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1. HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps

Author:
Yuxuan Du; Fengzhu Sun
Source:
Genome biology 2022 v.23 no.1 pp. 63
ISSN:
1474-760X
Subject:
chromosomes,   etc   ; algorithms; genome; metagenomics;     Show all 4 Subjects
Abstract:
... Recovering high-quality metagenome-assembled genomes (MAGs) from complex microbial ecosystems remains challenging. Recently, high-throughput chromosome conformation capture (Hi-C) has been applied to simultaneously study multiple genomes in natural microbial communities. We develop HiCBin, a novel open-source pipeline, to resolve high-quality MAGs utilizing Hi-C contact maps. HiCBin employs the Hi ...
DOI:
10.1186/s13059-022-02626-w

2. A parallelized hybrid genetic algorithm with differential evolution for heat exchanger network retrofit

Author:
Jan A. Stampfli; Donald G. Olsen; Beat Wellig; René Hofmann
Source:
MethodsX 2022 v.9 pp. 101711
ISSN:
2215-0161
Subject:
chromosomes,   etc   ; algorithms; heat; heat exchangers; topology;     Show all 5 Subjects
Abstract:
... The challenge of heat exchanger network retrofit is often addressed using deterministic algorithms. However, the complexity of the retrofit problems, combined with multi-period operation, makes it very difficult to find any feasible solution. In contrast, stochastic algorithms are more likely to find feasible solutions in complex solution spaces. This work presents a customized evolutionary based ...
DOI:
10.1016/j.mex.2022.101711

3. Candidate sex-associated gene identification in Trachinotus ovatus (Carangidae) using an integrated SLAF-seq and bulked segregant analysis approach

Author:
Pingping He; Pinyuan Wei; Yuan Ma; Shenhua Hu; Jiuxiang Yao; Xiaozhen Jiang; Youhou Xu; Peng Zhu; Mingli Wei; Weiming Jiang; Jinxia Peng
Source:
Gene 2022 v.809 pp. 146026
ISSN:
0378-1119
Subject:
chromosomes,   etc   ; DNA; Trachinotus ovatus; genes; single nucleotide polymorphism;     Show all 5 Subjects
Abstract:
... It is difficult to distinguish the sexes of Trachinotus ovatus based on appearance, and little data about sex-determining genes are available for this species. Here, we generated 200 F2 individuals using the parents R404 and R403. DNA samples were collected from 50 individuals of each sex and aggregated into sex-specific DNA pools. Specific-locus amplified fragment sequencing was integrated with b ...
DOI:
10.1016/j.gene.2021.146026

4. Combined GWAS and QTL mapping revealed candidate genes and SNP network controlling recovery and tolerance traits associated with drought tolerance in seedling winter wheat

Author:
Ahmed Sallam; Shamseldeen Eltaher; Ahmad M. Alqudah; Vikas Belamkar; P. Stephen Baenziger
Source:
Genomics 2022 v.114 no.3 pp. 110358
ISSN:
0888-7543
Subject:
chromosomes,   etc   ; drought tolerance; genes; genomics; seedlings; winter wheat;     Show all 6 Subjects
Abstract:
... To date, very little research on drought tolerance has been conducted at the seedling stage in winter wheat. In this study, two types of traits, namely tolerance and recovery traits, associated with drought tolerance were scored in biparental mapping population (BPP) and association mapping population (A-set). The results of this study revealed no or weak significant correlation between the two ty ...
DOI:
10.1016/j.ygeno.2022.110358

5. Chromosome-level genome sequence data and analysis of the white koji fungus, Aspergillus luchuensis mut. kawachii IFO 4308

Author:
Kazuki Mori; Chihiro Kadooka; Ken Oda; Kayu Okutsu; Yumiko Yoshizaki; Kazunori Takamine; Kosuke Tashiro; Masatoshi Goto; Hisanori Tamaki; Taiki Futagami
Source:
Data in Brief 2022 v.41 pp. 107888
ISSN:
2352-3409
Subject:
chromosomes,   etc   ; Aspergillus; fungi; genome; koji; mitochondrial DNA; nucleotide sequences;     Show all 7 Subjects
Abstract:
... Aspergillus luchuensis mut. kawachii is used primarily in the production of shochu, a traditional Japanese distilled alcoholic beverage. Here, we report the chromosome-level genome sequence of A. luchuensis mut. kawachii IFO 4308 (NBRC 4308) and a comparison of the sequence with that of A. luchuensis RIB2601. The genome of strain IFO 4308 was assembled into nine contigs consisting of eight chromos ...
DOI:
10.1016/j.dib.2022.107888

6. Fish genomics and its impact on fundamental and applied research of vertebrate biology

Author:
Syed Farhan Ahmad; Maryam Jehangir; Kornsorn Srikulnath; Cesar Martins
Source:
Reviews in fish biology and fisheries 2022 v.32 no.2 pp. 357-385
ISSN:
0960-3166
Subject:
chromosomes,   etc   ; applied research; data collection; ecology; fish; genome; genomics;     Show all 7 Subjects
Abstract:
... The living fishes span a unique and interesting set of animals because of their vast diversity, morphology, ecology, genetics and genomics, and higher importance to biology, economy and culture. During the past decade, the remarkable increase in fish genome sequencing has revolutionized comparative and evolutionary genomics, with the outcome of stimulating insights into vertebrate genome biology. ...
DOI:
10.1007/s11160-021-09691-7

7. Genome Resource of a Hypervirulent Strain C9-3 of Xanthomonas oryzae pv. oryzae Causing Bacterial Blight of Rice

Author:
Xiaolin Chen; Qili Li; Jinkai Wang; Yu Zhang; Lihua Tang; Suiping Huang; Jianyou Mo; Tangxun Guo
Source:
Plant disease 2022 v.106 no.2 pp. 741-744
ISSN:
0191-2917
Subject:
chromosomes,   etc   ; DNA; Xanthomonas oryzae pv. oryzae; blight; rice; virulence;     Show all 6 Subjects
Abstract:
... Xanthomonas oryzae pv. oryzae is the causal agent of bacterial blight, one of the most devastating diseases of rice. Here, a hypervirulent strain, C9-3, defeating Xa1, Xa10, xa13, and Xa23 resistance genes, was used to extract genomic DNA for single molecule real-time (SMRT) sequencing. After assembly, the genome consists of a single-circular chromosome with the size of 4,924,298 bp with G+C conte ...
DOI:
10.1094/PDIS-07-21-1565-A

8. Homoploid hybrids, allopolyploids, and high ploidy levels characterize the evolutionary history of a western North American quillwort (Isoëtes) complex

Author:
Jacob S. Suissa; Sylvia P. Kinosian; Peter W. Schafran; Jay F. Bolin; W. Carl Taylor; Elizabeth A. Zimmer
Source:
Molecular phylogenetics and evolution 2022 v.166 pp. 107332
ISSN:
1055-7903
Subject:
chromosomes,   etc   ; DNA; allopolyploidy; cytotypes; data collection; hybridization; phylogeny; tetraploidy;     Show all 8 Subjects
Abstract:
... Polyploidy and hybridization are important processes in seed-free plant evolution. However, a major gap lies in our understanding of how these processes affect the evolutionary history of high-ploidy systems. The heterosporous lycophyte genus Isoëtes is a lineage with many putative hybrids and high-level polyploid taxa (ranging from tetraploid to dodecaploid). Here, we use a complex of western Nor ...
DOI:
10.1016/j.ympev.2021.107332

9. Regulation of miR-30b in cancer development, apoptosis, and drug resistance

Author:
Zhen-Jie Fu; Yan Chen; Yu-Qin Xu; Mei-Ai Lin; Hang Wen; Yi-Tao Chen; Pei-Lei Pan
Source:
Open life sciences 2022 v.17 no.1 pp. 102-106
ISSN:
2391-5412
Subject:
chromosomes,   etc   ; antineoplastic agents; apoptosis; carcinogenesis; drug resistance; genes; neoplasms;     Show all 7 Subjects
Abstract:
... miR-30b, which is encoded by the gene located on chromosome 8q24.22, plays an important role in a variety of diseases. In most types of tumors, miR-30b significantly inhibits the proliferation, migration, and invasion of cancer cells through the regulation of target genes. Moreover, miR-30b can inhibit the PI3K/AKT signaling pathway through the regulation of EGFR, AKT, Derlin-1, GNA13, SIX1, and o ...
DOI:
10.1515/biol-2022-0017

10. TetR-Type Regulator Lp_2642 Positively Regulates Plantaricin EF Production Based on Genome-Wide Transcriptome Sequencing of Lactiplantibacillus plantarum 163

Author:
Deyin Zhao; Qian Wang; Fanqiang Meng; Fengxia Lu; Xiaomei Bie; Zhaoxin Lu; Yingjian Lu
Source:
Journal of agricultural and food chemistry 2022 v.70 no.14 pp. 4362-4372
ISSN:
1520-5118
Subject:
chromosomes,   etc   ; biosynthesis; food chemistry; plantaricins; plasmids; transcription (genetics); transcriptome;     Show all 7 Subjects
Abstract:
... Whole-genome and transcriptome sequences of Lactiplantibacillus plantarum 163 are provided. There was one circular chromosome and four circular plasmids, with sizes of 3,131,367; 56,674; 49,140; 43,628; and 36,387 bp, respectively, in L. plantarum 163. The regulator Lp_2642 was selected from the genome data, the overexpression of which increased the transcriptional levels of related genes in plant ...
DOI:
10.1021/acs.jafc.2c00206

11. Conversion between duplicated genes generated by polyploidization contributes to the divergence of poplar and willow

Author:
Jianyu Wang; Lan Zhang; Jiaqi Wang; Yanan Hao; Qimeng Xiao; Jia Teng; Shaoqi Shen; Yan Zhang; Yishan Feng; Shoutong Bao; Yu Li; Zimo Yan; Chendan Wei; Li Wang; Jinpeng Wang
Source:
BMC plant biology 2022 v.22 no.1 pp. 298
ISSN:
1471-2229
Subject:
chromosomes,   etc   ; Populus trichocarpa; Salix; evolution; gene conversion; genomics; plant biology;     Show all 7 Subjects
Abstract:
... BACKGROUND: Gene conversion has an important effect on duplicate genes produced by polyploidization. Poplar (Populus trichocarpa) and willow (Salix brachista) are leading models and excellent green plants in the Salicaceae. Although much attention has been paid to the evolution of duplicated genes in poplar and willow, the role of conversion between duplicates generated from polyploidization remai ...
DOI:
10.1186/s12870-022-03684-9

12. Genetic Markers of Karachaevsky Sheep Identified by Genome-Wide Association Study

Author:
A. Yu. Krivoruchko; O. A. Yatsyk; A. V. Skokova; A. A. Kanibolotskaya
Source:
Russian journal of genetics 2022 v.58 no.2 pp. 164-170
ISSN:
1022-7954
Subject:
chromosomes,   etc   ; DNA; exons; genome-wide association study; introns; phenotype; sheep;     Show all 7 Subjects
Abstract:
... A genome-wide association study (GWAS) was carried out in Karachaevsky sheep using Illumina Ovine Infinium HD BeadChip 600K DNA biochips to identify single nucleotide polymorphisms (SNPs) associated with the breed. On the basis of the analysis, more than 100 SNPs were identified that have highly significant differences in the frequency of occurrence in animals of the Karachaevsky breed; for subseq ...
DOI:
10.1134/S1022795422020090

13. New record of chromosome count and B- chromosome in Tinantia erecta (Jacq.) Fenzl collected from different localities of Mussoorie, Uttarakhand (India)

Author:
Arneet Grewal; Poonam Rani
Source:
Nucleus 2022 v.65 no.1 pp. 73-79
ISSN:
0029-568X
Subject:
B chromosomes,   etc   ; chromatin; chromosome number; gametophytes; males; meiosis; stickiness; India;     Show all 8 Subjects
Abstract:
... Plants of Tinantia erecta (Jacq.) Fenzl were collected from four localities of Mussoorie, Uttarakhand (India) to investigate their cytological status and course of male meiosis. Three populations revealed the presence of n = 32 and one population showed the presence of n = 34 as the gametophytic chromosome count which is being reported for the first time from India. Presence of B- chromosomes (n = ...
DOI:
10.1007/s13237-021-00359-y

14. Plasmid and chromosomal copies of blaCMY-2 mediate resistance to third-generation cephalosporins in Escherichia coli from food animals in China

Author:
Xing-Run Zheng; Yin-Huan Sun; Man-Xia Chang; Hong-Xia Jiang
Source:
Veterinary microbiology 2022 v.271 pp. 109493
ISSN:
0378-1135
Subject:
chromosomes,   etc   ; Escherichia coli; cephalosporins; genes; growth curves; hybridization; plasmids; China;     Show all 8 Subjects
Abstract:
... The use of antimicrobials in food animals is the major determinant for the propagation of resistant bacteria in the animal reservoir. The objective of this study was to investigate the presence and distribution of third-generation cephalosporin (3GC) -resistant and plasmid-mediated AmpC (pAmpC)-producing Escherichia coli isolated from food animals in Southern China. In total, 744 3GC-resistant and ...
DOI:
10.1016/j.vetmic.2022.109493

15. Aneusomaty and Chromosomal Chimeras in Male Track of Coccinia grandis (L.) Voigt

Author:
Priya Sharma; Namrata Sharma
Source:
National Academy science letters 2022 v.45 no.2 pp. 191-194
ISSN:
0250-541X
Subject:
chromosomes,   etc   ; Coccinia grandis; chromosome number; males; meiosis; mitosis; pollen viability; India;     Show all 8 Subjects
Abstract:
... In our present study, three wild ♂ accessions of Coccinia grandis from Jammu, Samba and Kathua of Jammu province (J&K, India) have been worked out for cytological details. To determine the chromosome behavior, both meiotic and mitotic details were worked out for plants of all three locations. While Samba and Kathua accessions had somatic cells with uniform chromosome count of 2n = 24, few plants o ...
DOI:
10.1007/s40009-021-01089-0

16. C9orf72 knockdown alleviates hepatic insulin resistance by promoting lipophagy

Author:
Xiaomin Cang; Yu Wang; Jia Zeng; Jingwen Gao; Qianqian Yu; Chunfeng Lu; Feng Xu; Jiaxi Lin; Jinzhou Zhu; Xueqin Wang
Source:
Biochemical and biophysical research communications 2022 v.588 pp. 15-22
ISSN:
0006-291X
Subject:
chromosomes,   etc   ; autophagy; cell division; glucose; hepatocytes; insulin resistance; liver; research; therapeutics;     Show all 9 Subjects
Abstract:
... Insulin resistance (IR) attributed by the deficiency of lipophagy, is an abnormal state of downregulation of insulin-mediated glucose uptake and use into the liver. Chromosome 9 open reading frame 72 (C9orf72) variously modulates autophagy. We investigated the role and the downstream pathway of C9orf72 in hepatic IR. We found that C9orf72 knockdown alleviated hepatic IR by lipophagy promotion in T ...
DOI:
10.1016/j.bbrc.2021.12.018

17. Complete genome sequence of a psychrotolerant and piezotolerant bacterium Parasedimentitalea marina W43T, isolated from deep sea water of the New Britain trench

Author:
Hongge Zhang; Jiasong Fang; Hongcai Zhang; Junwei Cao
Source:
Marine genomics 2022 v.61 pp. 100915
ISSN:
1874-7787
Subject:
chromosomes,   etc   ; RNA; Rhodobacteraceae; bacteria; cold; genomics; lifestyle; nucleotide sequences; plasmids; seawater;     Show all 10 Subjects
Abstract:
... Parasedimentitalea marina W43ᵀ is a novel psychrotolerant and piezotolerant Rhodobacteraceae bacterium isolated from deep-sea water (4000 m) of the New Britain Trench. Here we present the first complete genome sequence of the bacterial genus Parasedimentitalea, which contains a circular chromosome and four plasmids. The 5,080,916 bp long genome exhibits a G + C content of 55.9 mol% and contains 50 ...
DOI:
10.1016/j.margen.2021.100915

18. Crystal structure of the chromosome partition protein MukE homodimer

Author:
Jia-Wei Qian; Xiao-Yan Wang; Kai Deng; De-Feng Li; Lu Guo
Source:
Biochemical and biophysical research communications 2022 v.589 pp. 229-233
ISSN:
0006-291X
Subject:
chromosomes,   etc   ; Escherichia coli; amino acid sequences; chromosome morphology; crystal structure; research;     Show all 6 Subjects
Abstract:
... The SMC (structural maintenance of chromosomes) proteins are known to be involved in chromosome pairing or aggregation and play an important role in cell cycle and division. Different from SMC–ScpAB complex maintaining chromosome structure in most bacteria, the MukB–MukE–MukF complex is responsible for chromosome condensation in E. coli and some γ-proteobacter. Though different models were propose ...
DOI:
10.1016/j.bbrc.2021.12.032

19. Development of Oligo-GISH kits for efficient detection of chromosomal variants in peanut

Author:
Pei Du; Liuyang Fu; Qian Wang; Tao Lang; Hua Liu; Suoyi Han; Chenyu Li; Bingyan Huang; Li Qin; Xiaodong Dai; Wenzhao Dong; Xinyou Zhang
Source:
crop journal 2022 pp. -
ISSN:
2214-5141
Subject:
chromosomes,   etc   ; Arachis; fish; genetic improvement; genomics; homozygosity; hybridization; irradiation; karyotyping; peanuts;     Show all 10 Subjects
Abstract:
... Oligo probe staining is a low-cost and efficient chromosome identification technique. In this study, oligo genomic in situ hybridization (Oligo-GISH) technology was established in peanut. Peanut A and B subgenome-specific interspersed repeat (IR) oligo probe sets were developed based on clustering and electronic localization of tandem repeat sequences in the reference genome of Tifrunner. The Olig ...
DOI:
10.1016/j.cj.2022.03.014

20. Fine mapping and candidate gene analysis of dwarf gene Rht14 in durum wheat (Triticum durum)

Author:
Shan Duan; Chunge Cui; Liang Chen; Zujun Yang; Yin-Gang Hu
Source:
Functional & integrative genomics 2022 v.22 no.2 pp. 141-152
ISSN:
1438-793X
Subject:
chromosomes,   etc   ; DNA methylation; Triticum turgidum subsp. durum; alleles; durum wheat; genomics;     Show all 6 Subjects
Abstract:
... Semi-dwarf and dwarf genes were widely used in wheat breeding for improving lodging resistant and increasing yield. Rht14 dwarf gene was identified and deployed in durum wheat, where it showed advantage on important agronomic potential. The reciprocal F₂ populations derived of Castelporziano (CP) and Langdon (L) were used for mapping of Rht14, which was located in intervals 4.8 cM and 10.38 cM by ...
DOI:
10.1007/s10142-021-00825-5