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Chickpea is a globally important food legume, but its productivity is significantly constrained by low-temperature stress, particularly during autumn and winter sowing, as well as by sudden temperature fluctuations in late spring. Although wild relatives of chickpea exhibit enhanced cold tolerance, their molecular responses to freezing stress remain poorly understood. In this study, we compared cold-tolerant and cold-sensitive cultivated chickpea genotypes ILC8262 and ILC533 along with three wild relatives, Cicer bijugum , Cicer reticulatum , and Cicer echinospermum , using de novo transcriptome analysis through RNA sequencing. A total of 1.38 billion raw reads were generated, resulting in the assembly of 181,756 transcripts and 56,556 unigenes. Between 9,921 and 11,149 DEGs were identified per genotype under freezing stress. Functional annotation identified 453 unigenes related to cold response, while 519 DEGs were associated with cold or freezing tolerance based on gene ontology enrichment. Wild Cice r species showed a broader and more dynamic transcriptional response to freezing stress, including the activation of key calcium signaling components such as glutamate receptor-like channels, calmodulin-like proteins, CBL-CIPK modules, and calcium-dependent protein kinases, as well as MAPK cascades and genes in the ICE-CBF-COR pathway. Among the wild species, C. bijugum exhibited the highest number of species-specific DEGs and TFs, suggesting a distinct and potentially powerful cold adaptation strategy. In addition, we identified 8659 SSRs and 232,271 SNPs, with a subset validated as polymorphic markers. This study provides novel and comprehensive insights into the molecular mechanisms of freezing tolerance in chickpea and offers valuable genomic resources for breeding freezing-tolerant varieties.

Plum pox virus (PPV) is the most devastating viral disease of the stone fruits worldwide. Inefficiency of the traditional control measures against PPV along with its globally widespread distribution and the economic importance of stone fruits, signify the necessity and importance of PPV resistance programs. In the present study, Agrobacterium-mediated transformation of Nicotiana benthamiana Domin was performed using four inverted repeat constructs derived from UTR/P1, HCPro, HCPro/P3, and CP regions of PPV-T isolate KyEsAp301. The efficacy of the constructs for inducing virus resistance in transgenic plants was evaluated by inoculation with PPV-D, -M, and -T strains. The potential of hairpin structures in the production of siRNAs and miRNAs in both wild-type and transgenic plants was compared by small RNA high-throughput sequencing. Although the four PPV genomic regions were used for transgenic resistance in previous experiments, small RNA high-throughput sequencing was first time used in this study to demonstrate the efficacy of the PPV constructs and to determine expression profiles of siRNAs and miRNAs. The results revealed that the potentials of hairpin constructs in producing siRNAs and their accumulation in target regions were significantly different. Expression profiles of several known and novel miRNAs were dramatically changed in response to PPV infection in both wild-type and transgenic plants, demonstrating plausible involvement of these miRNAs in plant-virus interactions. Based on the abundance of siRNAs and lack of PPV virus accumulation in transgenic plants harboring UTR/P1 and CP hairpin construct, we have concluded that UTR/P1 and CP are likely the best viral regions for induction of resistance against PPV.

Formaldehyde (FA) is commonly used for hatchery disinfection, where it reduces microbial growth, ensures successful egg hatch and enhances healthy production, but its specific effects on embryonic development remain unclear. MicroRNAs (miRNAs) regulate gene expression post-transcriptionally and may mediate FA-induced transcriptional responses. Here, we investigated the impact of FA treatment on miRNA profiles in chicken embryo liver. Small RNA-seq libraries were constructed and sequenced using the Illumina NextSeq platform. Reads were trimmed and quantified using miRDeep2 version 2.0.0.3. Differential expression analysis was performed with DESeq2 (p-adjusted < 0.05 and |log2FC| > 1). Target genes of differentially expressed miRNAs (DEMs) were predicted with miRDB, and GO/KEGG/Reactome enrichment was conducted. Out of 662 total mature miRNAs detected, differential expression analysis identified 30 DEMs (11 up-regulated, 19 down-regulated). The highest fold increase was determined for gga-miR-3533 (log2FC = 4.45), and the most significant decrease was determined for gga-miR-133b (log2FC = −3.38). Pathway analysis revealed miRNAs affecting signaling pathways along with modules related to post-translational protein modification, immune system, and oxidative stress pathways. Our study demonstrates that FA treatment can affect critical biological processes by altering miRNA-mediated regulation in the developing embryonic liver and point to the need for functional validation of miRNA-target interactions to help determine mechanisms for FA benefits. Long term, these data may help serve as reference to identify new treatments with optimized response profiles.

Gliridae and Sciuridae, the most impressive mammalian radiations within the suborder Sciuromorpha, encompass a total of 327 extant species. This study aimed to: (i) characterize the mitogenomes of three sciurid (Spermophilus citellus, Spermophilus taurensis, and Spermophilus xanthoprymnus) and three glirid (Glis glis, Dryomys nitedula, and Dryomys laniger) species from Türkiye; (ii) elucidate the phylogeographic relationships within D. laniger and D. nitedula using both mitogenomes and mitochondrial cytochrome b (CYTB) sequences; and (iii) reconstruct the phylogenetic relationships among extant members of the suborder Sciuromorpha. Sixteen new mitogenomes were sequenced from Turkish samples, containing 37 genes (2 ribosomal RNAs, 13 protein‐coding genes, 22 transfer RNAs), exhibiting similarity to those of other Gliridae and Sciuridae species. Based on mitogenomic data, Bayesian Inference and Maximum Likelihood phylogenetic analyses revealed two major phylogroups corresponding to the two families, Gliridae and Sciuridae, which were both monophyletic. Analyses of mitogenomic and CYTB sequences revealed at least two major lineages (i: Anatolia and ii: Lesser Caucasus and Alborz) of D. nitedula in the Anatolian region of Türkiye. The mitochondrial CYTB data indicated that D. laniger exhibited at least two major lineages (Eastern and Western), whereas D. nitedula comprised multiple lineages and sublineages. The mean genetic distance between the two mitogenomic lineages of D. nitedula was 7.69%. Based on the CYTB data, the mean genetic distance between the Eastern and Western lineages of D. laniger was 7%, whereas the mean genetic distances among the lineages of D. nitedula ranged from 6% to 13%. Major lineages of both D. laniger and D. nitedula might be considered distinct species throughout the species' range. This study demonstrates that complete mitogenomes for reconstructing the Gliridae phylogeny provides important information for revealing phylogenetic and phylogeographic relationships. This study presents mitogenomic analyses of three squirrel (Sciuridae) and three dormouse (Gliridae) species from Türkiye, uncovering significant phylogenetic and phylogeographic insights within the suborder Sciuromorpha. Phylogenetic analyses positioned Gliridae as the basal group within the suborder, and mitogenomic and CYTB data revealed distinct genetic lineages for Dryomys laniger and Dryomys nitedula, suggesting potential species‐level distinctions. These findings underscore the value of complete mitogenomes in understanding the evolutionary and taxonomic relationships in Gliridae.

This study investigated genetic diversity, phylogenetic relationships, and evolutionary history of domestic goats from Türkiye and Iraq, along with wild goat and chamois species, using newly obtained mitogenomic sequences. Phylogenetic and phylogeographic analyses revealed a complex genetic structure among domestic goats, shaped by widespread distribution and gene flow. While haplotype A was predominant among domesticated breeds from both Türkiye and Iraq, haplotype G was also detected in the Turkish breeds. Notably, Turkish samples exhibited relatively higher nucleotide diversity (0.00133) compared to those from Iraq (0.00081), indicating greater genetic variability in the former population. Wild goat populations in Türkiye were clustered into two distinct lineages: (i) the Aegagrus lineage included the Artvin sample, some ancient genomes from the Taurus Mountains, and Iranian goats, and (ii) the Caucasian lineage contained Konya and Antalya samples, and some ancient genomes from the Taurus Mountains that were clustered closely with wild goats from the Caucasus. These findings suggest that geographic and ecological factors, such as the Anatolian Diagonal, influenced their diversification. Divergence time analyses indicated that the Caprinae began diversifying approximately 8.18 Mya, with initial splits in the Capra occurring around 3.22 Mya during the climatic fluctuations of the Late Pliocene/Early Pleistocene. The study also estimated the divergence of C. aegagrus and C. hircus at approximately 0.89 Mya in the Calabrian, with genetic diversification within domestic goats commencing 0.29 Mya in the Chibanian. The results provided robust evidence supporting Türkiye's role as a significant genetic center for goat domestication during the Neolithic period (~10,000 years ago). This hypothesis was further supported by the widespread presence of the common haplotype A in domestic goats, the high genetic diversity observed among domestic goats, and the region's proximity to the Fertile Crescent. The study underscored the importance of comprehensive genetic analyses in elucidating the evolutionary processes underlying goat domestication and highlighted the necessity for larger datasets and additional molecular markers to resolve the taxonomic complexities of wild goat populations in Türkiye, Iraq, and surrounding regions. This study explores the genetic diversity, phylogenetic relationships, and evolutionary history of domestic (Capra hircus) and wild goats (Capra aegagrus), as well as chamois (Rupicapra rupicapra) from Türkiye and Iraq, using complete mitochondrial genomes. The findings reveal two distinct wild goat lineages in Türkiye, shaped by geographic factors such as the Anatolian Diagonal, and highlight Türkiye's role as a key genetic center for goat domestication during the Neolithic period. Divergence time estimates suggest that C. aegagrus and C. hircus split around 0.89 million years ago, reinforcing the evolutionary significance of the region.

Plum pox virus strain Recombinant (PPV-Rec) is hypothetically considered as homologous recombinant between strains PPV-M and PPV-D. The nucleotide position 8450 up to end of genome is considered to come from PPV-M, and the remaining major genomic part is PPV-D-derived. It is regarded as third major PPV strain due to its wide distribution and prevalence in Europe. However, among over a thousand PPV isolates genetically identified in Turkey, only 10 of them (<1%) were characterized as PPV-Rec. The nearly complete genome of eight of the PPV-Rec isolates from European part of Turkey were obtained and analyzed together with PPV-Rec isolates of other countries. All major genomic features were conserved among Turkish PPV-Rec isolates. The genetic diversity of PPV-Rec isolates in Turkey (n = 8, 0.015 ± 0.001%) was found to be comparable to that observed for the isolates from eight countries (n = 10, 0.014 ± 0.001%). Particularly, genetic diversity of the minor recombinant fragment for Turkish PPV-Rec isolates was apparently higher (0.016 ± 0.001%) than the value for the 10 isolates from eight countries (0.011 ± 0.001%). The high genetic diversity was also demonstrated by high phylogenetic variation in Turkish isolates, indicating a long evolutionary history of PPV-Rec isolates in Turkey. After including Turkish isolates in the recombination analysis, the major putative recombination event of PPV-Rec isolates with a breakpoint around position 8450 was identified again, however the other recently reported putative recombination events were not supported in this study by the algorithms implemented in the RDP software.

In the past several years, a limited number of isolates of a diverse group of Plum pox virus (PPV) strain -M were discovered in the European part of Istanbul, Turkey. In this study, stone fruit samples were collected from the European part of Istanbul and investigated by PCR typing and sequence analyses for determining prevalence and genetic diversity of this divergent PPV-M isolates. Out of the 230 sampled trees, 97 were determined to be infected with PPV. Strains of 88 isolates were identified and 67 of them (76%) were divergent PPV-M isolates, detected in apricot, peach and plum trees revealing that they could be evolutionarily successful divergent PPV-M isolates prevalent in Istanbul. The divergent Istanbul M isolates formed a monophyletic clade thereby named as PPV-MIs. Additionally, recombination analysis suggested that PPV-MIs isolates could be the donor of the PPV-M-type recombinant fragment of the PPV-Rec strain.

Genotyping by sequencing (GBS), which is a highly promising technique for molecular breeding, has been implemented in apricots, including Turkish, European, and Plum Pox Virus -resistant accessions. DNA samples were digested with the ApeKI restriction enzyme to construct a genome-complexity-reduced 90-plex GBS library. After filtering the raw sequences, approximately 28 G of clean data were generated, and 17,842 high-quality single-nucleotide polymorphism (SNP) loci were discovered. A total of 561 SNP loci with 0 or 1 missing reads for the 90 accessions produced 1162 markers that were used for the cluster and population structure analysis of the same collection. The results of the SNP analysis indicated that the relation of the European accessions with the western Turkish apricots was accurately positioned. The resistant accessions from different sources were clustered together, confirming the previous finding that SEO/Harlayne-type resistance probably originated from the same source. The Malatya accessions produce most of the world’s dried apricots and are likely to be a genetically distinct group. Simple sequence repeat (SSR) and self-incompatibly (SI) locus characterization of the accessions was also included. SI genotyping supported the SNP findings, demonstrating both the reliability of SNP genotyping and the usefulness of SI genotyping for understanding the history of apricot breeding. The SSR genotyping revealed a characterization similar to that of SNP genotyping with a slightly lower resolution in the dendrogram. In conclusion, the GBS approach was validated in apricots, with the discovery of a large number of SNPs, and was demonstrated to be reliable by fingerprinting the accessions in a more informative manner.