI:
10.1186/s13059-022-02666-2

14. Integrated serum pharmacochemistry and network pharmacology analyses reveal the bioactive metabolites and potential functional mechanism of ground cherry (Physalis pruinosa L.) in treatment of type 2 diabetes mellitus in rats

Author:
Asmaa Mahana; Hala M. Hammoda; Asmaa A. Khalifa; Samar S. Elblehi; Fathallah M. Harraz; Eman Shawky
Source:
Journal of ethnopharmacology 2023 v.300 pp. 115750
ISSN:
0378-8741
Subject:
genome,   etc   ; Physalis pruinosa; atherosclerosis; blood serum; calyx; cherries; gene ontology; glucose; glycemic effect; high fat diet; histopathology; immunoblotting; insulin; lipid metabolism; lipids; mechanism of action; metabolites; models; noninsulin-dependent diabetes mellitus; pharmacology; quercetin; rats; streptozotocin; traditional medicine;     Show all 24 Subjects
Abstract:
... Different Physalis plants have been widely employed in traditional medicine for management of diabetes mellitus. Previous studies with respect to the in vivo antidiabetic activity of Physalis plants illustrated that they improved glucose and lipid metabolism in streptozotocin (STZ) -induced diabetic rats yet the mechanism of action of bioactive constituents of the different organs of Physalis plan ...
DOI:
10.1016/j.jep.2022.115750

15. Validation of reference-assisted assembly using existing and novel Heliothine genomes

Author:
Rong Guo; Alexie Papanicolaou; Megan L. Fritz
Source:
Genomics 2022 v.114 no.5 pp. 110441
ISSN:
0888-7543
Subject:
genome; genome assembly,   etc   ; Heliothis; genomics; host plants; insects;     Show all 6 Subjects
Abstract:
... Chloridea subflexa and Chloridea virescens are a pair of closely related noctuid species exhibiting pheromone-based sexual isolation and divergent host plant preferences. We produced a novel Illumina short read C. subflexa genome assembly and an improved C. virescens genome assembly, which offer opportunities to study the genomic basis for evolutionarily important traits in this lepidopteran famil ...
DOI:
10.1016/j.ygeno.2022.110441
CHORUS:
10.1016/j.ygeno.2022.110441

16. Draft genome assembly and sequencing dataset of the marine diatom Skeletonema cf. costatum RCC75

Author:
Maria Sorokina; Emanuel Barth; Mahnoor Zulfiqar; Michiel Kwantes; Georg Pohnert; Christoph Steinbeck
Source:
Data in Brief 2022 v.41 pp. 107931
ISSN:
2352-3409
Subject:
genome; genome assembly,   etc   ; Bacillariophyceae; Skeletonema costatum; data collection; phytoplankton;     Show all 6 Subjects
Abstract:
... Diatoms (Bacillariophyceae) are a major constituent of the phytoplankton and have a universally recognized ecological importance. Between 1,000 and 1,300 diatom genera have been described in the literature, but only 10 nuclear genomes have been published and made available to the public up to date. Skeletonema costatum is a cosmopolitan marine diatom, principally occurring in coastal regions, and ...
DOI:
10.1016/j.dib.2022.107931

17. Whole-genome sequence data of cellulase-producing fungi Trichoderma asperellum PK1J2, isolated from palm empty fruit bunch in Riau, Indonesia

Author:
Fela Laila Nur Hidayati; Dian Anggraini Suroto; Sardjono; Muhammad Nur Cahyanto; Jaka Widada
Source:
Data in Brief 2022 v.45 pp. 108607
ISSN:
2352-3409
Subject:
genome; genome assembly,   etc   ; Trichoderma asperellum; computer software; fruits; fungi; Indonesia;     Show all 7 Subjects
Abstract:
... Trichoderma asperellum PK1J2 is a promising cellulase-producing fungus isolated from a palm empty fruit bunch in Riau, Indonesia. Presented here is the genome assembly of T. asperellum PK1J2. The whole genome of the fungi was sequenced using Illumina NovaSeq PE150. The genome assembly was performed using SOAPdenovo, SPAdes, and Abyss software, and the assembly results of the three types of softwar ...
DOI:
10.1016/j.dib.2022.108607

18. The entire chloroplast genome sequence of Asparagus cochinchinensis and genetic comparison to Asparagus species

Author:
Wentao Sheng
Source:
Open life sciences 2022 v.17 no.1 pp. 893-906
ISSN:
2391-5412
Subject:
chloroplast genome; genome assembly,   etc   ; chloroplasts; codons; genomics; medicinal plants; phylogeny;     Show all 7 Subjects
Abstract:
... Asparagus cochinchinensis is a traditional Chinese medicinal plant. The chloroplast (cp) genome study on A. cochinchinensis is poorly understood. In this research, we collected the data from the cp genome assembly and gene annotation of A. cochinchinensis, followed by further comparative analysis with six species in the genus Asparagus. The cp genome of A. cochinchinensis showed a circular quadrip ...
DOI:
10.1515/biol-2022-0098

19. Genetic diversity, population structure, linkage disequilibrium and GWAS for resistance to WSSV in Pacific white shrimp (Litopenaeus vannamei) using a 50K SNP chip

Author:
Thania Medrano-Mendoza; Baltasar F. García; Alejandra Caballero-Zamora; José M. Yáñez; Leobardo Montoya-Rodríguez; Juan C. Quintana-Casares; Marina Durán-Aguilar; Gabriel R. Campos-Montes
Source:
Aquaculture 2023 v.562 pp. 738835
ISSN:
0044-8486
Subject:
genome-wide association study,   etc   ; DNA-directed RNA polymerase; Litopenaeus vannamei; White spot syndrome virus; aquaculture; arylsulfatase; chromosomes; death; genetic variance; genetic variation; genotyping; hepatopancreas; humoral immunity; immune response; linkage disequilibrium; marker-assisted selection; necrotizing hepatopancreatitis; oxidoreductases; population structure; principal component analysis; quality control; Ecuador; Panama;     Show all 23 Subjects
Abstract:
... The objectives of this research were to assess the genetic diversity, population structure, linkage disequilibrium and perform a genome-wide association study (GWAS) to search for single nucleotide polymorphisms (SNPs) that associate with the resistance of Pacific white shrimp (Litopenaeus vannamei) to White Spot Syndrome Virus (WSSV). The line here analyzed was formerly founded with animals origi ...
DOI:
10.1016/j.aquaculture.2022.738835

20. Effects of geographic isolation on the Bulbophyllum chloroplast genomes

Author:
Jiapeng Yang; Fuwei Zhang; Yajie Ge; Wenhui Yu; Qiqian Xue; Mengting Wang; Hongman Wang; Qingyun Xue; Wei Liu; Zhitao Niu; Xiaoyu Ding
Source:
BMC plant biology 2022 v.22 no.1 pp. 201
ISSN:
1471-2229
Subject:
chloroplast genome; mitochondrial genome; nuclear genome,   etc   ; Bulbophyllum; Crassulacean acid metabolism; Oligocene epoch; chloroplasts; phylogeny; plant biology; Asia; Australia; South America;     Show all 12 Subjects
Abstract:
... BACKGROUND: Because chloroplast (cp) genome has more conserved structures than nuclear genome and mitochondrial genome, it is a useful tool in estimating the phylogenetic relationships of plants. With a series of researches for cp genomes, there have been comprehensive understandings about the cp genome features. The genus Bulbophyllum widely distributed in Asia, South America, Australia and other ...
DOI:
10.1186/s12870-022-03592-y