Genetic diversity and structure in natural populations of Cajui from Brazilian Cerrado

Cajui (Anacardium spp.) is a native fruit tree (small cashew) of the Brazilian Cerrado and possesses the potential for commercialization. However, cajui exploitation occurs exclusively through extractivism in the absence of conservation strategies. The lack of conservation strategies may lead to a decrease in genetic diversity of Anacardium. In this work, the genetic diversity and population structure of three natural populations in Sete Cidades National Park (PNSC; PI, Brazil) were assessed using ISSR analysis of 56 cajui accessions and two A. occidentale accessions (outgroup) from Pacajus (CE, Brazil). A total of 112 markers were obtained, 93 (83.04%) of which were polymorphic. The diversity indices of these populations indicated moderate levels of genetic diversity. According to AMOVA, 96.17% of the genetic variability lay within populations, with low genetic differentiation among populations (ΦST = 0.03828). Furthermore, STRUCTURE analysis indicated the existence of four connected genetic groups. The findings show that the individuals from the three collection sites did not represent different subpopulations, likely due to the high gene flow (Nm = 6.7) favored by the floral biology of Anacardium, pollinators and small-animal seed dispersers. This research identifies genetically divergent individuals (C-03, C-05, C-22, C-26, C-34 and C-39), which should be considered priority individuals for conservation and can inform conservation programs for Anacardium spp.

Season-long infection of diverse hosts by the entomopathogenic fungus Batkoa major

Populations of the entomopathogenic fungus Batkoa major were analyzed using sequences of four genomic regions and evaluated in relation to their genetic diversity, insect hosts and collection site. This entomophthoralean pathogen killed numerous insect species from 23 families and five orders in two remote locations during 2019. The host list of this biotrophic pathogen contains flies, true bugs, butterflies and moths, beetles, and barkflies. Among the infected bugs (Order Hemiptera), the spotted lanternfly ( Lycorma delicatula ) is a new invasive planthopper pest of various woody plants that was introduced to the USA from Eastern Asia. A high degree of clonality occurred in the studied populations and high gene flow was revealed using four molecular loci for the analysis of population structure. We did not detect any segregation in the population regarding host affiliation (by family or order), or collection site. This is the first description of population structure of a biotrophic fungus-generalist in the entomopathogenic Order Entomophthorales. This analysis aimed to better understand the potential populations of entomopathogen-generalists infecting emerging invasive hosts in new ecosystems.

Highly Effective Crosslinker for Redox-Sensitive Gene Carriers

Polyethyleneimine (PEI) has been extensively used as a common gene carrier due to its high gene transfection efficiency. PEI1.8k shows significantly lower cytotoxicity than its high molecular weight counterparts. However, it also has the problem of low gene transfection efficiency. To address the dilemma, a highly effective crosslinker (DTME) was synthesized to react with PEI1.8k to obtain CS-PEI1.8k. The reaction showed several advantages, such as a fast process in room temperature within nine hours with the product which can directly complex with DNA after removing the solvent. The ability of CS-PEI1.8k to agglomerate with DNA was proven by particle size, zeta potential, and gel retardation assays. The cytotoxic in vitro transfection ability and cell internalization capacity of CS-PEI1.8k were tested to verify the transfection capacity of CS-PEI1.8k. Moreover, we also studied the mechanism of the relatively high level of gene transfection by this binary complex compared with PEI25k.

Population genetics of Anopheles arabiensis, the primary malaria vector in the Republic of Sudan

Background Anopheles arabiensis is a member of Anopheles gambiae complex and the main malaria vector in Sudan. There is insufficient population genetics data available on An. arabiensis for an understanding of vector population structure and genetics, which are important for the malaria vector control programmes in this country. The objective of this investigation is to study the population structure, gene flow and isolation by distance among An. arabiensis populations for developing control strategies. Methods Mosquitoes were collected from six sites located in three different states in Sudan, Khartoum, Kassala and Sennar, using pyrethrum spray catch of indoor resting mosquitoes. Anopheline mosquitoes were identified morphologically and based on species specific nucleotide sequences in the ribosomal DNA intergenic spacers (IGS). Seven published An. gambiae microsatellite loci primers were used to amplify the DNA of An. arabiensis samples. Results PCR confirmed that An. arabiensis was the main malaria vector found in the six localities. Of the seven microsatellite loci utilized, six were found to be highly polymorphic across populations, with high allelic richness and heterozygosity with the remaining one being monomorphic. Deviation from Hardy–Weinberg expectations were found in 21 out of 42 tests in the six populations due to heterozygote deficiency. Bayesian clustering analysis revealed two gene pools, grouping samples into two population clusters; one includes four and the other includes two populations. The clusters were not grouped according to the three states but were instead an admixture. The genetic distances between pairs of populations ranged from 0.06 to 0.24. Significant FST was observed between all pairwise analyses of An. arabiensis populations. The Kassala state population indicated high genetic differentiation (FST ranged from 0.17 to 0.24) from other populations, including one which is also located in the same state. High gene flow (Nm = 1.6–8.2) was detected among populations within respective clusters but limited between clusters particularly with respect to Kassala state. There was evidence of a bottleneck event in one of the populations (Al Haj Yousif site). No isolation by distance pattern was detected among populations. Conclusions This study revealed low levels of population differentiation with high gene flow among the An. arabiensis populations investigated in Sudan, with the exception of Kassala state.

The haplotype-resolved chromosome pairs and transcriptome of a heterozygous diploid African cassava cultivar

Background: Cassava (Manihot esculenta) is an important clonally propagated food crop in tropical and sub-tropical regions worldwide. Genetic gain by molecular breeding is limited because cassava has a highly heterozygous, repetitive and difficult to assemble genome. Findings: Here we demonstrate that Pacific Biosciences high-fidelity (HiFi) sequencing reads, in combination with the assembler hifiasm, produced genome assemblies at near complete haplotype resolution with higher continuity and accuracy compared to conventional long sequencing reads. We present two chromosome scale haploid genomes phased with Hi-C technology for the diploid African cassava variety TME204. Genome comparisons revealed extensive chromosome re-arrangements and abundant intra-genomic and inter-genomic divergent sequences despite high gene synteny, with most large structural variations being LTR-retrotransposon related. Allele-specific expression analysis of different tissues based on the haplotype-resolved transcriptome identified both stable and inconsistent alleles with imbalanced expression patterns, while most alleles expressed coordinately. Among tissue-specific differentially expressed transcripts, coordinately and biasedly regulated transcripts were functionally enriched for different biological processes. We use the reference-quality assemblies to build a cassava pan-genome and demonstrate its importance in representing the genetic diversity of cassava for downstream reference-guided omics analysis and breeding. Conclusions: The haplotype-resolved genome allows the first systematic view of the heterozygous diploid genome organization in cassava. The completely phased and annotated chromosome pairs will be a valuable resource for cassava breeding and research. Our study may also provide insights into developing cost-effective and efficient strategies for resolving complex genomes with high resolution, accuracy and continuity.

Chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architecture and interaction alterations

Background Three-dimensional (3D) chromatin organization provides a critical foundation to investigate gene expression regulation and cellular homeostasis. Results Here, we present the first 3D genome architecture maps in wild type and mutant allotetraploid peanut lines, which illustrate A/B compartments, topologically associated domains (TADs), and widespread chromatin interactions. Most peanut chromosomal arms (52.3%) have active regions (A compartments) with relatively high gene density and high transcriptional levels. About 2.0% of chromosomal regions switch from inactive to active (B-to-A) in the mutant line, harboring 58 differentially expressed genes enriched in flavonoid biosynthesis and circadian rhythm functions. The mutant peanut line shows a higher number of genome-wide cis-interactions than its wild-type. The present study reveals a new TAD in the mutant line that generates different chromatin loops and harbors a specific upstream AP2EREBP-binding motif which might upregulate the expression of the GA2ox gene and decrease active gibberellin (GA) content, presumably making the mutant plant dwarf. Conclusions Our findings will shed new light on the relationship between 3D chromatin architecture and transcriptional regulation in plants.

MCT1 is a Predictive Marker for Lenalidomide Maintenance Therapy in Multiple Myeloma

Biomarkers that predict response to lenalidomide maintenance therapy in patients with multiple myeloma (MM) have remained elusive. We have shown that IMiDs exert anti-MM activity via destabilization of MCT1 and CD147. Here, samples of 654 patients receiving lenalidomide (n=455), thalidomide (n=98) or bortezomib (n=101) maintenance were assessed using gene expression profiling and RNA-sequencing, followed by correlation of MCT1 and CD147 expression with progression-free (PFS) and overall survival (OS) data. Patients with high gene expression levels of MCT1 showed significantly reduced PFS (31.9 vs. 48.2 months in MCT1high vs. MCT1low, P=.03) and OS (75.9 months vs. not reached (NR) months in MCT1high vs. MCT1low; P=.001) in case of lenalidomide maintenance, whereas MCT1 expression had no significant impact on PFS or OS in patients with bortezomib maintenance. We validated the predictive role of MCT1 for IMiD-based maintenance in an independent cohort of patients receiving thalidomide (OS 83.6 months vs. NR in MCT1high vs. MCT1low; P=.03). Functional validation showed that MCT1 overexpression in human MM cell lines significantly reduced efficacy of lenalidomide, while no change was observed upon bortezomib treatment, both in vitro and in an MM xenograft model. Together, we establish MCT1-expression as a predictive marker for response to lenalidomide-based maintenance treatment.

Phylogeography of the Common New Zealand Wrasse Species, Notolabrus Celidotus, and the Phylogenetics of the Pseudolabrine Tribe

<p>The New Zealand coastline and marine environment is a diverse place and presents plenty of dispersal obstacles to many of the organisms that live there. This thesis investigates the phylogeography of one of the most common fish species around the coast of New Zealand, the endemic wrasse Notolabrus celidotus, using the mitochondrial DNA control region and compares genetic variability to another common New Zealand wrasse, Notolabrus fucicola in a local setting. These species are part of a tribe of temperate fish, the pseudolabrines, which can be found throughout the South and North-West Pacific. The phylogeny of this tribe was also analysed using the mitochondrial 16S gene to investigate the relationships among the New Zealand pseudolabrines and to those species elsewhere. The results suggest that pseudolabrines from mainland New Zealand are closely related and are likely to have originated from southern Australia while species from the Kermadec Islands and other northern islands are more closely related to the species of eastern Australia. The Notolabrus and Pseudolabrus genera should be reviewed to remedy paraphyly of Pseudolabrus. Furthermore, N. celidotus shows no population structuring throughout its range and appears to be rapidly expanding. Genetic variability was similar for both N. celidotus and N. fucicola. The results suggest that the pseudolabrine tribe has made multiple migrations to New Zealand where Notolabrus celidotus was able to spread around the three main islands and, likely facilitated by a long planktonic larval duration, was able to maintain high gene flow among populations.</p>

Phylogeography of the Common New Zealand Wrasse Species, Notolabrus Celidotus, and the Phylogenetics of the Pseudolabrine Tribe

<p>The New Zealand coastline and marine environment is a diverse place and presents plenty of dispersal obstacles to many of the organisms that live there. This thesis investigates the phylogeography of one of the most common fish species around the coast of New Zealand, the endemic wrasse Notolabrus celidotus, using the mitochondrial DNA control region and compares genetic variability to another common New Zealand wrasse, Notolabrus fucicola in a local setting. These species are part of a tribe of temperate fish, the pseudolabrines, which can be found throughout the South and North-West Pacific. The phylogeny of this tribe was also analysed using the mitochondrial 16S gene to investigate the relationships among the New Zealand pseudolabrines and to those species elsewhere. The results suggest that pseudolabrines from mainland New Zealand are closely related and are likely to have originated from southern Australia while species from the Kermadec Islands and other northern islands are more closely related to the species of eastern Australia. The Notolabrus and Pseudolabrus genera should be reviewed to remedy paraphyly of Pseudolabrus. Furthermore, N. celidotus shows no population structuring throughout its range and appears to be rapidly expanding. Genetic variability was similar for both N. celidotus and N. fucicola. The results suggest that the pseudolabrine tribe has made multiple migrations to New Zealand where Notolabrus celidotus was able to spread around the three main islands and, likely facilitated by a long planktonic larval duration, was able to maintain high gene flow among populations.</p>

Phylogeny, Connectivity and Dispersal Patterns of the Giant Kelp Macrocystis (Phaeophyceae)

<p>Macrocystis represents the most widely distributed kelp genus, providing structure and energy for one of the most productive ecosystems on earth. Despite its ecological and economical importance, many aspects of its taxonomy, distribution and dispersal still remain unknown. Using different molecular markers I studied the taxonomy, phylogeography and dispersal patterns of Macrocystis. The analysis involves samples from different populations throughout the world. Using the DNA barcoding method I, confirmed previous suggestions that the genus must be considered as monospecific, M. pyrifera being the only species. The effects of historical and contemporary events on the haplotype distribution were determined by analyzing samples from the southeastern Pacific (SEP) using the atp8-S mitochondrial marker. The last glacial maximum as well as oceanographic anomalies (El Niño phenomena) may be important factors driving the genetic pattern along the SEP. The genetic structure in southern Chile was also analyzed in more detail, especially in the Chilean Fjords. Samples from attached and floating kelp individuals revealed that dispersal via kelp rafts is possible. Finally, a global analysis using COI sequences showed shared haplotypes along vast distances in the Northern and Southern hemispheres, recent dispersal and high gene flow can explain such genetic homogeneity. Additionally, microsatellite analysis confirmed that gene flow along the Southern Ocean is occurring over ecological time scales, where rafting of detached reproductive kelps seems to be facilitated by the Antarctic Circumpolar Current connecting populations in the Southern Hemisphere. This study has provided valuable genetic evidence to understand factors shaping the genetic structure of this important ecologically and economically species. It also contributes important knowledge for conservation and management strategies, especially in places where M. pyrifera has been harvested. In summary, the results of this study confirm previous suggestions of high gene flow among M. pyrifera populations at different scales. It also provides evidence suggesting that kelp rafts act as an important dispersal mechanism in this species, thus giving important information to understand the factors shaping the evolution of the largest seaweed on earth.</p>