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Article: Comparative genomics analysis of Pediococcus acidilactici species

Li, Zhenzhen / Song, Qi / Wang, Mingming / Ren, Junli / Liu, Songling / Zhao, Shancen

journal of microbiology. 2021 June, v. 59, no. 6

2021

Abstract: Pediococcus acidilactici is a reliable bacteriocin producer and a promising probiotic species with wide application in the food and health industry. However, the underlying genetic features of this species have not been analyzed. In this study, we ... ...

Abstract	Pediococcus acidilactici is a reliable bacteriocin producer and a promising probiotic species with wide application in the food and health industry. However, the underlying genetic features of this species have not been analyzed. In this study, we performed a comprehensive comparative genomic analysis of 41 P. acidilactici strains from various ecological niches. The bacteriocin production of 41 strains were predicted and three kinds of bacteriocin encoding genes were identified in 11 P. acidilactici strains, namely pediocin PA-1, enterolysin A, and colicin-B. Moreover, whole-genome analysis showed a high genetic diversity within the population, mainly related to a large proportion of variable genomes, mobile elements, and hypothetical genes obtained through horizontal gene transfer. In addition, comparative genomics also facilitated the genetic explanation of the adaptation for host environment, which specify the protection mechanism against the invasion of foreign DNA (i.e. CRISPR/Cas locus), as well as carbohydrate fermentation. The 41 strains of P. acidilactici can metabolize a variety of carbon sources, which enhances the adaptability of this species and survival in different environments. This study evaluated the antibacterial ability, genome evolution, and ecological flexibility of P. acidilactici from the perspective of genetics and provides strong supporting evidence for its industrial development and application.
Keywords	DNA ; Pediococcus acidilactici ; bacteriocins ; carbohydrates ; carbon ; evolution ; fermentation ; genetic variation ; genomics ; horizontal gene transfer ; industrialization ; industry ; loci ; probiotics
Language	English
Dates of publication	2021-06
Size	p. 573-583.
Publishing place	The Microbiological Society of Korea
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2012399-1
ISSN	1225-8873
ISSN	1225-8873
DOI	10.1007/s12275-021-0618-6
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Comparative genomics analysis of Pediococcus acidilactici species.

Li, Zhenzhen / Song, Qi / Wang, Mingming / Ren, Junli / Liu, Songling / Zhao, Shancen

Journal of microbiology (Seoul, Korea)

2021 Volume 59, Issue 6, Page(s) 573–583

Abstract	Pediococcus acidilactici is a reliable bacteriocin producer and a promising probiotic species with wide application in the food and health industry. However, the underlying genetic features of this species have not been analyzed. In this study, we performed a comprehensive comparative genomic analysis of 41 P. acidilactici strains from various ecological niches. The bacteriocin production of 41 strains were predicted and three kinds of bacteriocin encoding genes were identified in 11 P. acidilactici strains, namely pediocin PA-1, enterolysin A, and colicin-B. Moreover, whole-genome analysis showed a high genetic diversity within the population, mainly related to a large proportion of variable genomes, mobile elements, and hypothetical genes obtained through horizontal gene transfer. In addition, comparative genomics also facilitated the genetic explanation of the adaptation for host environment, which specify the protection mechanism against the invasion of foreign DNA (i.e. CRISPR/Cas locus), as well as carbohydrate fermentation. The 41 strains of P. acidilactici can metabolize a variety of carbon sources, which enhances the adaptability of this species and survival in different environments. This study evaluated the antibacterial ability, genome evolution, and ecological flexibility of P. acidilactici from the perspective of genetics and provides strong supporting evidence for its industrial development and application.
MeSH term(s)	Anti-Bacterial Agents/biosynthesis ; Bacteriocins/biosynthesis ; Genome, Bacterial ; Genomics ; Pediococcus acidilactici/classification ; Pediococcus acidilactici/genetics ; Pediococcus acidilactici/metabolism
Chemical Substances	Anti-Bacterial Agents ; Bacteriocins
Language	English
Publishing date	2021-05-15
Publishing country	Korea (South)
Document type	Journal Article
ZDB-ID	2012399-1
ISSN	1976-3794 ; 1225-8873
ISSN (online)	1976-3794
ISSN	1225-8873
DOI	10.1007/s12275-021-0618-6
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Critical metabolic pathways and SAD/FADs, WRI1s, and DGATs cooperate for high-oleic acid oil production in developing oil tea (

Yang, Jihong / Chen, Beibei / Manan, Sehrish / Li, Penghui / Liu, Chun / She, Guangbiao / Zhao, Shancen / Zhao, Jian

Horticulture research

2022 Volume 9, Page(s) uhac087

Abstract: Oil tea trees produce high-quality edible oils with desirably high oleic acid (18:1) and low linoleic (18:2) and linolenic (18:3) fatty acid (FA) levels, but limited understanding of tea oil biosynthesis and regulation has become a significant obstacle ... ...

Abstract	Oil tea trees produce high-quality edible oils with desirably high oleic acid (18:1) and low linoleic (18:2) and linolenic (18:3) fatty acid (FA) levels, but limited understanding of tea oil biosynthesis and regulation has become a significant obstacle for the breeding of high-yield and -quality oil tea varieties. By integrating metabolite and transcriptome analyses of developing oil tea seeds, we dissected the critical metabolic pathways, including glycolysis, fatty acid, and triacylglycerol (TAG) biosynthesis, as well as genes essential for tea seed oil production. Two plastidic stearoyl-acyl carrier protein desaturases (CoSAD1 and 2) and two endoplasmic reticulum-localized FA desaturases (CoFAD2 and 3) were functionally characterized as responsible for high 18:1 and low 18:2 and 18:3 proportions in tea oils. Two diacylglycerol
Language	English
Publishing date	2022-04-21
Publishing country	England
Document type	Journal Article
ISSN	2662-6810
ISSN	2662-6810
DOI	10.1093/hr/uhac087
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Article: Genomic regions controlling yield-related traits in spring wheat: a mini review and a case study for rainfed environments in Australia and China

Liu, Hui / Mullan, Daniel / Zhao, Shancen / Zhang, Yong / Ye, Jun / Wang, Yong / Zhang, Aimin / Zhao, Xiaoqing / Liu, Guannan / Zhang, Chi / Chan, Kenneth / Lu, Zhanyuan / Yan, Guijun

Genomics. 2022 Mar., v. 114, no. 2

2022

Abstract: A genome-wide association study (GWAS) was performed in six environments to identify major or consistent alleles responsible for wheat yield traits in Australia and North China where rainfed farming system is adopted. A panel of 228 spring wheat ... ...

Abstract	A genome-wide association study (GWAS) was performed in six environments to identify major or consistent alleles responsible for wheat yield traits in Australia and North China where rainfed farming system is adopted. A panel of 228 spring wheat varieties were genotyped by double digest restriction-site associated DNA genotyping-by-sequencing. A total of 223 significant marker-trait association (MTAs) and 46 candidate genes for large- or consistent-effect MTAs were identified. The results were compared with previous studies based on a mini-review of 23 GWAS analyses on wheat yield. A phenomenon seldom reported in previous studies was that MTAs responsible for the trait tended to cluster together at certain chromosome segments, and many candidate genes were in the form of gene clusters. Although linkage disequilibrium (LD) might contribute to the co-segregation of the regions, it also suggested that marker-assisted selection (MAS) or transgenic method targeting a single gene might not be as effective as MAS targeting a larger genomic region where all the genes or gene clusters underlying play important roles.
Keywords	DNA ; case studies ; chromosomes ; genetic engineering ; genome-wide association study ; genomics ; genotyping by sequencing ; linkage disequilibrium ; marker-assisted selection ; spring wheat ; Australia ; China
Language	English
Dates of publication	2022-03
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	356334-0
ISSN	1089-8646 ; 0888-7543
ISSN (online)	1089-8646
ISSN	0888-7543
DOI	10.1016/j.ygeno.2022.110268
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Tea plant roots respond to aluminum-induced mineral nutrient imbalances by transcriptional regulation of multiple cation and anion transporters

Hao, Jing / Peng, Anqi / Li, Yingying / Zuo, Hao / Li, Ping / Wang, Jinsong / Yu, Keke / Liu, Chun / Zhao, Shancen / Wan, Xiaochun / Pittman, Jon K. / Zhao, Jian

BMC Plant Biol. 2022 Dec., v. 22, no. 1 p.203-203

2022

Abstract: BACKGROUND: Tea is one of the most popular non-alcoholic beverages in the world for its flavors and numerous health benefits. The tea tree (Camellia sinensis L.) is a well-known aluminum (Al) hyperaccumulator. However, it is not fully understood how tea ... ...

Abstract	BACKGROUND: Tea is one of the most popular non-alcoholic beverages in the world for its flavors and numerous health benefits. The tea tree (Camellia sinensis L.) is a well-known aluminum (Al) hyperaccumulator. However, it is not fully understood how tea plants have adapted to tolerate high concentrations of Al, which causes an imbalance of mineral nutrition in the roots. RESULTS: Here, we combined ionomic and transcriptomic profiling alongside biochemical characterization, to probe the changes of metal nutrients and Al responsive genes in tea roots grown under increasing concentrations of Al. It was found that a low level of Al (~ 0.4 mM) maintains proper nutrient balance, whereas a higher Al concentration (2.5 mM) compromised tea plants by altering micro- and macro-nutrient accumulation into roots, including a decrease in calcium (Ca), manganese (Mn), and magnesium (Mg) and an increase in iron (Fe), which corresponded with oxidative stress, cellular damage, and retarded root growth. Transcriptome analysis revealed more than 1000 transporter genes that were significantly changed in expression upon Al exposure compared to control (no Al) treatments. These included transporters related to Ca and Fe uptake and translocation, while genes required for N, P, and S nutrition in roots did not significantly alter. Transporters related to organic acid secretion, together with other putative Al-tolerance genes also significantly changed in response to Al. Two of these transporters, CsALMT1 and CsALS8, were functionally tested by yeast heterologous expression and confirmed to provide Al tolerance. CONCLUSION: This study shows that tea plant roots respond to high Al-induced mineral nutrient imbalances by transcriptional regulation of both cation and anion transporters, and therefore provides new insights into Al tolerance mechanism of tea plants. The altered transporter gene expression profiles partly explain the imbalanced metal ion accumulation that occurred in the Al-stressed roots, while increases to organic acid and Al tolerance gene expression partly explains the ability of tea plants to be able to grow in high Al containing soils. The improved transcriptomic understanding of Al exposure gained here has highlighted potential gene targets for breeding or genetic engineering approaches to develop safer tea products.
Keywords	Camellia sinensis ; aluminum ; calcium ; cations ; gene expression ; genes ; heterologous gene expression ; hyperaccumulators ; ionomics ; iron ; magnesium ; manganese ; nutrient balance ; oxidative stress ; root growth ; secretion ; tea ; transcription (genetics) ; transcriptomics ; trees ; yeasts
Language	English
Dates of publication	2022-12
Size	p. 203.
Publishing place	BioMed Central
Document type	Article ; Online
ZDB-ID	2059868-3
ISSN	1471-2229
ISSN	1471-2229
DOI	10.1186/s12870-022-03570-4
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Article ; Online: CRISPR/Cas9-mediated seamless gene replacement in protoplasts expands the resistance spectrum to TMV-U1 strain in regenerated Nicotiana tabacum.

Li, Yanli / Huang, Changjun / Liu, Yong / Zeng, Jianmin / Yu, Haiqin / Tong, Zhijun / Yuan, Xinjie / Sui, Xueyi / Fang, Dunhuang / Xiao, Bingguang / Zhao, Shancen / Yuan, Cheng

Plant biotechnology journal

2023 Volume 21, Issue 12, Page(s) 2641–2653

Abstract: CRISPR/Cas-based genome editing is now extensively used in plant breeding and continues to evolve. Most CRISPR/Cas current applications in plants focus on gene knock-outs; however, there is a pressing need for new methods to achieve more efficient ... ...

Abstract	CRISPR/Cas-based genome editing is now extensively used in plant breeding and continues to evolve. Most CRISPR/Cas current applications in plants focus on gene knock-outs; however, there is a pressing need for new methods to achieve more efficient delivery of CRISPR components and gene knock-ins to improve agronomic traits of crop cultivars. We report here a genome editing system that combines the advantages of protoplast technologies with recent CRISPR/Cas advances to achieve seamless large fragment insertions in the model Solanaceae plant Nicotiana tabacum. With this system, two resistance-related regions of the N' gene were replaced with homologous fragments from the N'alata gene to confer TMV-U1 resistance in the T0 generation of GMO-free plants. Our study establishes a reliable genome-editing tool for efficient gene modifications and provides a detailed description of the optimization process to assist other researchers adapt this system for their needs.
MeSH term(s)	Nicotiana/genetics ; CRISPR-Cas Systems/genetics ; Protoplasts ; Plant Breeding ; Gene Editing/methods ; Plants/genetics ; Genome, Plant
Language	English
Publishing date	2023-08-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2136367-5
ISSN	1467-7652 ; 1467-7652
ISSN (online)	1467-7652
ISSN	1467-7652
DOI	10.1111/pbi.14159
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Article ; Online: The complete mitochondrial genome of the drill (Mandrillus leucophaeus).

Zhang, Kai / Xiang, Hai-Tao / Zhao, Shan-Cen

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis

2017 Volume 28, Issue 1, Page(s) 69–70

Abstract: The drill (Mandrillus leucophaeus) is a primate of the family Cercopithecidae (Old World monkeys). Drills are among Africa's most endangered mammals, and are listed by the IUCN as the highest conservation priority of all African primates and are used as ... ...

Abstract	The drill (Mandrillus leucophaeus) is a primate of the family Cercopithecidae (Old World monkeys). Drills are among Africa's most endangered mammals, and are listed by the IUCN as the highest conservation priority of all African primates and are used as a model for cytomegalovirus vaccine and antiviral development. Here, we describe the complete mitochondrial genome (mitogenome) sequence of M. leucophaeus. The genome is 16 547 bp in length, comprising 13 protein-coding genes, 22 tRNAs, 2 rRNAs and a major non-coding region. The gene content and order is in accord with the common vertebrate form. All PCGs share the start codon ATG except ND2(ATC), ND3(ATT) and ND5(ATA). ND1, ND2 and ATP8 use ATG as the end codon. COX1, COX2, ATP6, ND4L and ND5 employ ATT as the end codon. The other five PCGs share the end codon T--. Phylogenic tree was constructed based on the complete mitogenome of M. leucophaeus and 12 closely related species to estimate their phylogenic relationship. We present an important genetic resource for the family Cercopithecidae in general.
Language	English
Publishing date	2017-01
Publishing country	England
Document type	Journal Article
ISSN	2470-1408
ISSN (online)	2470-1408
DOI	10.3109/19401736.2015.1110802
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Article: Clinical Characteristics and Risk of Diabetic Complications in Data-Driven Clusters Among Type 2 Diabetes.

Xing, Lin / Peng, Fangyu / Liang, Qian / Dai, Xiaoshuang / Ren, Junli / Wu, Han / Yang, Shufen / Zhu, Yaxin / Jia, Lijing / Zhao, Shancen

Frontiers in endocrinology

2021 Volume 12, Page(s) 617628

Abstract: Background: This study aimed to cluster newly diagnosed patients and patients with long-term diabetes and to explore the clinical characteristics, risk of diabetes complications, and medication treatment related to each cluster.: Research design and ... ...

Abstract	Background: This study aimed to cluster newly diagnosed patients and patients with long-term diabetes and to explore the clinical characteristics, risk of diabetes complications, and medication treatment related to each cluster. Research design and methods: K-means clustering analysis was performed on 1,060 Chinese patients with type 2 diabetes based on five variables (HbA1c, age at diagnosis, BMI, HOMA2-IR, and HOMA2-B). The clinical features, risk of diabetic complications, and the utilization of elven types of medications agents related to each cluster were evaluated with the chi-square test and the Tukey-Kramer method. Results: Four replicable clusters were identified, severe insulin-resistant diabetes (SIRD), severe insulin-deficient diabetes (SIDD), mild obesity-related diabetes (MOD), and mild age-related diabetes (MARD). In terms of clinical characteristics, there were significant differences in blood pressure, renal function, and lipids among clusters. Furthermore, individuals in SIRD had the highest prevalence of stages 2 and 3 chronic kidney disease (CKD) (57%) and diabetic peripheral neuropathy (DPN) (67%), while individuals in SIDD had the highest risk of diabetic retinopathy (32%), albuminuria (31%) and lower extremity arterial disease (LEAD) (13%). Additionally, the difference in medication treatment of clusters were observed in metformin (p = 0.012), α-glucosidase inhibitor (AGI) (p = 0.006), dipeptidyl peptidase 4 inhibitor (DPP-4) (p = 0.017), glucagon-like peptide-1 (GLP-1) (p <0.001), insulin (p <0.001), and statins (p = 0.006). Conclusions: The newly diagnosed patients and patients with long-term diabetes can be consistently clustered into featured clusters. Each cluster had significantly different patient characteristics, risk of diabetic complications, and medication treatment.
MeSH term(s)	Adult ; Aged ; Blood Pressure/physiology ; China ; Cluster Analysis ; Cross-Sectional Studies ; Diabetes Mellitus, Type 2/complications ; Diabetes Mellitus, Type 2/drug therapy ; Diabetes Mellitus, Type 2/physiopathology ; Diabetic Nephropathies/physiopathology ; Diabetic Neuropathies/physiopathology ; Female ; Humans ; Hypoglycemic Agents/therapeutic use ; Kidney/physiopathology ; Male ; Metformin/therapeutic use ; Middle Aged ; Risk Factors
Chemical Substances	Hypoglycemic Agents ; Metformin (9100L32L2N)
Language	English
Publishing date	2021-06-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2592084-4
ISSN	1664-2392
ISSN	1664-2392
DOI	10.3389/fendo.2021.617628
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Article: Major genomic regions responsible for wheat yield and its components as revealed by meta-QTL and genotype–phenotype association analyses

Liu, Hui / Mullan, Daniel / Zhang, Chi / Zhao, Shancen / Li, Xin / Zhang, Aimin / Lu, Zhanyuan / Wang, Yong / Yan, Guijun

Planta. 2020 Oct., v. 252, no. 4

2020

Abstract: MAIN CONCLUSION: Meta-QTL (MQTL) analysis was done for yield-related traits in wheat. Candidate genes were identified within the refined MQTL and further validated by genotype–phenotype association analysis. Extensive studies have been undertaken on ... ...

Abstract	MAIN CONCLUSION: Meta-QTL (MQTL) analysis was done for yield-related traits in wheat. Candidate genes were identified within the refined MQTL and further validated by genotype–phenotype association analysis. Extensive studies have been undertaken on quantitative trait locus/loci (QTL) for wheat yield and its component traits. This study conducted a meta-analysis of 381 QTL related to wheat yield under various environments, including irrigated, drought- and/or heat-stressed conditions. Markers flanking meta-QTL (MQTL) were mapped on the wheat reference genome for their physical positions. Putative candidate genes were examined for MQTL with a physical interval of less than 20 Mbp. A total of 86 MQTL were identified as responsible for yield, of which 34 were for irrigated environments, 39 for drought-stressed environments, 36 for heat-stressed environments, and 23 for both drought- and heat-stressed environments. The high-confidence genes within the physical positions of the MQTL flanking markers were screened in the reference genome RefSeq V1.0, which identified 210 putative candidate genes. The phenotypic data for 14 contrasting genotypes with either high or low yield performance—according to the Australian National Variety Trials—were associated with their genotypic data obtained through ddRAD sequencing, which validated 18 genes or gene clusters associated with MQTL that had important roles for wheat yield. The detected and refined MQTL and candidate genes will be useful for marker-assisted selection of high yield in wheat breeding.
Keywords	genomics ; genotype-phenotype correlation ; irrigation ; marker-assisted selection ; meta-analysis ; phenotype ; quantitative trait loci ; water stress ; wheat
Language	English
Dates of publication	2020-10
Size	p. 65.
Publishing place	Springer Berlin Heidelberg
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	208909-9
ISSN	1432-2048 ; 0032-0935 ; 1866-2749
ISSN (online)	1432-2048
ISSN	0032-0935 ; 1866-2749
DOI	10.1007/s00425-020-03466-3
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Article ; Online: Evolution of Disease Defense Genes and Their Regulators in Plants.

Zhang, Rongzhi / Zheng, Fengya / Wei, Shugen / Zhang, Shujuan / Li, Genying / Cao, Peijian / Zhao, Shancen

International journal of molecular sciences

2019 Volume 20, Issue 2

Abstract: Biotic stresses do damage to the growth and development of plants, and yield losses for some crops. Confronted with microbial infections, plants have evolved multiple defense mechanisms, which play important roles in the never-ending molecular arms race ... ...

Abstract	Biotic stresses do damage to the growth and development of plants, and yield losses for some crops. Confronted with microbial infections, plants have evolved multiple defense mechanisms, which play important roles in the never-ending molecular arms race of plant⁻pathogen interactions. The complicated defense systems include pathogen-associated molecular patterns (PAMP) triggered immunity (PTI), effector triggered immunity (ETI), and the exosome-mediated cross-kingdom RNA interference (CKRI) system. Furthermore, plants have evolved a classical regulation system mediated by miRNAs to regulate these defense genes. Most of the genes/small RNAs or their regulators that involve in the defense pathways can have very rapid evolutionary rates in the longitudinal and horizontal co-evolution with pathogens. According to these internal defense mechanisms, some strategies such as molecular switch for the disease resistance genes, host-induced gene silencing (HIGS), and the new generation of RNA-based fungicides, have been developed to control multiple plant diseases. These broadly applicable new strategies by transgene or spraying ds/sRNA may lead to reduced application of pesticides and improved crop yield.
MeSH term(s)	Disease Resistance/genetics ; Evolution, Molecular ; Genes, Plant ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Plant Diseases/genetics ; Stress, Physiological/genetics
Chemical Substances	MicroRNAs
Language	English
Publishing date	2019-01-15
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms20020335
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