Specificity Patterns Research Articles

Parasite–host network analysis provides insights into the evolution of two mistletoe lineages (Loranthaceae and Santalaceae)

Mistletoes are ecologically important parasitic plants, with > 1600 species from five lineages worldwide. Mistletoe lineages exhibit distinct patterns of species diversification and host specificity, however, the mechanisms underlying these differences are poorly understood. In this study, we analysed a comprehensive parasite–host network, including 280 host species from 60 families and 22 mistletoe species from two lineages (Santalaceae and Loranthaceae) in Xishuangbanna, located in a biodiversity hotspot of tropical Asia. We identified the factors that predict the infection strength of mistletoes. We also detected host specificity and the phylogenetic signal of mistletoes and their hosts. We found that this interaction network could be largely explained by a model based on the relative abundance of species. Host infection was positively correlated with diameter at breast height and tree coverage, but negatively correlated with wood density. Overall, closely related mistletoe species tend to interact more often with similar hosts. However, the two lineages showed a significantly different network pattern. Rates of host generality were higher in Loranthaceae than in Santalaceae, although neither lineage showed phylogenetic signal for host generality. This study demonstrates that the neutral interaction hypothesis provides suitable predictions of the mistletoe–host interaction network, and mistletoe species show significant phylogenetic signals for their hosts. Our findings also indicate that high species diversification in Loranthaceae may be explained by high rates of host generality and the evolutionary history shared by Loranthaceae species with diverse host plants in the tropics.

A set of closely related methyltransferases for site-specific tailoring of anthraquinone pigments

Modification of the polyketide anthraquinone AQ-256 in the entomopathogenic Photorhabdusluminescens involves several O-methylations, but the biosynthetic gene cluster antA-I lacks corresponding tailoring enzymes. We here describe the identification of five putative, highly homologous O-methyltransferases encoded in the genome of P.luminescens. Activity assays invitro and deletion experiments invivo revealed that three of them account for anthraquinone tailoring by producing three monomethylated and two dimethylated species of AQ-256. X-ray structures of all five enzymes indicate high structural and mechanistic similarity. As confirmed by structure-based mutagenesis, a conserved histidine at the active site likely functions as a general base for substrate deprotonation and subsequent methyl transfer in all enzymes. Eight complex structures with AQ-256 as well as mono- and dimethylated derivatives confirm the substrate specificity patterns found invitro and visualize how single amino acid differences in the active-site pockets impact substrate orientation and govern site-specific methylation.

Diversity and structure of feather mite communities on seabirds from the north–east Atlantic and Mediterranean Sea

The richness and structure of symbiont assemblages are shaped by many factors acting at different spatial and temporal scales. Among them, host phylogeny and geographic distance play essential roles. To explore drivers of richness and structure of symbiont assemblages, feather mites and seabirds are an attractive model due to their peculiar traits. Feather mites are permanent ectosymbionts and considered highly host-specific with limited dispersal abilities. Seabirds harbour species-rich feather mite communities and their colonial breeding provides opportunities for symbionts to exploit several host species. To unravel the richness and test the influence of host phylogeny and geographic distance on mite communities, we collected feather mites from 11 seabird species breeding across the Atlantic Ocean and Mediterranean Sea. Using morphological criteria, we identified 33 mite species, of which 17 were new or recently described species. Based on community similarity analyses, mite communities were clearly structured by host genera, while the effect of geography within host genera or species was weak and sometimes negligible. We found a weak but significant effect of geographic distance on similarity patterns in mite communities for Cory’s shearwaters Calonectris borealis. Feather mite specificity mainly occurred at the host-genus rather than at host-species level, suggesting that previously inferred host species-specificity may have resulted from poorly sampling closely related host species. Overall, our results show that host phylogeny plays a greater role than geography in determining the composition and structure of mite assemblages and pinpoints the importance of sampling mites from closely-related host species before describing mite specificity patterns.

The evolution of partner specificity in mutualisms.

Mutualistic species vary in their level of partner specificity, which has important evolutionary, ecological, and management implications. Yet, the evolutionary mechanisms which underpin partner specificity are not fully understood. Most work on specialization focuses on the trade-off between generalism and specialism, where specialists receive more benefits from preferred partners at the expense of benefits from non-preferred partners, while generalists receive similar benefits from all partners. Because all mutualisms involve some degree of both cooperation and conflict between partners, we highlight that specialization to a mutualistic partner can be cooperative, increasing benefit to a focal species and a partner, or antagonistic, increasing resource extraction by a focal species from a partner. We devise an evolutionary game theoretic model to assess the evolutionary dynamics of cooperative specialization, antagonistic specialization, and generalism. Our model shows that cooperative specialization leads to bistability: stable equilibria with a specialist host and its preferred partner excluding all others. We also show that under cooperative specialization with spatial effects, generalists can thrive at the boundaries between differing specialist patches. Under antagonistic specialization, generalism is evolutionarily stable. We provide predictions for how a cooperation-antagonism continuum may determine the patterns of partner specificity that develop within mutualistic relationships.

Multi-tissue RNA-Seq Analysis and Long-read-based Genome Assembly Reveal Complex Sex-specific Gene Regulation and Molecular Evolution in the Manila Clam.

The molecular factors and gene regulation involved in sex determination and gonad differentiation in bivalve molluscs are unknown. It has been suggested that doubly uniparental inheritance (DUI) of mitochondria may be involved in these processes in species such as the ubiquitous and commercially relevant Manila clam, Ruditapes philippinarum. We present the first long-read-based de novo genome assembly of a Manila clam, and a RNA-Seq multi-tissue analysis of 15 females and 15 males. The highly contiguous genome assembly was used as reference to investigate gene expression, alternative splicing, sequence evolution, tissue-specific co-expression networks, and sexual contrasting SNPs. Differential expression (DE) and differential splicing (DS) analyses revealed sex-specific transcriptional regulation in gonads, but not in somatic tissues. Co-expression networks revealed complex gene regulation in gonads, and genes in gonad-associated modules showed high tissue specificity. However, male gonad-associated modules showed contrasting patterns of sequence evolution and tissue specificity. One gene set was related to the structural organization of male gametes and presented slow sequence evolution but high pleiotropy, whereas another gene set was enriched in reproduction-related processes and characterized by fast sequence evolution and tissue specificity. Sexual contrasting SNPs were found in genes overrepresented in mitochondrial-related functions, providing new candidates for investigating the relationship between mitochondria and sex in DUI species. Together, these results increase our understanding of the role of DE, DS, and sequence evolution of sex-specific genes in an understudied taxon. We also provide resourceful genomic data for studies regarding sex diagnosis and breeding in bivalves.

Identification of the GAPDH gene family in Citrullus lanatus and functional characteristics of ClGAPC2 in Arabidopsis thaliana.

Members of the GAPDH family play important roles in plant growth and development, as well as in stress responses. Our aim was to identify stress resistance genes through systematic analysis of the GAPDH family in watermelon. This could not only provide genetic resources for stress resistance breeding, but also form a basis for the study of plant stress resistance mechanisms. Eight GAPDHs representing four types of plant GAPDH in watermelon were identified (ClGAPA/B, ClGAPC1-3, ClGAPCp1-2 and ClGAPN). A comprehensive analysis of physicochemical properties, chromosome distribution, evolutionary relationships, exon-intron structure and conserved motifs of watermelon GAPDHs was performed using bioinformatics. Expression characteristics were assessed by RT-qPCR. Based on RT-qPCR results, ClGAPC2 was screened as a candidate for subcellular localization analysis and functional verification in Arabidopsis thaliana. Eight GAPDHs were classified into four subfamilies. GAPDHs in each subgroup were generally conserved and shared similarities in structure and conserved motifs. ClGAPDHs had notable tissue specificity and different expression patterns in response to H2 O2 , chilling, salt, osmotic stress, heat, salicylic acid, gibberellin, brassinosterol, ethylene and abscisic acid treatments. Three ClGAPC genes, especially ClGAPC2, were markedly induced by several treatments. ClGAPC2 was located in the nucleus and cytoplasm of tabacum epidermal cells. The ClGAPC2 transgenic Arabidopsis showed enhanced tolerance to salinity at the germination stage. We suggest that ClGAPC2 plays important roles in the adaptation of watermelon to salinity. Our findings provided candidate genes for further improving the salt tolerance of watermelon.

Genome-Wide Identification and Expression Profiling of Heat Shock Protein 20 Gene Family in Sorbus pohuashanensis (Hance) Hedl under Abiotic Stress.

Small heat shock proteins (HSP20s) are a significant factor in plant growth and development in response to abiotic stress. In this study, we investigated the role of HSP20s' response to the heat stress of Sorbus pohuashanensis introduced into low-altitude areas. The HSP20 gene family was identified based on the genome-wide data of S. pohuashanensis, and the expression patterns of tissue specificity and the response to abiotic stresses were evaluated. Finally, we identified 38 HSP20 genes that were distributed on 16 chromosomes. Phylogenetic analysis of HSP20s showed that the closest genetic relationship to S. pohuashanensis (SpHSP20s) is Malus domestica, followed by Populus trichocarpa and Arabidopsis thaliana. According to phylogenetic analysis and subcellular localization prediction, the 38 SpHSP20s belonged to 10 subfamilies. Analysis of the gene structure and conserved motifs indicated that HSP20 gene family members are relatively conserved. Synteny analysis showed that the expansion of the SpHSP20 gene family was mainly caused by segmental duplication. In addition, many cis-acting elements connected with growth and development, hormones, and stress responsiveness were found in the SpHSP20 promoter region. Analysis of expression patterns showed that these genes were closely related to high temperature, drought, salt, growth, and developmental processes. These results provide information and a theoretical basis for the exploration of HSP20 gene family resources, as well as the domestication and genetic improvement of S. pohuashanensis.

Cytohistopathological Correlation of 884 Cervical Pap Smears as Bethesda System 2014: A Hospital-Based Study

Cervical carcinoma is most common in Indian women of which Rural women are predominantly affected. The most common etiological factor is human papillomavirus (HPV ). The present study aims to assess the diagnostic accuracy, sensitivity, specificity, and different patterns of cervical Pap smears by comparing histological findings. The index study is a retrospective cross-sectional analytical study. The data was collected at the pathology department from May 2017 to December 2019 according to hospital ethical protocol. Cervical Pap smears received by the pathology department underwent Pap staining. A total of 884 Pap smears were satisfactory and included in the study. The age of enrolled women was 46.4 ± 9.7 years. 800 cervical Pap smears were reported as negative for intraepithelial lesion (NILM), and 84 Pap smears were reported as abnormal. Abnormal pap smears included 64 (7.1%) atypical squamous cell-undetermined significance (ASC-US), 9 (1.01%) low-grade squamous intraepithelial (LSIL), 5 (0.56%) high-grade squamous intraepithelial lesion cannot be ruled out (ASC-H), 3 cases (0.33%) of high grade squamous intraepithelial lesion (HSIL), 2 cases (0.22%) of atypical glandular cell-not specific otherwise (AGC-NOS) and 1 case (0.11%) of squamous cell carcinoma. The cytohistological correlation was found in 56 patients, including 41.07% with chronic cervicitis, 26.75% with chronic cervicitis with squamous metaplasia, 5.35% with cervical polyps, 3.57% with CIN-1, 14.28% with carcinoma in situ, 7.14% with squamous cell carcinoma (keratinizing), 1.78% with squamous cell carcinoma (non-keratinizing) patients. Cytohistological correlation of 56 cases revealed sensitivity (83.33%), specificity (94.73%), PPV (88.23%), NPV (92.3%) and accuracy (91.07%). The cervical Pap test is cost-effective, almost as sensitive, and accurate as histology in screening for cervical lesions.

Culturable endophytic fungal assemblages from Styrax sumatrana and Stryax benzoin and their potential as antifungal, antioxidant, and alpha-glucosidase inhibitory resources.

Benzoin resin, produced by the native Indonesian trees Styrax sumatrana and Styrax benzoin, has been incorporated into medical practices to treat wounds, erythema, and many other conditions for centuries. Endophytic fungi that reside within medicinal plants have antimicrobial, antioxidant, and α-glucosidase inhibitory capacities, contributing to plant health and derivative products. In this study, we determined the antifungal, antioxidant, and α-glucosidase inhibitory capacities of endophytic fungal isolates from three different tissues (leaves, bark, and stems) of S. sumatrana and S. benzoin trees. The genera of fungal isolates were determined by phylogenetic analysis of internal transcribed spacer sequences. A total of 58 fungal isolates were classified into 15 different fungal genera from eight taxonomic orders-Hypocreales, Botryosphaeriales, Glomerellales, Diaphortales, Pleosporales, Eurotiales, Xylariales, and Mucorales-with a pattern of host species specificity. Among these isolates, Trichoderma sp. 6407 consistently exhibited high inhibition of the growth of plant pathogens Fusarium sp., Trichoderma viride, and Aspergillus niger. With respect to antioxidant activity, Phyllosticta sp. 6454 consistently showed 2,2-diphenyl-1-picrylhydrazyl inhibition (37.59 ± 0.05%), 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid)-based antioxidant activity (25.04 ± 0.27 mgTE/g), and α-glucosidase inhibitory activity (52.15 ± 10.08%). Neopestalotiopsis sp. 6431 was notably potent in 2,2-diphenyl-1-picrylhydrazyl inhibition (49.65 ± 0.80%), ferric reducing antioxidant power-based antioxidant activity (197.49 ± 8.65 mgTE/g), and α-glucosidase inhibitory activity (52.88 ± 4.93%). This study revealed that Trichoderma sp. 6407, Phyllosticta sp. 6454, and Neopestalotiopsis sp. 6431 exhibited antifungal, antioxidant, and α-glucosidase inhibitory activities.

A comprehensive atlas of epigenetic regulators reveals tissue-specific epigenetic regulation patterns

ABSTRACT Epigenetic machinery contributes to gene regulation in eukaryotic species. However, the machinery including more than 600 epigenetic regulator (ER) genes responsible for reading, writing, and erasing histone modifications and DNA modifications remains largely uncharacterized across species. We compile a comprehensive list of ERs based on an evolutionary analysis across 23 species, which is the most comprehensive ER list in various species until recently. We further perform comparative transcriptomic analyses across different tissues in humans, mice, as well as other amniote species. We observe a consistent tissue-of-origin expression specificity pattern of duplicated ER genes across species and suggest links between expression specificity and ER gene evolution as well as ER function. Additional analyses further suggest that ER duplication can generate tissue-specific ER genes with the same epigenetic substrates, which may be closely related to their regulatory specificity in tissue development. Our work can serve as a foundation to better comprehend the tissue-specific expression patterns of ER genes from an evolutionary perspective and also the functional implications of ERs in tissue-specific epigenetic regulation.

A humanized mouse model for in vivo evaluation of invariant Natural Killer T cell responses.

Invariant natural killer T (iNKT) cells mediate immune responses when stimulated by glycolipid agonists presented by CD1d. In extensive studies of synthetic analogues of α-galactosyl ceramides, we identified numerous examples of significant differences in the recognition of specific glycolipids in wild type mice versus human iNKT cell clones or PBMC samples. To predict human iNKT cell responses more accurately in a mouse model, we derived a mouse line in which compound genetic modifications were used to express a human-like iNKT cell TCR along with human CD1d in place of the endogenous mouse proteins. Detailed transcriptional and phenotypic profiling demonstrated that these partially humanized mice developed an expanded population of T cells recognizing CD1d-presented glycolipid antigens, among which a subset characterized by expression of chemokine receptor CXCR6 had features characteristic of authentic iNKT cells. Responses to iNKT cell activating glycolipids in these mice generated cytokine production in vitro and in vivo that showed a pattern of fine specificity that closely resembled that of cultured human iNKT cell clones. Anti-tumor responses to variants of α-galactosyl ceramide in VαKI mice also correlated with their potency for stimulating human iNKT cells. This genetically modified mouse line provides a practical model for human presentation and recognition of iNKT cell activators in the context of a normally functioning immune system, and may furnish valuable opportunities for preclinical evaluation of iNKT cell-based therapies.

Morphological and molecular characterization of the ciliate parasite Tetrahymena rostrata infecting the renal organ of the dusky slug (Arion fuscus)

The histophagous ciliate Tetrahymena rostrata (Kahl, 1926) is a facultative parasite of the renal organ of land snails and slugs. The possibility of transovum transmission and the lack of heteroparental sex make T. rostrata an interesting model for studying host specificity and distribution patterns in pathogenic ciliates. We recorded mass Tetrahymena infection in the dusky slug ( Arion fuscus (O.F. Müller, 1774)) collected in Slovakia, Central Europe. Based on the mitochondrial 16S rRNA gene and barcoding cytochrome c oxidase subunit I (COI) sequences, Slovak isolates belong to the TRO-1 subgroup. Strains of T. rostrata, however, do not cluster according to the relatedness of their gastropod hosts, i.e., various phylogenetically unrelated snails and slugs are parasitized by members of both T. rostrata subclades (TRO-1 and TRAUS). Invasion of adult gastropods through the integumentary pouch might be thus a more important transmission way than the transovum route. Geographic distances of T. rostrata isolates are not correlated with divergences in COI sequences. The absence of a clear relationship between genetic and geographic distances might have been, however, also caused by the human-mediated transmission of invasive gastropods.

Specificity of Stenurus (Metastrongyloidea: Pseudaliidae) infections in odontocetes stranded along the north-west Spanish coast.

Parasites extracted from the lungs and the pterygoid sinus complex of 6 species of odontocetes stranded along the north-west Spanish coast (Northeast Atlantic) between 2009 and 2019 were morphologically identified. The samples belonged to 14 specimens, including 3 harbour porpoises, Phocoena phocoena, 6 short-finned pilot whales, Globicephala macrorhynchus, 1 long-finned pilot whale, Globicephala melas, 1 Risso's dolphin, Grampus griseus, 1 striped dolphin, Stenella coeruleoalba and 2 bottlenose dolphins, Tursiops truncatus. All animals (14/14) were infected by nematodes of the genus Stenurus spp.; moreover, two of them presented a mixed lung nematode infection by Stenurus spp. and Halocercus spp., and another two a mixed infection by Stenurus spp. and the trematode Nasitrema spp. in the pterygoid sinuses. The morphological characterization of the Stenurus specimens revealed the existence of three different species: Stenurus minor, present in the pterygoid sinuses of harbour porpoises with a mean intensity of 43.0 ± 9.0; Stenurus globicephalae, in the pterygoid sinuses of pilot whales and the Risso's dolphin (370.3 ± 579.4); and Stenurus ovatus infecting bottlenose and striped dolphins’ lungs (47.7 ± 76.5). This is the first citation of S. minor and S. ovatus in odontoceti from the Galician coast. Nematodes of the genus Stenurus are frequent in odontocetes stranded along the north-west Spanish coast. A clear host-parasite association was observed between S. minor and the Phocoenidae family, between S. globicephalae and the subfamily Globicephalinae and between S. ovatus and subfamily Delphininae. Different trophic position and niche segregation may lead to different patterns of specificity.

In-Depth Characterization of greenflesh Tomato Mutants Obtained by CRISPR/Cas9 Editing: A Case Study With Implications for Breeding and Regulation.

Gene editing has already proved itself as an invaluable tool for the generation of mutants for crop breeding, yet its ultimate impact on agriculture will depend on how crops generated by gene editing technologies are regulated, and on our ability to characterize the impact of mutations on plant phenotype. A starting operational strategy for evaluating gene editing-based approaches to plant breeding might consist of assessing the effect of the induced mutations in a crop- and locus-specific manner: this involves the analysis of editing efficiency in different cultivars of a crop, the assessment of potential off-target mutations, and a phenotypic evaluation of edited lines carrying different mutated alleles. Here, we targeted the GREENFLESH (GF) locus in two tomato cultivars (‘MoneyMaker’ and ‘San Marzano’) and evaluated the efficiency, specificity and mutation patterns associated with CRISPR/Cas9 activity for this gene. The GF locus encodes a Mg-dechelatase responsible for initiating chlorophyll degradation; in gf mutants, ripe fruits accumulate both carotenoids and chlorophylls. Phenotypic evaluations were conducted on two transgene-free T2 ‘MoneyMaker’ gf lines with different mutant alleles (a small insertion of 1 nucleotide and a larger deletion of 123 bp). Both lines, in addition to reduced chlorophyll degradation, showed a notable increase in carotenoid and tocopherol levels during fruit ripening. Infection of gf leaves and fruits with Botrytis cinerea resulted in a significant reduction of infected area and pathogen proliferation compared to the wild type (WT). Our data indicates that the CRISPR/Cas9-mediated mutation of the GF locus in tomato is efficient, specific and reproducible and that the resulting phenotype is robust and consistent with previously characterized greenflesh mutants obtained with different breeding techniques, while also shedding light on novel traits such as vitamin E overaccumulation and pathogen resistance. This makes GF an appealing target for breeding tomato cultivars with improved features for cultivation, as well as consumer appreciation and health.

Specificity within bird–parasite–parasitoid food webs: A novel approach for evaluating potential biological control agents of the avian vampire fly

Abstract Quantitative food web analyses can provide insights into the specificity of consumers such as herbivores, parasites and parasitoids. Understanding such patterns can be useful in forecasting the potential benefits and risks of biological control agents being considered for introduction against invasive species. The avian vampire fly, Philornis downsi (Diptera: Muscidae), is a neotropical bird parasite that is invasive in the Galapagos Islands, where it is causing substantial mortality of endemic bird species. We used a novel in‐field experimental food web approach within the native range of P. downsi in Ecuador to test the hypotheses that pupal parasitoids known to attack P. downsi specialize on members of the genus Philornis, which occur only in bird nests. We deployed pupae of non‐Philornis fly species adjacent to bird nests to assess specificity of the parasitoids and used two indices to assess specificity: Resource Range (RR), which evaluates the breadth of host use, and Pair Difference Index (PDI), which evaluates interaction strength. The results revealed very strong compartmentalization within the guild of pupal fly parasitoids, with four species attacking only Philornis spp. Both specificity indices indicated significant levels of specificity towards the genus Philornis for two of these species: Conura annulifera and Trichopria sp. novus. We also assessed the specificity of the two dominant Philornis species attacking 11 bird species and preference of the two dominant parasitoid species for bird species. Although there was some significant preference for particular bird species by the Philornis spp., there was no indication that this drove specificity patterns by the parasitoids. Policy implications. Our results confirm previous laboratory studies indicating specificity by C. annulifera and support the hypothesis that this species would produce few, if any, nontarget impacts if released into Galapagos to suppress populations of the P. downsi. These results can inform an environmental risk assessment framework to guide governmental agencies in deliberation on potential field releases of parasitoids in the Galapagos Islands.

Parasite–copepod interactions in Svalbard: diversity, host specificity, and seasonal patterns

Copepods of the genera Calanus and Pseudocalanus are important components of Arctic marine ecosystems. Despite the key roles of these zooplankters, little is known about the organisms they interact with most intimately, their parasites and symbionts. We applied metabarcode sequencing to uncover eukaryotic parasites present within these two copepod genera from three areas around the high Arctic archipelago of Svalbard. Ten distinct parasite groups were observed: four different Apostome ciliates, four different dinoflagellates (Chytriodinium sp., Ellobiopsis sp., Thalassomyces sp., and Hematodinium sp.), a Paradinium sp., and a trematode. Apostome ciliates closely related to Pseudocollinia spp. were the most commonly observed parasite, with overall infection rates of 21.5% in Calanus and 12.5% in Pseudocalanus. Infection by these ciliates varied seasonally, with no infections observed in early winter, but infection rates exceeding 75% in spring. Host specificity varied between parasites, with significant differences in infection rate between the two host copepod genera for four parasites (two ciliates, Chytriodinium, and a trematode). The diverse assemblage of parasites observed in these copepods, and the frequency of infection, with over one in five copepod individuals infected, suggest parasites may be playing a greater role in Arctic plankton communities than generally acknowledged.

Assembly of wood-inhabiting archaeal, bacterial and fungal communities along a salinity gradient: common taxa are broadly distributed but locally abundant in preferred habitats.

Wood decomposition in water is a key ecosystem process driven by diverse microbial taxa that likely differ in their affinities for freshwater, estuarine and marine habitats. How these decomposer communities assemble in situ or potentially colonize from other habitats remains poorly understood. At three watersheds on Coiba Island, Panama, we placed replicate sections of branch wood of a single tree species on land, and in freshwater, estuarine and marine habitats that constitute a downstream salinity gradient. We sequenced archaea, bacteria and fungi from wood samples collected after 3, 9 and 15 months to examine microbial community composition, and to examine habitat specificity and abundance patterns. We found that these microbial communities were broadly structured by similar factors, with a strong effect of salinity, but little effect of watershed identity on compositional variation. Moreover, common aquatic taxa were also present in wood incubated on land. Our results suggest that either taxa dispersed to both terrestrial and aquatic habitats, or microbes with broad habitat ranges were initially present in the wood as endophytes. Nonetheless, these habitat generalists varied greatly in abundance across habitats suggesting an important role for habitat filtering in maintaining distinct aquatic communities in freshwater, estuarine and marine habitats.

Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle

BackgroundA comprehensive analysis of gene expression profiling across tissues can provide necessary information for an in-depth understanding of their biological functions. We performed a large-scale gene expression analysis and generated a high-resolution atlas of the transcriptome in beef cattle.ResultsOur transcriptome atlas was generated from 135 bovine tissues in adult beef cattle, covering 51 tissue types of major organ systems (e.g., muscular system, digestive system, immune system, reproductive system). Approximately 94.76% of sequencing reads were successfully mapped to the reference genome assembly ARS-UCD1.2. We detected a total of 60,488 transcripts, and 32% of them were not reported before. We identified 2654 housekeeping genes (HKGs) and 477 tissue-specific genes (TSGs) across tissues. Using weighted gene co-expression network analysis, we obtained 24 modules with 237 hub genes (HUBGs). Functional enrichment analysis showed that HKGs mainly maintain the basic biological activities of cells, while TSGs were involved in tissue differentiation and specific physiological processes. HKGs in bovine tissues were more conserved in terms of expression pattern as compared to TSGs and HUBGs among multiple species. Finally, we obtained a subset of tissue-specific differentially expressed genes (DEGs) between beef and dairy cattle and several functional pathways, which may be involved in production and health traits.ConclusionsWe generated a large-scale gene expression atlas across the major tissues in beef cattle, providing valuable information for enhancing genome assembly and annotation. HKGs, TSGs, and HUBGs further contribute to better understanding the biology and evolution of multiple tissues in cattle. DEGs between beef and dairy cattle also fill in the knowledge gaps about differential transcriptome regulation of bovine tissues underlying economically important traits.

Genome-Wide Identification and Characterization of CDPK Family Reveal Their Involvements in Growth and Development and Abiotic Stress in Sweet Potato and Its Two Diploid Relatives.

Calcium-dependent protein kinase (CDPKs) is one of the calcium-sensing proteins in plants. They are likely to play important roles in growth and development and abiotic stress responses. However, these functions have not been explored in sweet potato. In this study, we identified 39 CDPKs in cultivated hexaploid sweet potato (Ipomoea batatas, 2n = 6x = 90), 35 CDPKs in diploid relative Ipomoea trifida (2n = 2x = 30), and 35 CDPKs in Ipomoea triloba (2n = 2x = 30) via genome structure analysis and phylogenetic characterization, respectively. The protein physiological property, chromosome localization, phylogenetic relationship, gene structure, promoter cis-acting regulatory elements, and protein interaction network were systematically investigated to explore the possible roles of homologous CDPKs in the growth and development and abiotic stress responses of sweet potato. The expression profiles of the identified CDPKs in different tissues and treatments revealed tissue specificity and various expression patterns in sweet potato and its two diploid relatives, supporting the difference in the evolutionary trajectories of hexaploid sweet potato. These results are a critical first step in understanding the functions of sweet potato CDPK genes and provide more candidate genes for improving yield and abiotic stress tolerance in cultivated sweet potato.

Diversity and Functional Evolution of Terpene Synthases in Rosaceae.

Terpenes are organic compounds and play important roles in plant development and stress response. Terpene synthases (TPSs) are the key enzymes for the biosynthesis of terpenes. For Rosaceae species, terpene composition represents a critical quality attribute, but limited information is available regarding the evolution and expansion occurring in the terpene synthases gene family. Here, we selected eight Rosaceae species with sequenced and annotated genomes for the identification of TPSs, including three Prunoideae, three Maloideae, and two Rosoideae species. Our data showed that the TPS gene family in the Rosaceae species displayed a diversity of family numbers and functions among different subfamilies. Lineage and species-specific expansion of the TPSs accompanied by frequent domain loss was widely observed within different TPS clades, which might have contributed to speciation or environmental adaptation in Rosaceae. In contrast to Maloideae and Rosoideae species, Prunoideae species owned less TPSs, with the evolution of Prunoideae species, TPSs were expanded in modern peach. Both tandem and segmental duplication significantly contributed to TPSs expansion. Ka/Ks calculations revealed that TPSs genes mainly evolved under purifying selection except for several pairs, where the divergent time indicated TPS-e clade was diverged relatively anciently. Gene function classification of TPSs further demonstrated the function diversity among clades and species. Moreover, based on already published RNA-Seq data from NCBI, the expression of most TPSs in Malus domestica, Prunus persica, and Fragaria vesca displayed tissue specificity and distinct expression patterns either in tissues or expression abundance between species and TPS clades. Certain putative TPS-like proteins lacking both domains were detected to be highly expressed, indicating the underlying functional or regulatory potentials. The result provided insight into the TPS family evolution and genetic information that would help to improve Rosaceae species quality.