Ecological Genetics and Genomics最新文献

Mycoplasma capricolum subsp. capricolum (Mcc) is an etiological agent of Contagious Agalactia (CA) in small ruminants and belongs to Mycoplasma mycoides cluster. Until today, six strains genomes and candidates of Mcc were sequenced in Germany, USA, France and China. The aim of the present study is to analyze the genomic sequence of Mcc MOR20 strain and to compare it with the other sequenced strains. Indeed, the genome sequence of Mcc MOR20 strain was obtained using Illumina NovaSeq 6000 platform. NGS sequencing reads were assembled de novo using CLC genomics v12 (Qiagen). The variant calling on MOR20 strain was conducted using SNIPPY tools. The phylogenomic analysis of Mcc MOR20 strain was performed using BuscoPhylo pipeline. Thus, the genome of Mcc MOR20 characterized by 960,401 bp and encoded for 820 protein-coding genes, 15 rRNA genes (5S, 16S, and 23S), 34 tRNA genes, and three ncRNA genes. In addition, Mcc MOR20 is genetically closer to Mcc isolate human case with percentage of 98.58 %. In addition, the Mcc MOR20 show a genomic relationship with Mccp clade, and they share the same must of potential virulence genes that were identified, including variable surface lipoproteins and metabolic enzymes. The results of this study could be of interest for contagious agalactia vaccine development and the conserved gene might be taken as candidate for new markers for Mcc diagnosis.

Understanding the genetic diversity and population structure of anguillid eels is crucial for effective management. In this study, we used the mitochondrial DNA (mtDNA) D-loop marker to identify anguillid glass eels and assessed their genetic diversity across six sampling sites spanning three Southeast Asian countries. We also examined the population structures of Anguilla marmorata and A. celebesensis. We validated nine distinct species and subspecies of anguillid eels from 465 specimens collected in Indonesia (n = 246), the Philippines (n = 119), and Vietnam (n = 100). High gene diversities were observed across the species, ranging from 0.979 (A. celebesensis) to 1.000 (A. bicolor bicolor, A. marmorata, and A. interioris). Correspondingly, nucleotide diversity values were relatively low, varying from 0.036 (A. marmorata) to 0.057 (A. interioris). A. marmorata (n = 162) displayed a broad distribution, being observed across all six sites, with a significant yet low average fixation index of 0.05755. Pairwise comparisons of FST values between Cimandiri and other locations (except for Cagayan) were relatively high and statistically significant (p < 0.01), indicating significant genetic differentiation of Cimandiri samples compared to most locations in this study. On the other hand, A. celebesensis (n = 110), exhibited a non-significant and low fixation index (0.007), indicating no genetic differentiation in samples from Poso and Poigar Rivers, Indonesia. Our findings highlight the essential need for coordinated management strategies among regions that share common stocks. Additionally, this study underscores the efficacy of the mtDNA D-loop in precisely identifying glass eel species/subspecies and elucidating the genetic diversity and population structure of tropical anguillid eels.

Genotype plus genotype-by-environment (GGE) and additive main effects and multiplicative interaction (AMMI) analyses are recognized as the two most effective approaches for assessing genotype × environment interaction. In this investigation, forty-three spearmint (Mentha spicata L.) half-sib seed progenies were evaluated for the stability of agro-morphological and biochemical characteristics. For leaf-to-stem ratio, limonene and carvone contents, the analysis of variance uncovered the presence of a significant genotype-by-environment interaction, this finding illustrates that Mentha spicata genotypes exhibited diverse levels of performance across the three environments. The genotypes OPSP-95, OPSP-96, OPSP-78, OPSP-46, and OPSP-86 excelled in carvone per cent in each environment, as indicated by the “which-won-where” polygon. The optimal genotypes for carvone content determined by the genotype ranking are as follows OPSP-46, OPSP-35, OPSP-86, OPSP-78, OPSP-66 and OPSP-106 and for limonene content OPSP-86, OPSP-66, OPSP-47, OPSP-56, OPSP-59 and OPSP-106. Three genotypes OPSP-50, OPSP-112, and OPSP-16 showed both high oil yield per plot couples with stability across tested environments. Based on the mean trait stability index, genotypes OPSP-92, OPSP-76, OPSP-96, OPSP-94, OPSP-95, and OPSP-117 were stable and best based on all observed characters across the three environments. Spearmint genotypes that are stable and high-yield can be cultivated commercially and utilized as base populations for upcoming breeding initiatives.

The current study used two harvesting periods (2020-21 and 2021–2022) to investigate the effects of organic and inorganic fertilizers applied to the soil on Kalmegh growth, productivity, and economic viability. The study looked at a variety of growth parameters, including plant height, the number of primary and secondary branches, plant spread, leaf area, dry matter accumulation, and fresh, dry, and seeded herbage output. T6 (RDF + VAM + Vermicompost) produced much higher growth metrics and yields than other treatments, exhibiting consistently better performance. The improved outcomes were attributed to the combined effects of inorganic fertilizers, mycorrhizal association (VAM), and organic supplementation (vermicompost). T2 (RDF + vermicompost) displayed a similar performance. On the other hand, the T7 control group had the lowest values across all metrics. The economic study determined that T6 was the most economically viable choice due to its higher gross and net returns. This emphasizes the importance of coordinated nutrient management in achieving optimal agricultural output and economic sustainability. According to the study's findings, T6, which has a balanced mix of inorganic and organic amendments, is a promising technique for increasing kalmegh variety CIM Megha production. This technique provides higher crops, financial rewards, and improved soil nutrient levels.

The research was conducted in north Wello and south Gonder zones of Amhara region with the aim of investigating phenotypic diversity of cattle. The study areas were selected based on prior experience where Smada cattle breed breeding track can be found and other areas were selected based on agroecology, area and population distribution. Both morphological and metric value were recorded from 178 male and 272 female. The morphological data were entered to SPSS for conducting chi-square test procedure. The morphometric data were subjected to SAS GLM procedures by fitting sex, agro ecology, districts and agro ecology interaction with districts. Except body length (BL) and ear length (EL) other morphometric characteristics of cattle has variation (P < 0.05) based on the sex of cattle. Population difference also observed within agro ecology of the study areas. Accordingly, in highland part of the study areas; BL, heart girth (HG) and pelvic width (PW) are better (P < 0.05) than midland of the study areas. However, population difference (P < 0.05) along districts lacks consistency. Black and red coat color covers major observation along the study areas. Black coat color is not preferred culturally, and the price of such cattle is lower. The red coat color is the next observed and culturally preferred color for farmers. Including such coat color in trait preference of farmers for conducting improvement programs along with other traits is crucial. Moreover, cattle population along districts has no variation based on morphometric and morphological results. Therefore, considering this cattle population as Smada cattle breed is recommended.

Drosophila bipectinata and D. malerkotliana are found to be distributed all along the Oriental-Australian continents and have common phylogenetic descent. The genetic divergence of these two species have been studied by using genetic markers like chromosome inversions and allozyme variants to establish the extent of variation they have experienced since their speciation. In this study, microsatellite variations have been considered to observe the genetic differentiation among the seven natural populations of D. bipectinata and six populations of D. malerkotliana. Results pertaining to both the species indicate that the level of average heterozygosity increases from north to south. Distinct genetic differentiation has been observed between north and south populations of both the species giving an indication that north and south populations have undergone genetic structuring due to absence of gene flow between them and varying environmental conditions. Based on the frequencies of microsatellite variants of the two species, we have computed the level of variation between these two species. The analysis in this regard shows an almost similar trend of genetic variation being experienced by these two species which could be a kind of parallel evolution occurring due to similar ecological niches occupied by them and similar impact of evolutionary forces.

Male sterility (MS) is powerful tool for improvement of various traits of economic importance. MS has not been characterized in Solanum villosum, and molecular mechanism underlying mutation change have not yet been studied. In this study, Sanger sequence platform was employed to amplify the MS genic region using mt ATPase marker. The molecular mechanism governing sterility was studied, and the results detected the amplification region at 1150bp. The sequence query was 97 % identical with atp subunit 6 gene loci. Significance mutation detected in this study was deletion GG (delGG) and deletion C (delC) occurring between 536bp and 542bp position in atp6 gene transcript. The mutation score was 16 for delGG and 17 for delC, with a 90 % mutation confidence interval. The study observed that SNP changes due to base deletions in the atp6 gene region were the main cause of male sterility in the studied mutants due to anticipated frameshifts of the open reading frame (ORF) of the mitochondrial atp6 gene, this is regarded as cytoplasmic male sterility type (CMS). Deformed and low pollen count was morphological changes confirmed this study that associated with sterility. Disruption of the ATP synthesis in mitochondria, limits the energy supply for pollen grain formation and anticipated pollen sterility however, mitochondria nuclear gene interaction governing the CMS should be further studied in case of S.villosum. These findings shed-light on molecular mechanism underlying the CMS and can be utilized as a molecular marker for agronomic traits improvement of S.villosum.

Arbutin is a hydroquinone glucoside and a natural product present in microorganisms and plants. Arbutin inhibits the tyrosinase activity in skin cells and due to this property; this compound has been highly exploited in derma-pharmaceutical applications. Arbutin also possesses broad biological activities, which includes; anti-oxidative, anti-inflammatory, anti-microbial and anti-cancer properties. In this study, the arbutin biosynthesis gene was PCR amplified from the genomic DNA of deep sea halophilic bacteria, Shigella sp. NIOT-DSB91. The amplified gene was cloned and nucleotide sequences were determined. Sequencing results revealed that ascF gene is encoded by polynucleotides of 1458 bp. The ascF gene encodes proteins of 485 amino acids with calculated molecular mass of 51026 Da. In silico sequence and phylogenetic analysis of nucleotides and amino acids revealed that the ascF gene sequences of Shigella sp. NIOT-DSB91 were conserved in many eubacteria.

Amaranths are a type of plant that belongs to the NAD-malic enzyme-type C4 metabolism category. They have a unique C4 anatomy, which is present in their bracts, cotyledons, and leaves. This allows them to produce food through the C4 photosynthetic pathway and rapidly adapt to unfavorable environmental conditions. In this study, 120 amaranth genotypes were evaluated for physio-morphological traits, genetic variability, and growth performance assessment from Ethiopia. The results of the analysis of variance showed that all examined physio-morphological parameters, except the rate of photosynthesis and stomata conductance, had mean squares that varied considerably (P < 0.001) owing to genotypes. The estimates of genetic variability, heritability, and expected genetic advance indicated an incredible extent of genetic diversity among amaranth genotypes, with a significant selection pressure for these traits in the population to produce better genotypes for improved amaranth. Selection based on desirable features such as leaf-to-air vapor pressure deficit, transpiration rate, chlorophyll a, chlorophyll b, total chlorophyll, carotenoid, leaf area, plant height, leaf number, and root weight can be useful in achieving the intended genetic gains for improvement since these traits appear to be more controlled by additive gene activity. Thus, selection in amaranth genotypes may consider these desired yield-related features. Moreover, the study showed that certain genotypes (ALE-073) exhibited better intercellular CO₂ concentration (Ci), leaf-to-air vapor pressure deficit (VPD), transpiration rate (E), and leaf number (LN), resulting in better grain yield. Understanding the relationship between LA and E can help in selecting crops for high E and may provide an avenue to improve leaf yield. Furthermore, some of the selected genotypes in this study could be used as potential parents for improving the genetic gain in amaranth breeding programs. The study concluded that there was additive gene action present since the Ch a, Ch b, TCh, and Tca markers exhibited 100 % heritability. This showed that the use of these characteristics for selection, which indicated a potentially exploitable variation, would be more effective and successful in the long run in breeding programs than the use of other traits for splitting generations.

The species of genus Citrus mostly originated in Southeast Asia, a region with a remarkable diversity of Citrus species. They have been cultivated and harnessed worldwide and are commonly known as mandarins, oranges, lemons, and pomelos. The major products of the plants include the juice from fruits, leaves, and the rind as flavour enhancement of food in many regional culinary cultures. Different parts of the plants are commonly used in traditional medicines with a long history ascribed to the potential medicinal benefits, including antimicrobial, antihypertensive, anti-inflammatory, and antioxidant properties. In this article, we aim to provide a comprehensive review of studies on Citrus species in the following aspects. First, we reviewed studies on various Citrus species in different geographic regions of Asia including their uses in medicinal, culinary, and other cultural purposes. The phylogeny of the Citrus species was proposed to be complicated, which might be attributed to the extensive interbreeding between ancestral taxa and/or being cultivated for different economic strains. Secondly, we summarized and discussed the studies of Citrus depressa in Japan and Taiwan, emphasizing the maintenance of genetic diversity and the potential health benefits of bioactive compounds. Finally, we reviewed the studies discovering the species or cultivars that may provide a source of disease-resistant genes to help Citrus plants from Huanglongbing (HLB), a common disease of Citrus species. The use of the latest genomic biotechnology to introduce disease-resistant genes to cultivars will significantly reduce the damage to the soil and environment from using chemical reagents for disease prevention.