The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest.

BACKGROUND: Although native to North America, the invasion of the aphid-like grape phylloxera Daktulosphaira vitifoliae across the globe altered the course of grape cultivation. For the past 150 years, viticulture relied on grafting-resistant North American Vitis species as rootstocks, thereby limiting genetic stocks tolerant to other stressors such as pathogens and climate change. Limited understanding of the insect genetics resulted in successive outbreaks across the globe when rootstocks failed. Here we report the 294-Mb genome of D. vitifoliae as a basic tool to understand host plant manipulation, nutritional endosymbiosis, and enhance global viticulture. RESULTS: Using a combination of genome, RNA, and population resequencing, we found grape phylloxera showed high duplication rates since its common ancestor with aphids, but similarity in most metabolic genes, despite lacking obligate nutritional symbioses and feeding from parenchyma. Similarly, no enrichment occurred in development genes in relation to viviparity. However, phylloxera evolved > 2700 unique genes that resemble putative effectors and are active during feeding. Population sequencing revealed the global invasion began from the upper Mississippi River in North America, spread to Europe and from there to the rest of the world. CONCLUSIONS: The grape phylloxera genome reveals genetic architecture relative to the evolution of nutritional endosymbiosis, viviparity, and herbivory. The extraordinary expansion in effector genes also suggests novel adaptations to plant feeding and how insects induce complex plant phenotypes, for instance galls. Finally, our understanding of the origin of this invasive species and its genome provide genetics resources to alleviate rootstock bottlenecks restricting the advancement of viticulture.

Correction to: The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest.

An amendment to this paper has been published and can be accessed via the original article.

Mitochondrial DNA genome evidence for the existence of a third divergent lineage in the western Atlantic Ocean for the bull shark (Carcharhinus leucas).

We report for the first time a highly divergent lineage in the Caribbean Sea for the bull shark (Carcharhinus leucas) based on the analysis of 51 mitochondrial DNA genomes of individuals collected in the western North Atlantic. When comparing the mtDNA control region obtained from the mitogenomes to sequences reported previously for Brazil, the Caribbean lineage remained highly divergent. These results support the existence of a discrete population in Central America due to a phylogeographic break separating the Caribbean Sea from the western North Atlantic, Gulf of Mexico and South America.

Computational prediction of the phenotypic effects of genetic variants: basic concepts and some application examples in Drosophila nervous system genes.

Predicting the phenotypic impact of mutations is a central challenge in population and functional genetics. The analysis of DNA and amino acid sequence variation in an evolutionary context is a robust approach to infer the fitness effects of genetic variants. In this review, we discuss the most popular methods based on this approach, covering both theoretical and practical aspects, and introduce compelling software for predicting the functional effects of mutations, and to highlight functionally relevant nucleotide or amino acid candidate positions. Furthermore, we provide some examples of their application to Drosophila genes affecting significant aspects of the development, physiology and function of the nervous system.

Mesenchymal stem cells induce an immunosuppressive microenvironment in pituitary tumors.

BACKGROUND: The tumor microenvironment (TME) includes diverse cellular components such as mesenchymal stem cells (MSC) and immune cells among others. MSC have been isolated from different tumors and they favor tumor cell growth, however, their role in pituitary tumors (PT) remains unknown. Herein we report the presence of MSCs in 2 ACTH-secreting PT causing Cushing disease (MCU), 2 nonfunctioning adenomas of gonadotrope differentiation (MNF) and 2 non tumoral pituitary glands (MS). METHODS: We have analyzed their transcriptomic profiles by RNAseq and compared MSC in terms of their immunosuppressive effects against lymphoid T cell and macrophage populations by means of co-cultures and flow cytometry. RESULTS: Our transcriptomic analysis revealed molecular differences between MSC derived from non-tumoral pituitaries and MSC derived from PT. Two distinct subpopulations of MSC, one displaying immunosuppressive properties and the other with increased pro-proliferative capabilities, regardless of their origin. MSC derived from ACTH- and nonfunctioning PT, but not those derived from non-tumoral glands significantly inhibited the proliferation of activated T cells, favored the generation of Tregs and promote M2 macrophage polarization. Such immunosuppressive effects were correlated with an upregulation of programmed death ligand 1 and intracellular expression of macrophage colony stimulating factor (M-CSF) and IL-10. Importantly, MSC derived from ACTH-PT showed a higher immunosuppressive potential than MSC isolated from nonfunctioning tumors. CONCLUSION: This study demonstrates the presence of at least two MSC subpopulations in the pituitary gland and suggests that immunosuppressive effects of MSC may have important implications in PT growth.

Evaluating the monophyly of Mammillaria series Supertextae (Cactaceae).

Mammillaria (Cactaceae) taxonomy has been historically problematic due to the morphological variability and sympatry of the species. This has led to several proposals for infrageneric classification, including subgeneric, section and series categories. Mammillaria ser. Supertextae is one of 15 series and is made up of a variable set of species that are mainly distributed in southern Mexico and Central America. However, the phylogenetic relationships within M. ser. Supertextae and its relationship to other Mammillaria taxa are far from fully understood. Here we attempt to elucidate these relationships using complete terminal sampling and newly obtained chloroplast marker sequences and comparing them to Mammillaria species sequences from GenBank. Our phylogenetic analyses showed that M. ser. Supertextae comprises a well-supported monophyletic group that diverged approximately 2.1 Mya and has M. ser. Polyacanthae as its sister group; however, relationships within M. ser. Supertextae remain unresolved. The topology obtained within M. ser. Supertextae must also be interpreted under the distribution shared by these taxa, but it is difficult to differentiate ancestral polymorphisms from possible introgression, given the short time elapsed and the markers used. Our results show that the infrageneric units of M. haageana and M. albilanata can be considered independent evolutionary units. We also suggest that the relationship between M. haageana and M. albilanata is convoluted because their distribution overlaps (mainly towards southern Mexico), with genetic differences that possibly indicate they represent more than two taxonomic entities. One possible explanation is that there could still be gene flow between these taxa, and we might be witnessing an ongoing speciation process.

The chloroplast genome of the pincushion cactus Mammilllaria haageana subsp. san-a ngelensis, a Mexican endangered species.

The genus Mammillaria occupies diverse habitats and exhibits diverse growth patterns and a large range of morphologies. Most of the species of this genus are used as ornamental plants and are subject to mass habitat loss. Due to these factors, they are being submitted to selective pressure that might affect conservational efforts and management plans. We obtained the 133 gene chloroplast genome as part of the project of sequencing the complete genome of pincushion cactus, including 88 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The phylogenetic tree indicates the pincushion cactus is a sister species of M. supertexta and M. huitzilopochtli.

The draft genome sequence of the spider Dysdera silvatica (Araneae, Dysderidae): A valuable resource for functional and evolutionary genomic studies in chelicerates.

BACKGROUND: We present the draft genome sequence of Dysdera silvatica, a nocturnal ground-dwelling spider from a genus that has undergone a remarkable adaptive radiation in the Canary Islands. RESULTS: The draft assembly was obtained using short (Illumina) and long (PaciBio and Nanopore) sequencing reads. Our de novo assembly (1.36 Gb), which represents 80% of the genome size estimated by flow cytometry (1.7 Gb), is constituted by a high fraction of interspersed repetitive elements (53.8%). The assembly completeness, using BUSCO and core eukaryotic genes, ranges from 90% to 96%. Functional annotations based on both ab initio and evidence-based information (including D. silvatica RNA sequencing) yielded a total of 48,619 protein-coding sequences, of which 36,398 (74.9%) have the molecular hallmark of known protein domains, or sequence similarity with Swiss-Prot sequences. The D. silvatica assembly is the first representative of the superfamily Dysderoidea, and just the second available genome of Synspermiata, one of the major evolutionary lineages of the "true spiders" (Araneomorphae). CONCLUSIONS: Dysderoids, which are known for their numerous instances of adaptation to underground environments, include some of the few examples of trophic specialization within spiders and are excellent models for the study of cryptic female choice. This resource will be therefore useful as a starting point to study fundamental evolutionary and functional questions, including the molecular bases of the adaptation to extreme environments and ecological shifts, as well of the origin and evolution of relevant spider traits, such as the venom and silk.

The complete mitochondrial DNA of the silky shark (Carcharhinus falciformis).

The silky shark mitogenome (GeneBank accession number KF801102) has a total length of 17,774 bp, the base composition of the genomes was as follows: A (31.36%), T (30.18%), C (25.27%) and G (13.17%), which demonstrated an A + T-rich feature (61.64%), similar to other elasmobranch mitogenomes. The mitochondrial genome contained 13 protein-coding genes and 23 tRNA genes. The tRNA genes ranged from 70 to 72 bp. The gene order was the same as in other vertebrates and teleosts.

The complete mitochondrial DNA of white shark (Carcharodon carcharias) from Isla Guadalupe, Mexico.

The Isla Guadalupe white shark mitochondrial structure is similar to the one previously reported for a white shark individual from Taiwan with a total length of 16,745 and 16,742 bp respectively; the base composition of the genomes was as follow A (30.60%), T (28.67%), C (26.86%) and G (13.87%), contains 13 protein-coding genes and 24 tRNA genes and the non-coding control region. The tRNA genes range from 70-72 bp. Gene order is the same as in other vertebrates and teleosts.

A potential third Manta Ray species near the Yucatán Peninsula? Evidence for a recently diverged and novel genetic Manta group from the Gulf of Mexico.

We present genetic and morphometric support for a third, distinct, and recently diverged group of Manta ray that appears resident to the Yucatán coastal waters of the Gulf of Mexico. Individuals of the genus Manta from Isla Holbox are markedly different from the other described manta rays in their morphology, habitat preference, and genetic makeup. Herein referred to as the Yucatán Manta Ray, these individuals form two genetically distinct groups: (1) a group of mtDNA haplotypes divergent (0.78%) from the currently recognized Manta birostris and M. alfredi species, and (2) a group possessing mtDNA haplotypes of M. birostris and highly similar haplotypes. The latter suggests the potential for either introgressive hybridization between Yucatán Manta Rays and M. birostris, or the retention of ancestral M. birostris signatures among Yucatán Manta Rays. Divergence of the genetically distinct Yucatán Manta Ray from M. birostris appears quite recent (<100,000 YBP) following fit to an Isolation-with-Migration model, with additional support for asymmetrical gene flow from M. birostris into the Yucatán Manta Ray. Formal naming of the Yucatán Manta Ray cannot yet be assigned until an in-depth taxonomic study and further confirmation of the genetic identity of existing type specimens has been performed.

The complete mitochondrial DNA of the bull shark (Carcharhinus leucas).

The bull shark mitochondrial structure is similar to that of other elasmobranchs; it has a total length of 16,100 bp, the base composition of the genomes was as follows: A (31.35%), T (31.35%), C (24.38%) and G (12.90%). It contains 13 protein-coding genes and 23 tRNA genes. The tRNA genes range from 70-72 bp. Gene order is the same as in other vertebrates and teleosts.

The complete mitochondrial genome of the Giant Manta ray, Manta birostris.

The complete mitochondrial genome of the giant manta ray (Manta birostris), consists of 18,075 bp with rich A + T and low G content. Gene organization and length is similar to other species of ray. It comprises of 13 protein-coding genes, 2 rRNAs genes, 23 tRNAs genes and 1 non-coding sequence, and the control region. We identified an AT tandem repeat region, similar to that reported in Mobula japanica.

The complete mitogenome of the common dolphinfish (Coryphaena hippurus).

The complete mitochondrial genome of the dolphinfish (GeneBank accession number KF719178) structure is similar to that of other teleosts, has a total length of 15,733 bp, the base composition was as follows: A (28.78%), T (29.25%), C (25.45%) and G (16.50%), which demonstrated an A+T (58.04%) rich feature. It contains 13 protein-coding genes and 23 tRNA genes that range from 54 to 72 bp. We compared our mitogenome with the one reported by Miya and collaborators in 2013 and found that the average number of nucleotide differences was k: 47.000 resulting in a nucleotide diversity Pi(t) of 0.00299.