Genomic scanning using AFLP to detect loci under selection in the moss Funaria hygrometrica along a climate gradient in the Sierra Nevada Mountains, Spain

Genetic Diversity Analysis of Banana Cultivars (Musa sp.) in Saudi Arabia Based on AFLP Marker

Banana plantation has been introduced recently to a temperate zone in the southeastern parts of Saudi Arabia (Fifa, Dhamadh, and Beesh, located in Jazan province). The introduced banana cultivars were of a clear origin without a recorded genetic background. In the current study, the genetic variability and structure of five common banana cultivars (i.e., Red, America, Indian, French, and Baladi) were analyzed using the fluorescently labeled AFLP technique. Nine different primer pairs combinations yielded 1468 loci with 88.96% polymorphism. Among all locations, high expected heterozygosity under the Hardy–Weinberg assumption was found (0.249 ± 0.003), where Dhamadh was the highest, followed by Fifa and Beesh, respectively. Based on the PCoA and Structure analysis, the samples were not clustered by location but in pairs in accordance with the cultivar’s names. However, the Red banana cultivar was found to be a hybrid between the American and Indian cultivars. Based on ΦST, 162 molecular markers (i.e., loci under selection) were detected among cultivars. Identifying those loci using NGS techniques can reveal the genetic bases and molecular mechanisms involved in the domestication and selection indicators among banana cultivars.

Evaluation of environmental factors affecting the genetic diversity, genetic structure, and the potential distribution of Rhododendron aureum Georgi under changing climate

Understanding genetic variation and structure, adaptive genetic variation, and its relationship with environmental factors is of great significance to understand how plants adapt to climate change and design effective conservation and management strategies. The objective of this study was to (I) investigate the genetic diversity and structure by AFLP markers in 36 populations of R. aureum from northeast China, (Ⅱ) reveal the relative contribution of geographical and environmental impacts on the distribution and genetic differentiation of R. aureum, (Ⅲ) identify outlier loci under selection and evaluate the association between outlier loci and environmental factors, and (Ⅳ) exactly calculate the development trend of population of R. aureum, as it is confronted with severe climate change and to provide information for designing effective conservation and management strategies. We found high genetic variation (I = 0.584) and differentiation among populations (ΦST  = 0.703) and moderate levels of genetic diversity within populations of R. aureum. A significant relationship between genetic distance and environmental distance was identified, which suggested that the differentiation of different populations was caused by environmental factors. Using BayeScan and Dfdist, 42 outlier loci are identified and most of the outlier loci are associated with climate or relief factors, suggesting that these loci are linked to genes that are involved in the adaptability of R. aureum to the environment. Species distribution models (SDMs) showed that climate warming will cause a significant reduction in suitable areas for R. aureum, especially under the RCP 85 scenario. Our results help to understand the potential response of R. aureum to climatic changes and provide new perspectives for R. aureum resource management and conservation strategies.

High gene space divergence contrasts with frozen vegetative architecture in the moss family Funariaceae

A new paradigm has slowly emerged regarding the diversification of bryophytes, with inferences from molecular data highlighting a dynamic evolution of their genome. However, comparative studies of expressed genes among closely related taxa is so far missing. Here we contrast the dimensions of the vegetative transcriptome of Funaria hygrometrica and Physcomitrium pyriforme against the genome of their relative, Physcomitrium (Physcomitrella) patens. These three species of Funariaceae share highly conserved vegetative bodies, and are partially sympatric, growing on mineral soil in mostly temperate regions. We analyzed the vegetative gametophytic transcriptome of F. hygrometrica and P. pyriforme and mapped short reads, transcripts, and proteins to the genome and gene space of P. patens. Only about half of the transcripts of F. hygrometrica map to their ortholog in P. patens, whereas at least 90% of those of P. pyriforme align to loci in P. patens. Such divergence is unexpected given the high morphological similarity of the gametophyte but reflects the estimated times of divergence of F. hygrometrica and P. pyriforme from P. patens, namely 55 and 20 mya, respectively. The newly sampled transcriptomes bear signatures of at least one, rather ancient, whole genome duplication (WGD), which may be shared with one reported for P. patens. The transcriptomes of F. hygrometrica and P. pyriforme reveal significant contractions or expansions of different gene families. While transcriptomes offer only an incomplete estimate of the gene space, the high number of transcripts obtained suggest a significant divergence in gene sequences, and gene number among the three species, indicative of a rather strong, dynamic genome evolution, shaped in part by whole, partial or localized genome duplication. The gene ontology of their specific and rapidly-evolving protein families, suggests that the evolution of the Funariaceae may have been driven by the diversification of metabolic genes that may optimize the adaptations to environmental conditions, a hypothesis well in line with ecological patterns in the genetic diversity and structure in seed plants.

Evolutionary origin of the latitudinal diversity gradient in liverworts

A latitudinal diversity gradient towards the tropics appears as one most recurrent patterns in ecology, but the mechanisms underlying this pattern remain an area of controversy. In angiosperms, the tropical conservatism hypothesis proposes that most groups originated in the tropics and are adapted to a tropical climatic regime, and that relatively few species have evolved physiological adaptations to cold, dry or unpredictable climates. This mechanism is, however, unlikely to apply across land plants, and in particular, to liverworts, a group of about 7500 species, whose ability to withstand cold much better than their tracheophyte counterparts is at odds with the tropical conservatism hypothesis. Molecular dating, diversification rate analyses and ancestral area reconstructions were employed to explore the evolutionary mechanisms that account for the latitudinal diversity gradient in liverworts. As opposed to angiosperms, tropical liverwort genera are not older than their extra-tropical counterparts (median stem age of tropical and extra-tropical liverwort genera of 24.35 ± 39.65 Ma and 39.57 ± 49.07 Ma, respectively), weakening the 'time for speciation hypothesis'. Models of ancestral area reconstructions with equal migration rates between tropical and extra-tropical regions outperformed models with asymmetrical migration rates in either direction. The symmetry and intensity of migrations between tropical and extra-tropical regions suggested by the lack of resolution in ancestral area reconstructions towards the deepest nodes are at odds with the tropical niche conservatism hypothesis. In turn, tropical genera exhibited significantly higher net diversification rates than extra-tropical ones, suggesting that the observed latitudinal diversity gradient results from either higher extinction rates in extra-tropical lineages or higher speciation rates in the tropics. We discuss a series of experiments to help deciphering the underlying evolutionary mechanisms.

Evolutionary dynamism in bryophytes: Phylogenomic inferences confirm rapid radiation in the moss family Funariaceae

Rapid diversifications of plants are primarily documented and studied in angiosperms, which are perceived as evolutionarily dynamic. Recent studies have, however, revealed that bryophytes have also undergone periods of rapid radiation. The speciose family Funariaceae, including the model taxon Physcomitrella patens, is one such lineage. Here, we infer relationships among major lineages within the Entosthodon-Physcomitrium complex from virtually complete organellar exomes (i.e., 123 genes) obtained through high throughput sequencing of genomic libraries enriched in these loci via targeted locus capture. Based on these extensive exonic data we (1) reconstructed a robust backbone topology of the Funariaceae, (2) confirmed the monophyly of Funaria and the polyphyly of Entosthodon, Physcomitrella, and Physcomitrium, and (3) argue for the occurrence of a rapid radiation within the Entosthodon-Physcomitrium complex that began 28 mya and gave rise more than half of the species diversity of the family. This diversification may have been triggered by a whole genome duplication and coincides with global Eocene cooling that continued through the Oligocene and Miocene. The Funariaceae join a growing list of bryophyte lineages whose history is marked by at least one burst of diversification, and our study thereby strengthens the view that bryophytes are evolutionarily dynamic lineages and that patterns and processes characterizing the evolution of angiosperms may be universal among land plants.

Genetic diversity of three European Veratrum species revealed by Amplified Fragment Length Polymorphism

Chemical and genetic characterization of Veratrum species deposited in European collections is important for genepool preservation and identification of populations with desired metabolic properties. Veratrum album, V. lobelianum and V. nigrum are native to Europe, and in Poland are ranked as rare or threatened. Genetic variation of European Veratrum species was characterized by Amplified Fragment Length Polymorphism (AFLP) markers. The accumulation of jervine as a representative of steroidal alkaloids was measured in seeds. Distribution of 380 markers generated from eight primer combinations was useful for studying genetic relationships among and within species in the Veratrum genus and the most divergent populations were identified. Genetic variation between 12 populations of Veratrum species supports the classification of V. lobelianum as a subspecies of V. album. However, the results need further validation on extended material. A higher genetic diversity (22.3%) was observed between populations of V. nigrum as compared to V. album (14.5%). Contents of jervine allowed for discrimination of the studied Veratrum species and can be used as a potential chemotaxonomic marker. The highest jervine levels were found in V. album. V. nigrum seeds had only trace amounts and no jervine was detected in seeds of V. lobelianum.

The moss Funaria hygrometrica has cuticular wax similar to vascular plants, with distinct composition on leafy gametophyte, calyptra and sporophyte capsule surfaces

BACKGROUND AND AIMS

Aerial surfaces of land plants are covered with a waxy cuticle to protect against water loss. The amount and composition of cuticular waxes on moss surfaces had rarely been investigated. Accordingly, the degree of similarity between moss and vascular plant waxes, and between maternal and offspring moss structure waxes is unknown. To resolve these issues, this study aimed at providing a comprehensive analysis of the waxes on the leafy gametophyte, gametophyte calyptra and sporophyte capsule of the moss Funaria hygrometrica

METHODS

Waxes were extracted from the surfaces of leafy gametophytes, gametophyte calyptrae and sporophyte capsules, separated by gas chromatography, identified qualitatively with mass spectrometry, and quantified with flame ionization detection. Diagnostic mass spectral peaks were used to determine the isomer composition of wax esters.

KEY RESULTS

The surfaces of the leafy gametophyte, calyptra and sporophyte capsule of F. hygrometrica were covered with 0·94, 2·0 and 0·44 μg cm(-2) wax, respectively. While each wax mixture was composed of mainly fatty acid alkyl esters, the waxes from maternal and offspring structures had unique compositional markers. β-Hydroxy fatty acid alkyl esters were limited to the leafy gametophyte and calyptra, while alkanes, aldehydes and diol esters were restricted to the sporophyte capsule. Ubiquitous fatty acids, alcohols, fatty acid alkyl esters, aldehydes and alkanes were all found on at least one surface.

CONCLUSIONS

This is the first study to determine wax coverage (μg cm(-2)) on a moss surface, enabling direct comparisons with vascular plants, which were shown to have an equal amount or more wax than F. hygrometrica Wax ester biosynthesis is of particular importance in this species, and the ester-forming enzyme(s) in different parts of the moss may have different substrate preferences. Furthermore, the alkane-forming wax biosynthesis pathway, found widely in vascular plants, is active in the sporophyte capsule, but not in the leafy gametophyte or calyptra. Overall, wax composition and coverage on F. hygrometrica were similar to those reported for some vascular plant species, suggesting that the underlying biosynthetic processes in plants of both lineages were inherited from a common ancestor.

Genetic structure of Mugil cephalus L. populations from the northern coast of Egypt

AIM

The gray mullet, Mugil cephalus, has been farmed in semi-intensive ponds with tilapia and carps in Egypt for years. The current study used the fluorescent amplified fragment length polymorphism (F-AFLP) technique to search for genetic differences between the populations of M. cephalus in the northern region of Egypt and to detect the gene flow between sampled locations and the homogeneity within M. cephalus genetic pool in Egypt.

MATERIALS AND METHODS

To fulfill the study objectives 60 (15/location) samples were collected from four northern coast governorates of Egypt (Alexandria "sea," Kafr El-Sheikh "farm," Damietta "farm" and Port Said "sea"). Three replicates of bulked DNA (5 samples/replicate) for each location were successfully amplified using the standard AFLP protocol using fluorescent primers. DNA polymorphism, genetic diversity, and population structure were assessed while positive outlier loci were successfully detected among the sampled locations. Based on the geographical distribution of sampling sites, the gene flow, the genetic differentiation, and correlations to sampling locations were estimated.

RESULTS

A total of 1890 polymorphic bands were scored for all locations, where 765, 1054, 673, and 751 polymorphic bands were scored between samples from Alexandria, Kafr El-Sheikh, Damietta and Port Said, respectively. The effective number of alleles (ne) for all bulked samples combined together was 1.42. The expected heterozygosity under Hardy-Weinberg assumption (He) for all bulked samples combined together was 0.28. Bulked samples from Damietta yielded the lowest ne (1.35) and the lowest He (0.23) when inbreeding coefficient (FIS) = 1. Bulked samples from Kafr El-Sheikh scored the highest ne (1.55) and the highest He (0.37). Bulked samples from Alexandria scored 1.40 for ne and 0.26 for He, while bulked samples from Port Said scored 1.39 for ne and 0.26 for He. The observed bulked samples formed three sub-population groups, where none is limited to a certain sampling location. A high differentiation among locations was detected, however, is not fully isolating the locations. Gene flow was 0.58. Positive outliers loci (117) were detected among the four sampled locations while weak significant correlation (r=0.15, p=0.03) was found for the distance between them.

CONCLUSION

Even though this species is cultivated in Egypt, the wild population is still present and by the current study a flow of its genes is still exchanged through the northern coast of Egypt. Which contribute to the cultivated populations leading to heterogeneity in its genetic pool and consequently affects the production consistency of M. cephalus in Egypt.

Infraspecific variation within and across complete organellar genomes and nuclear ribosomal repeats in a moss

Bryophytes (mosses, liverworts, and hornworts) are diverse and ecologically and evolutionarily significant yet genome scale data sets and analyses remain extremely sparse relative to other groups of plants, and are completely lacking at the infraspecific level. By sequencing the complete organellar genomes and nuclear ribosomal repeat from seven patches of a South American sub-Antarctic neo-endemic non-model moss, we present the first characterization of infraspecific polymorphism within and across the three genomic compartments for a bryophyte. Diversity within patches is accounted for by both intraindividual and interindividual variation for the nuclear ribosomal repeat and plastid genome, respectively. This represents the most extensive infraspecific genomic dataset generated for an early land plant lineage thus far and provides insight into relative rates of substitution between organellar genomes, including high rates of nonsynonymous to synonymous substitutions.