Mitogenomic analyses provide further evidence for multiple miniaturization events during the evolution of Seychelles caecilian amphibians

Whole mitochondrial genomes have been helpful in estimating phylogenetic relationships in many organismal groups, including caecilian amphibians. Despite the increasing ease of obtaining mitochondrial genome sequences from high-throughput sequencing, several species of caecilian lack this important molecular resource. As part of a targeted-sequence capture project of nuclear ultraconserved elements for a small but substantially diverse radiation of caecilian amphibians found on the granitic Seychelles, we examined off-target sequences to determine if we captured enough mitochondrial fragments to reconstruct mitogenomes. We reconstructed (near-)complete mitogenomes for six of the eight species of Seychelles caecilians and completed 14 independent phylogenetic analyses (Bayesian inference and maximum likelihood) on different mitochondrial datasets assembled using different alignment techniques. As with other studies, we were unable to fully resolve internal phylogenetic relationships of the group. However, we found strong support in most analyses that a recently described miniaturized species, Hypogeophis pti, and another similarly-sized miniaturized species, H. brevis are not sister taxa. Our study suggests that miniature species of caecilians likely evolved at least twice on the Seychelles and highlights the need to revise genus-level taxonomy of Seychelles caecilians while providing further evidence that off-target sequences often contain enough mitochondrial fragments to reconstruct mitogenomes.

Everolimus in Invasive Malignant Renal Epithelioid Angiomyolipoma

BackgroundTo evaluate the efficacy and safety of everolimus, a mTOR inhibitor, on invasive malignant renal epithelioid angiomyolipoma (EAML).Materials and MethodsFrom Oct 2014 to May 2019, we collected data from seven patients with a definite (clinical and pathological) diagnosis of EAML received everolimus in our hospital. Targeted sequence capture array technique with next-generation of high throughput sequencing (NGS) were performed to detect mutations of TSC1/2 genes. All patients had received surgery and everolimus. The clinical efficacy and safety of the therapy were evaluated.ResultsMutations of TSC1 and TSC2 were detected in two and three patients though targeted sequence capture array technique with NGS, respectively. Among seven patients, three had missense mutations, one had nonsense mutation, and one had the large fragment deletion mutation. Five patients accompanied with tuberous sclerosis complex (TSC) were identified. All patients were administered 10mg everolimus once daily, the treatment duration lasted for 3 to 28 months. The objective response was assessed 3 months later, five partial response, two stable disease (SD), the mean greatest tumor diameter of all patients decreased from 9.6 to 5.2cm. Six patients stayed SD and one patient died during follow up. Patients accompanying with TSC had better responses to everolimus compared with non-TSC.ConclusionThe mTOR inhibitor can be an effective treatment for patients with invasive malignant renal EAML. Patients with TSC may benefit more from the therapy.

Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples

Shotgun metagenomic sequencing (SMg) enables the simultaneous detection and characterization of viruses in human, animal and environmental samples. However, lack of sensitivity still poses a challenge and may lead to poor detection and data acquisition for detailed analysis. To improve sensitivity, we assessed a broad scope targeted sequence capture (TSC) panel (ViroCap) in both human and animal samples. Moreover, we adjusted TSC for the Oxford Nanopore MinION and compared the performance to an SMg approach. TSC on the Illumina NextSeq served as the gold standard. Overall, TSC increased the viral read count significantly in challenging human samples, with the highest genome coverage achieved using the TSC on the MinION. TSC also improved the genome coverage and sequencing depth in clinically relevant viruses in the animal samples, such as influenza A virus. However, SMg was shown to be adequate for characterizing a highly diverse animal virome. TSC on the MinION was comparable to the NextSeq and can provide a valuable alternative, offering longer reads, portability and lower initial cost. Developing new viral enrichment approaches to detect and characterize significant human and animal viruses is essential for the One Health Initiative.

Herbarium-based phylogenomics reveals that the Andes are a biogeographic barrier for Otoba (Myristicaceae), an ecologically dominant Neotropical tree genus

Abstract•Premise of the studyUniversal probesets for targeted sequence capture have facilitated phylogenomic research into diverse plant groups with limited genomic resources, including from low-quality DNA typical of herbarium specimens. Here, we leverage the Angiosperms353 loci to infer the first phylogeny of Otoba (Myristicaceae), a Neotropical tree genus that is ecologically dominant in low-to-mid elevation wet forests, exclusively from herbarium specimens.•MethodsWe use a combination of Angiosperms353 loci, obtained via targeted sequence capture, and plastid sequences to resolve the phylogeny of Otoba using concatenated and species tree methods. We subsequently use this phylogeny to infer biogeography and trait evolution using phylogenetic comparative methods.•Key resultsRecovery success of loci is correlated with age of herbarium specimens and average annual precipitation. Despite a large amount of missing data, we resolve the phylogeny of Otoba into three major subclades, each structured by geography. We show that Otoba’s crown radiation occurred on the western slopes of the Andes in the late Miocene, and from there, migrated into Central America at least twice; the genus was only able to cross to the eastern slopes of the Andes a single time. Trait evolution has been dynamic across vegetative and reproductive traits, with multiple origins of most discrete traits investigated, including ecologically important aril color.•ConclusionsOtoba is recent, rapid radiation whose evolution is tied to landscape change, including Andean uplift, in the northern Neotropics. Its dynamic morphological evolution is consistent with sorting of ancestral traits during recent speciation events. In one of the first herbariomic studies exclusively using herbarium tissue from specimens collected in the wet tropics, this study demonstrates the promise of Angiosperms353 loci in resolving shallow species-level relationships, even from low-quality DNA.

New Compound Heterozygous CYP4V2 Mutations in Bietti Crystalline Corneoretinal Dystrophy

Background: Bietti crystalline corneoretinal dystrophy (BCD) is an autosomal recessive retinal dystrophy which is caused by the mutations of CYP4V2.Here we identified new CYP4V2compound heterozygous mutations in BCD.Methods:381 pathogenic genes related to retinal diseases were screened by targeted sequence capture array techniques and confirmed by Sanger sequencing.Results:Two female siblings with BCD carry two compound heterozygous mutations in CYP4V2. One was missense mutation c.1198C>T (p.R400C) and the other was frameshift mutation c.802-8_810delinsGC (p.V268_E329del).Optical coherence tomography (OCT) showed that the ellipsoid zone was absent in the macular regions and electroretinogram (ERG) revealed poor cone and rod responses. Conclusions:Newcompound heterozygous mutations in CYP4V2 are related to the BCD.Our study expands our knowledge of heterogenic phenotypes and genotypes through genetic diagnosis of the BCD patients.

Targeted sequence capture array for phylogenetics and population genomics in the Salicaceae

Premise of the studyThe family Salicaceae has proved taxonomically challenging, especially in the genus Salix, which is speciose and features frequent hybridization and polyploidy. Past efforts to reconstruct the phylogeny with molecular barcodes have failed to resolve the species relationships of many sections of the genus.MethodsWe used the wealth of sequence data in the family to design sequence capture probes to target regions of 300-1200 base pairs of exonic regions of 972 genes.ResultsWe recovered sequence data for nearly all of the targeted genes in three species of Populus and three species of Salix. We present a species tree, discuss concordance among gene trees, as well as some population genomic summary statistics for these loci.ConclusionsOur sequence capture array has extremely high capture efficiency within the genera Populus and Salix, resulting in abundant phylogenetic information. Additionally, these loci show promise for population genomic studies.