Ecological Genetics and Genomics最新文献

Hidden for many years and serendipitously discovered, giant viruses have emerged as a captivating subject of scientific interest, leading to significant discoveries and paradigm shifts in our understanding of viruses. The identification of Mimivirus in 2003 marked a turning point, leading to the exploration and characterization of various giant viruses, including Mimiviridae, Marseilleviridae, Pandoravirus, Pithovirus, Mollivirus, Faustovirus, and Cedratvirus. These viruses exhibit unique structural and genomic features, challenging our understanding of viral diversity and evolution. Metagenomic studies have revealed their presence in diverse environments, indicating their global distribution and suggesting the likelihood of further discoveries. The co-discovery of virophages, viruses associated with giant viruses, has added another layer of complexity to their interactions and ecological roles. The study of giant viruses has shed light on their impact on ecosystems and potential roles in eukaryotic evolution. However, many knowledge gaps persist, including understanding host-virus interactions, identifying original hosts, expanding isolation efforts, and investigating the implications of giant viruses for human health. Further research in these areas will contribute to our comprehensive understanding of these fascinating entities and their significance in virology and ecology.

Composting, a biologically driven process, can transform green waste into nutrient-rich soil amendments. Molecular biology is becoming increasingly popular among researchers for understanding microbial dynamics to understand the structure and function of biomolecules, such as DNA, RNA, proteins, and other macromolecules. Genomics is the favoured method of among researchers in environmental engineering, specifically during composting. It allows the researchers to analyse complex microbial communities at different stages of composting without the need for cultivation. Many researchers used 16S rRNA and 18S rRNA gene sequencing, ITS region sequencing, DGGE analysis, and whole genome shotgun (WGS) sequencing to analyse community dynamics of bacteria and fungi. The microbial communities vary concerning additives used with green waste composting and during the phases of composting. This mini-review summarises the techniques used for genomics study during the composting of green waste. It involves a type of substrate, the DNA extraction kit used, the region selected for the sequencing, and the primer selection. Microbial community dynamics during different phases of green waste composting are also discussed in this review.

Varietal identification of economically significant crops has acquired great importance in the global market especially in the terms of protection of plant varieties. Kerala is the home to several different specialty traditional rice varieties which is vital sources of nutritional and therapeutic properties. Traditional rice landraces are an integral part of the nutrition, medicine, and culture of Kerala. Most of these varieties possess similar morphological characteristics but differ in their nutritional and medicinal properties. It has become a challenge for a non-taxonomist to identify and recognize the traditional rice varieties accurately. DNA barcoding has been considered a standard method to identify species or variety which utilizes a unique pattern of variation in the DNA of the species. It can be adopted as a routine and faster approach to determine the molecular taxonomy when compared to morphological identification approaches. Currently, the most intensively applied two DNA barcode loci are maturase K (matK) and ribulose 1,5-biphosphate carboxylase (rbcL) for plant identification. But, the efficacy of these two loci in discriminating plant species may vary. Hence, in this study fifty-four traditional rice varieties collected from the Wayanad district of Kerala were used to generate and compare the two standard DNA barcode regions for plant matK and rbcL via PCR amplification. The varieties collected were varying in the husk color from black; red to brown and the brown rice varieties not display any morphological variation. The study identified that among the two selected markers rbcL was observed to have the potential to discriminate the intra and interspecific regions of the studied rice varieties and this would have been utilized to generate DNA barcodes for each variety. This study separates and identifies 28 traditional rice varieties among the 54 studied varieties as Oryza nivara, the wild progenitor of Asian cultivated rice. Along with other supporting information the data presented here could be used as a reference to check the authenticity and varietal purity of commercially significant rice varieties in the future.

Published and unpublished (MSc and PhD thesis works) were used to assess the achievements and limitations of phenotypic and molecular characterization studies towards breed differentiation of Ethiopian cattle. Accordingly, listing cattle breeds which are believed to exist, identification of their distribution areas, revealing their unique features, as well as reporting their morphometric measurement values were among the achievements of phenotypic characterization studies. However, the small area coverage, lack of uniform breed naming and lack of consistency during recording were the limitations of the phenotypic characterizations which contributed to their failure in quantification of the degree of relationships among adjacent breeds. On the other hand, molecular characterization studies achieved reporting the assessment of within breed genetic diversity and among breed differentiation. However, contradictions of the molecular studies to each other as well as contradictions to the traditional breed differentiation which was based on the phenotypic characteristics and geographical distances among the breeds was observed. Moreover, lack of using appropriate breed naming and the use of few sample size was observed as the limitations of the molecular characterization studies. The overall results of the phenotypic and molecular characterization studies undertaken so far were found to be less comprehensive mainly towards breed differentiation and registration. This lack of complete information on breed differentiation hinders the design of breed-specific conservation and sustainable utilization breeding programs. Therefore, further well-designed and inclusive phenotypic and molecular characterization using modern technologies with the objective of breed differentiation is recommended alongside the use of uniform breed naming.

Considering the genetic variability of bread wheat is essential for the development of improved, high-yielding germplasm. The extent of genetic variability, heritability and genotype-environment interaction in 180 bread wheat (Triticum aestivumL.) genotypes was investigated using field-based phenotyping of 12 agro-morphological traits. The experiment was positioned at alpha lattice design in two replications in Ethiopia at Kulmsa agricultural research center, Meraro (substation of Kulmsa agricultural research center) and Holeta agricultural research center. Moderate heritability and genetic advance were observed in plant height (50 %, 5.5 %), spick length (38 %, 5.3 %), number of kernels per spick (50 %, 5.23 %), and thousand kernel weights (41 %, 4.38 %), respectively. The analysis discovered that the mean performance of grain yield per-plot was the highest at Kulmsa, implying that Kulmsa could be better for bread wheat to perform well. Phenotypic and genotypic associations of grain yield with number of kernels per speculate (0.42 and 0.99), spick weight (0.91 and 0.99), leaf area (0.14 and 0.55) were positive and significant correlated both at phenotypic and genotypic levels. Analysis of variance showed that highly significant differences for environment and genotype in which grain yields were significantly affected by environment, counted 55.22 % of the total variation, whereas genotype and genotype environment interaction accounted for 27.46 % and 17.44 %, respectively. Moreover, genotypes 53, 68 and 168 are high performing valuable genetic resources to be used in further bread wheat breeding program. Inclusively, the study provided valuable information for the bread wheat improvement.

The current taxonomy of Streptococcus is primarily based on low-resolution methods such as biochemical analysis, single housekeeping gene-based phylogeny, or conserved sequence identity of species groups resulting in various amendments in the taxonomic positioning of their constituent species.. We reported genome similarities assessment and phylogeny using several methods to provide a robust taxonomic framework with inclusion of 115 type strains and 23 unclassified species. Phylogeny based on the 16S rRNA gene suggests no integrity of the earlier classified species groups, which cannot be used for taxonomic classification. The whole genome phylogeny does not support the existence of the earlier defined species groups. Genome similarity assessment suggests the presence of sixteen novel genomospecies, including some of the amendments in the earlier classified species and subspecies. A highly stringent antibiotic resistance gene search resulted in widespread fluoroquinolones resistance. It is noteworthy that among the 42 genomes analyzed, which include strains of probiotic significance such as S. thermophilus NCTC 12958T and S. salivarius NCTC 8618T, no properly curated antibiotic resistance genes were discovered. However, the presence of partial hits for resistance genes in such strains requires further experimental validation before their downstream application.

Bacteria promote mushroom growth by providing growth factors and vitamins, preventing pathogen growth, and enhancing spore distribution. Soil bacteria involved in the nitrogen cycle showed association with the abundance of ectomycorrhizal fungi. Uncultured microorganisms comprise a significant proportion of complex soil ecosystem. Nanopore sequencing Technologies used a genome-resolved metagenomics approach to evaluate the rhizospheric bacterial diversity of these mushrooms from the tropical forests of West Bengal (India) and the temperate forests of West Kameng districts in Arunachal Pradesh, India. The ectomycorrhizosphere soil of tropical forest has higher abundance of nitrogen fixing bacteria such as Bradyrhizobium diazoefficiens, B. erythrophlei, and B. elkanii whereas the ectomycorrhizosphere soil of temperate forest has higher abundance of Candidatus Solibacter usitatus, Rhodoplanes sp. Z2-YC6860, Candidatus Koribacter versatilis, Bacillus cereus, Granulicella tundricola, G. mallensis, Bradyrhizobium icense, Bradyrhizobium sp. SK17, Acidobacterium capsulatum, Bacillus weihaiensis, Terriglobus saanensis, Planococcus sp. MB-3u-03, Bradyrhizobium sp. CCGE-LA001, and Bradyrhizobium japonicum These microorganisms have deep impact in the growth and development of ectomycorrhizal partners (trees and mushrooms) and be called as mycorrhiza helper bacteria (MHB).

Gut microbiome variation has functional importance on host fitness, ecology, and evolution, but the scope and basis of microbial diversity for marine shrimp are still not fully understood. The aim of present study is to characterize the gut microbiomes of five Penaeus monodon broodstocks populations of wild and aquaculture environments within the Indo-Pacific region. We conducted data analysis of 16S rRNA gene amplicons using Qiime2 and Microbiomeanalyst and functional prediction by FAPROTAX (Functional Annotation of Prokaryotic Taxa). Our results identified considerable variation in the gut microbiomes of wild and cultured shrimps, presumably reflecting differences in diet, host genetic divergence, and host-bacteria co-evolution. While wild shrimp broodstocks had higher gut microbial diversity, a pronounced divergence of core microbiota was detected in PCOA analysis for both wild and cultured shrimp populations with altered community structure and predicted metabolic functions. Proteobacteria was observed to be dominated in the gut microbiome in all P. monodon populations, whereas Gracilibacteria and Fusobacteriia were only found in domesticated populations. Interestingly, probiotic bacteria such as genus Enterococcus and Lactobacillus were observed to be the core genus for both wild populations with range from 1.08% to 17.67%. LEfSe analysis detected significant enrichment of beneficial/opportunistic pathogens from the gut microbiome of each host population, suggesting possible biomarkers for host health monitoring. Our results provide insights into the deterministic factors contributing to the interpopulation variation in the P. monodon microbiome, highlighting potential future research directions in areas such as host-bacteria co-evolution and holobiome, which may enable the assessment of host-species genomic divergence across environmental gradients.

Oat (Avena sativa L.) is one of the most important dual-purpose cereal crops cultivated under diverse environmental conditions in Ethiopia. The fodder dry matter yield stability analysis was conducted using twenty-four oat genotypes across nine environments in a randomized complete block design with three replications. The study aimed to evaluate the magnitude of genotype by environment interaction and determine the stability of oat genotypes for fodder yield using 14 univariate stability parameters. The pooled analysis of variance revealed that the genotype, environment, and their interaction effects had variation (p < 0.001) for fodder yield. The contribution of environment for the total fodder yield variation was the highest (67.45%) followed by the interaction (22.73%) and genotypic (9.82%) effects. The results of stability analysis showed that high fodder yield-producing genotypes had stable performance using the stability parameters of genotypic superiority index (P_i), yield stability index (YSI), coefficient of determination (R²), and coefficient of variability (CV_i), demonstrating that selection of oat genotypes using these stability parameters would be effective for fodder yield improvement. Moreover, Spearman's rank correlation coefficients indicated that the stability parameters of P_i, YSI, R², and CV_i had a significant positive association with fodder dry matter yield (FDMY). On the contrary, the FDMY had non-significant inverse relations with the remaining stability parameters except B_i, suggesting that the selection of oat genotypes using these stability parameters would not be effective for fodder yield improvement. Therefore, G6, G7, G9, G10, and G23 were desirable genotypes for fodder yield improvement programs in Ethiopia.

Tamarix aphylla (L.) H. Karst. is an evergreen, haloxeric, ecologically and economically important tree species of the Indian Thar desert. Genetic diversity analysis of this tree species is vital as it survives in extreme climatic conditions. In this study, we employed first time two gene-targeted CAAT box-derived polymorphism (CBDP) and start codon-targeted (SCoT) polymorphism markers for the analysis of the genetic diversity in Tamarix aphylla. A total of 47 wild genotypes of T. aphylla from eight populations of the Indian Thar Desert were analyzed using 12 primers, six from each CBDP and SCoT markers. The percent polymorphism was higher for CBDP (94.84%) than for the SCoT (76.57%) markers. The average PIC value for CBDP and SCoT marker was 0.601 and 0.409, respectively. Both CBDP and SCoT markers demonstrated high levels of genetic differentiation, low gene flow, and high fixation index. Using both marker systems, AMOVA revealed the percent molecular variation was higher in the case of within population than among population. The clustering pattern based on UPGMA and PCoA plots clearly showed that the grouping of genotypes is associated with their geographical origin and habitat. However, few genotypes were significantly diverse from their respective population and grouped in separate clusters with the genotypes of other populations. The findings observed in the present study can be further exploited in the breeding and conservation programs of T. aphylla.