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1.
Microorganisms ; 10(10)2022 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-36296261

RESUMO

The cell membrane of Lactiplantibacillus plantarum is a key structure for cell survival. In this study, we aimed to improve the lyophilization resistance of L. plantarum by regulating the cell membrane structure. Unsaturated fatty acids or cell membrane-regulating substances were added during culturing to determine their effect on the composition of cell membrane fatty acids and the survival rate of the cells after freeze-drying. The results showed that Tween 80, ß-carotene and melatonin increased the lyophilization survival rate of L. plantarum by 9.44, 14.53, and 18.34%, respectively. After adding a lyophilization protective agent at a concentration of 21.49% at a 1:1 ratio, a combination of Tween 80, melatonin, and ß-carotene was added to regulate the cell membrane, which increased the lyophilization survival rate by 32.08-86.05%. This study proposes new research directions and ideas for improving the survival rate of probiotics for industrial production.

2.
Plants (Basel) ; 11(18)2022 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-36145832

RESUMO

The genus Nymphaea L. (water lily) is the most diverse genus in the family Nymphaeaceae, with more than 50 species worldwide, including 11 species distributed in Africa. The complex and variable morphology of Nymphaea makes it extremely difficult to accurately identify species based on morphological characteristics alone. DNA barcoding has the potential to identify species accurately. In this study, 158 Nymphaea populations from seven African countries were collected for species identification by ITS, trnT-trnF and rpl16. Additionally, the three candidate DNA barcodes were evaluated for genetic distance and barcoding gap. Based on the comprehensive analysis of sequence similarity, genetic distance method and phylogenetic tree, a total of 137 populations of seven Nymphaea species from African were well-identified, including N. lotus, N. petersiana, N. zenkeri, N. nouchali var. caerulea, N. micrantha and N. guineensis. ITS has more obvious advantages over trnT-trnF, rpl16 and trnT-trnF+rpl16 in the intraspecific and interspecific variation differences and barcoding gap and can identify most species. trnT-trnF and rpl16 can identify some species that cannot be identified by ITS. The results showed that it is more appropriate to apply the combination of ITS and trnT-trnF (or rpl16) as the DNA barcoding of Nymphaea. Additionally, this study further enriches the DNA barcoding database of Nymphaea and provides a reference basis for studying taxonomy, phylogenetics and evolutionary origin of Nymphaea.

3.
DNA Res ; 29(4)2022 Jun 25.
Artigo em Inglês | MEDLINE | ID: mdl-35751614

RESUMO

Nymphoides indica, an aquatic plant, is an invasive species that causes both ecological and economic damage in North America and elsewhere. However, the lack of genomic data of N. indica limits the in-depth analysis of this invasive species. Here, we report a chromosome-level genome assembly of nine pseudochromosomes of N. indica with a total size of ∼ 520 Mb. More than half of the N. indica genome consists of transposable elements (TEs), and a higher density of TEs around genes may play a significant role in response to an ever-changing environment by regulating the nearby gene. Additionally, our analysis revealed that N. indica only experienced a gamma (γ) whole-genome triplication event. Functional enrichment of the N. indica-specific and expanded gene families highlighted genes involved in the responses to hypoxia and plant-pathogen interactions, which may strengthen the ability to adapt to external challenges and improve ecological fitness. Furthermore, we identified 160 members of the nucleotide-binding site and leucine-rich repeat gene family, which may be linked to the defence response. Collectively, the high-quality N. indica genome reported here opens a novel avenue to understand the evolution and rapid invasion of Nymphoides spp.


Assuntos
Cromossomos , Elementos de DNA Transponíveis , Sítios de Ligação , Genoma de Planta , Filogenia , Domínios Proteicos
4.
Mol Ecol Resour ; 22(7): 2732-2743, 2022 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-35620935

RESUMO

Pistia stratiotes (Araceae), commonly referred to as water lettuce, is one of the most notorious weeds that cause severe damage to the economy and natural ecosystems of infested areas. In order to explore the mechanism of its rapid invasion, here, we assembled a high-quality chromosome-level genome for P. stratiotes based on the Illumina sequencing, PacBio sequencing, and Hi-C scaffolding technology. The assembled genome is 311.87 Mb in size with a contig N50 of 1.08 Mb. The contigs were further anchored on 14 pseudochromosomes with a scaffold N50 of 21.21 Mb. A total of 20,356 protein-coding genes were predicted, of which 79.35% were functionally annotated here. Evolutionary analysis showed that P. stratiotes and Colocasia esculenta were clustered together as sister lineages that diverged approximately 61 Ma. The synteny analyses indicated that two whole-genome duplication (WGD) events occurred within a short period in P. stratiotes. Moreover, comparative genome analysis indicated that the expansion of gene families corresponding to disease resistance might contribute to rapid invasion in P. stratiotes. Also, we analysed the disease-resistance gene family (NBS-LRR) involved in plant defence. A genome-wide search in P. stratiotes genome identified 85 NBS-LRR genes in this study. In conclusion, this study provides some new insights into the evolution of the invasive aquatic plant P. stratiotes. Our reference genome will also provide valuable resources for future invasion genomic research programmes.


Assuntos
Araceae , Araceae/genética , Cromossomos , Ecossistema , Genoma , Genômica , Filogenia
5.
Genomics ; 113(4): 2583-2590, 2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-34111522

RESUMO

Pterocarya stenoptera is a tree species that occurs along rivers and has high tolerance to waterlogging. Identification of waterlogging response genes in the aboveground part of P. stenoptera will increase understanding of tolerance mechanisms under root waterlogging conditions. In this study, we employed four physiological indicators and comparative transcriptome sequencing to investigate the waterlogging tolerance mechanism in P. stenoptera. The physiological results showed that the aboveground part of P. stenoptera was not obviously affected by waterlogging. P. stenoptera enhanced waterlogging tolerance by increasing the synthesis of alpha-Linolenic acids and flavonoids and activating the jasmonic acid, ethylene, and auxin signaling pathways. Our results confirmed our hypothesis that P. stenoptera, a species that is widely distributed along rivers, has evolved a range of mechanisms in response to waterlogging. Our research will provide new insights for understanding the tolerance mechanism of species to waterlogging.


Assuntos
Rios , Estresse Fisiológico , Estresse Fisiológico/genética
6.
Front Genet ; 10: 1089, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31737056

RESUMO

The geological events, past climatic fluctuations, and river systems played key roles in the spatial distribution, population dynamics, and genetic differentiation of species. In this work, we selected Pterocarya stenoptera, a widespread tree species in China, to test the roles of these factors. Four noncoding spacers, eight microsatellite (simple sequence repeat) markers, and species distribution modeling were used to examine the phylogeographical pattern of P. stenoptera. Based on chloroplast DNA data, populations of P. stenoptera were clearly clustered into three groups. The divergence time of these groups fell into the stage of the Qinghai-Tibet Movement, 1.7-2.6 Ma. For simple sequence repeat data, only one western marginal population YNYB could be separated from other populations, whereas other populations were mixed together. Our results indicated that the environmental heterogeneity resulting from the Qinghai-Tibet movement might be response for this genetic divergence. The climatic fluctuations in the Pleistocene did not cause the substantial range shift of P. stenoptera, while the fluctuations affected its population size. Moreover, we also confirmed the river systems did not act as channels or barrier of dispersal for P. stenoptera.

7.
BMC Evol Biol ; 19(1): 160, 2019 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-31370777

RESUMO

BACKGROUND: Understanding the genetic basis of local adaptation has long been the concern of biologists. Identifying these adaptive genetic variabilities is crucial not only to improve our knowledge of the genetic mechanism of local adaptation but also to explore the adaptation potential of species. RESULTS: Using 10 natural populations and 12 start codon targeted (SCoT) markers, a total of 430 unambiguous loci were yielded. The Bayesian analysis of population structure clearly demonstrated that the 10 populations of P. bungeana could be subdivided into three groups. Redundancy analysis showed that this genetic divergence was caused by divergence selection from environmental variables related to the ecological habitats of "avoidance of flooding" and "avoidance of high temperature and humidity." LFMM results indicated that Bio1, Bio5, Bio8, Bio12, Bio14, and Bio16, which are related to the ecological habitat of P. bungeana, were correlated with the highest numbers of environment-associated loci (EAL). CONCLUSIONS: The results of EAL characterization in P. bungeana clearly supported the hypothesis that environmental variations related to the ecological habitat of species are the key drivers of species adaptive divergence. Moreover, a method to calculate the species landscape adaptation index and quantify the adaptation potential of species was proposed and verified using ecological niche modeling. This model could estimate climatically suitable areas of species spatial distribution. Taking the results together, this study improves the current understanding on the genetic basis of local adaptation.


Assuntos
Adaptação Fisiológica/genética , Ecossistema , Variação Genética , Pinus/genética , Teorema de Bayes , Clima , Deriva Genética , Loci Gênicos , Genética Populacional , Geografia
8.
BMC Plant Biol ; 18(1): 306, 2018 Nov 27.
Artigo em Inglês | MEDLINE | ID: mdl-30482158

RESUMO

BACKGROUND: The investigation of the genetic basis of local adaptation in non-model species is an interesting focus of evolutionary biologists and molecular ecologists. Identifying these adaptive genetic variabilities on the genome responsible can provide insight into the genetic mechanism of local adaptation. RESULTS: We investigated the spatial distribution of genetic variation in 22 natural populations of Pterocarya stenoptera across its distribution area in China to provide insights into the complex interplay between multiple environmental variables and adaptive genetic differentiation. The Bayesian analysis of population structure showed that the 22 populations of P. stenoptera were subdivided into two groups. Redundancy analysis demonstrated that this genetic differentiation was caused by the divergent selection of environmental difference. A total of 44 outlier loci were mutually identified by Arlequin and BayeScan, 43 of which were environment-associated loci (EAL). The results of latent factor mixed model analysis showed that solar radiation in June (Sr6), minimum temperature of the coldest month (Bio6), temperature seasonality (Bio4), and water vapor pressure in January (Wvp1) were associated with the highest numbers of EAL. Sr6 was associated with the ecological habitat of "prefered light", and Bio6 and Wvp1 were associated with the ecological habitat of "warm and humid environment". CONCLUSIONS: Our results provided empirical evidence that environmental variables related to the ecological habitats of species play key roles in driving adaptive differentiation of species genome.


Assuntos
Adaptação Fisiológica/genética , Interação Gene-Ambiente , Variação Genética , Juglandaceae/genética , China , Marcadores Genéticos , Genética Populacional , Genoma de Planta
9.
Appl Plant Sci ; 6(12): e01205, 2018 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-30598863

RESUMO

PREMISE OF THE STUDY: Microsatellite markers of Pterocarya stenoptera (Juglandaceae) were developed for future studies on the population genetic diversity and spatial genetic structure of the species. METHODS AND RESULTS: Based on Illumina sequencing of the transcriptome of P. stenoptera, a total of 2452 microsatellites were identified from 83,674 assembled unigenes. One hundred microsatellites were randomly selected to design amplification primer pairs. Of these, 15 were successfully amplified and displayed polymorphism. For these markers, the number of alleles per locus and population ranged from one to six. The levels of observed and expected heterozygosity varied from 0.000 to 1.000 and 0.000 to 0.718, respectively. Furthermore, all of the 15 loci were successfully cross-amplified in another congeneric species (P. hupehensis) and were demonstrated to be polymorphic. CONCLUSIONS: The microsatellite loci described here can be used for future population genetic and landscape genetic studies on P. stenoptera.

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