scholarly journals Peer Review #3 of "De novo oviduct transcriptome of the moor frog Rana arvalis: a quest for maternal effect candidate genes (v0.1)"

2018 ◽  
Author(s):  
D Jeffries
Keyword(s):  
Peer Review ◽  
Candidate Genes ◽  
Maternal Effect ◽  
De Novo ◽  
Rana Arvalis ◽  
Moor Frog

scholarly journals De novo oviduct transcriptome of the moor frog Rana arvalis: a quest for maternal effect candidate genes

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5452
Author(s):  
Longfei Shu ◽  
Jie Qiu ◽  
Katja Räsänen
Keyword(s):  
Candidate Genes ◽  
Maternal Effects ◽  
De Novo ◽  
Full Range ◽  
Natural Populations ◽  
Population Variation ◽  
Adaptive Divergence ◽  
Rana Arvalis ◽  
Egg Jelly ◽  
Moor Frog

Maternal effects can substantially affect ecological and evolutionary processes in natural populations. However, as they often are environmentally induced, establishing their genetic basis is challenging. One important, but largely neglected, source of maternal effects are egg coats (i.e., the maternally derived extracellular matrix that surrounds the embryo). In the moor frog, the gelatinous egg coats (i.e., egg jelly) are produced in the mother’s oviduct and consist primarily of highly glycosylated mucin type O-glycans. These O-glycans affect jelly water balance and, subsequently, contribute to adaptive divergence in embryonic acid tolerance. To identify candidate genes for maternal effects, we conducted RNAseq transcriptomics on oviduct samples from seven R. arvalis females, representing the full range of within and among population variation in embryonic acid stress tolerance across our study populations. De novo sequencing of these oviduct transcriptomes detected 124,071 unigenes and functional annotation analyses identified a total of 57,839 unigenes, of which several identified genes likely code for variation in egg jelly coats. These belonged to two main groups: mucin type core protein genes and five different types of glycosylation genes. We further predict 26,711 gene-linked microsatellite (simple sequence repeats) and 231,274 single nucleotide polymorphisms. Our study provides the first set of genomic resources for R. arvalis, an emerging model system for the study of ecology and evolution in natural populations, and gives insight into the genetic architecture of egg coat mediated maternal effects.

scholarly journals The ‘Tommy Atkins’ mango genome reveals candidate genes for fruit quality

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ian S. E. Bally ◽  
◽  
Aureliano Bombarely ◽  
Alan H. Chambers ◽  
Yuval Cohen ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Fruit Quality ◽  
De Novo ◽  
Mapping Population ◽  
Mangifera Indica ◽  
Consensus Sequence ◽  
Fruit Size ◽  
Hybrid Population ◽  
High Molecular Weight Dna ◽  
Tropical Fruit

Abstract Background Mango, Mangifera indica L., an important tropical fruit crop, is grown for its sweet and aromatic fruits. Past improvement of this species has predominantly relied on chance seedlings derived from over 1000 cultivars in the Indian sub-continent with a large variation for fruit size, yield, biotic and abiotic stress resistance, and fruit quality among other traits. Historically, mango has been an orphan crop with very limited molecular information. Only recently have molecular and genomics-based analyses enabled the creation of linkage maps, transcriptomes, and diversity analysis of large collections. Additionally, the combined analysis of genomic and phenotypic information is poised to improve mango breeding efficiency. Results This study sequenced, de novo assembled, analyzed, and annotated the genome of the monoembryonic mango cultivar ‘Tommy Atkins’. The draft genome sequence was generated using NRGene de-novo Magic on high molecular weight DNA of ‘Tommy Atkins’, supplemented by 10X Genomics long read sequencing to improve the initial assembly. A hybrid population between ‘Tommy Atkins’ x ‘Kensington Pride’ was used to generate phased haplotype chromosomes and a highly resolved phased SNP map. The final ‘Tommy Atkins’ genome assembly was a consensus sequence that included 20 pseudomolecules representing the 20 chromosomes of mango and included ~ 86% of the ~ 439 Mb haploid mango genome. Skim sequencing identified ~ 3.3 M SNPs using the ‘Tommy Atkins’ x ‘Kensington Pride’ mapping population. Repeat masking identified 26,616 genes with a median length of 3348 bp. A whole genome duplication analysis revealed an ancestral 65 MYA polyploidization event shared with Anacardium occidentale. Two regions, one on LG4 and one on LG7 containing 28 candidate genes, were associated with the commercially important fruit size characteristic in the mapping population. Conclusions The availability of the complete ‘Tommy Atkins’ mango genome will aid global initiatives to study mango genetics.

scholarly journals An Overview of the Helminths of Moor Frog Rana arvalis Nilsson, 1842 (Amphibia: Anura) in the Volga Basin

Diversity ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 61
Author(s):  
Igor V. Chikhlyaev ◽  
Alexander B. Ruchin
Keyword(s):  
Systematic Position ◽  
Helminth Fauna ◽  
Helminth Species ◽  
Volga Basin ◽  
Rana Arvalis ◽  
Amphibian Species ◽  
Volga River ◽  
Spirometra Erinacei ◽  
First Time ◽  
Moor Frog

This is the first review of the helminth fauna of the moor frog Rana arvalis Nilsson, 1842 from the Volga river basin (Russia). The article summarizes the authors’ and literature data on the helminthic fauna of this species. The method of complete helminthological dissection was used. Thirthy-eight helminth species were recorded from three classes: Cestoda (1), Trematoda (28), and Chromadorea (9). Nine helminth species are new to the moor frog in Russia: trematodes Gorgodera varsoviensis Sinitzin, 1905, Strigea falconis Szidat, 1928, larvae, Neodiplostomum spathoides Dubois, 1937, larvae, Tylodelphys excavata (Rudolphi, 1803), larvae, Pharyngostomum cordatum (Diesing, 1850), larvae, Astiotrema monticelli Stossich, 1904, larvae and Encyclometra colubrimurorum (Rudolphi, 1819), larvae, nematodes Strongyloides spiralis Grabda-Kazubska, 1978 and Icosiella neglecta (Diesing, 1851). The cestode Spirometra erinacei (Rudolphi, 1918), larvae were observed of this amphibian species in the Volga basin for the first time. The nematodes Rhabdias bufonis, Oswaldocruzia filiformis, Cosmocerca ornata and the trematode Haplometra cylindracea form the core of the helminth fauna of the moor frog. Information on species of helminths includes systematic position, localization, areas of detection, type and scheme of life cycle, geographical distribution, and degree of specificity to host amphibians.

scholarly journals Rare variant analysis of 4241 pulmonary arterial hypertension cases from an international consortium implicates FBLN2, PDGFD, and rare de novo variants in PAH

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Na Zhu ◽  
◽  
Emilia M. Swietlik ◽  
Carrie L. Welch ◽  
Michael W. Pauciulo ◽  
...  
Keyword(s):  
Pulmonary Arterial Hypertension ◽  
Candidate Genes ◽  
Rare Variant ◽  
De Novo ◽  
Risk Genes ◽  
International Consortium ◽  
Rare Variant Analysis ◽  
New Genes ◽  
Pulmonary Arterial ◽  
Variant Analysis

Abstract Background Pulmonary arterial hypertension (PAH) is a lethal vasculopathy characterized by pathogenic remodeling of pulmonary arterioles leading to increased pulmonary pressures, right ventricular hypertrophy, and heart failure. PAH can be associated with other diseases (APAH: connective tissue diseases, congenital heart disease, and others) but often the etiology is idiopathic (IPAH). Mutations in bone morphogenetic protein receptor 2 (BMPR2) are the cause of most heritable cases but the vast majority of other cases are genetically undefined. Methods To identify new risk genes, we utilized an international consortium of 4241 PAH cases with exome or genome sequencing data from the National Biological Sample and Data Repository for PAH, Columbia University Irving Medical Center, and the UK NIHR BioResource – Rare Diseases Study. The strength of this combined cohort is a doubling of the number of IPAH cases compared to either national cohort alone. We identified protein-coding variants and performed rare variant association analyses in unrelated participants of European ancestry, including 1647 IPAH cases and 18,819 controls. We also analyzed de novo variants in 124 pediatric trios enriched for IPAH and APAH-CHD. Results Seven genes with rare deleterious variants were associated with IPAH with false discovery rate smaller than 0.1: three known genes (BMPR2, GDF2, and TBX4), two recently identified candidate genes (SOX17, KDR), and two new candidate genes (fibulin 2, FBLN2; platelet-derived growth factor D, PDGFD). The new genes were identified based solely on rare deleterious missense variants, a variant type that could not be adequately assessed in either cohort alone. The candidate genes exhibit expression patterns in lung and heart similar to that of known PAH risk genes, and most variants occur in conserved protein domains. For pediatric PAH, predicted deleterious de novo variants exhibited a significant burden compared to the background mutation rate (2.45×, p = 2.5e−5). At least eight novel pediatric candidate genes carrying de novo variants have plausible roles in lung/heart development. Conclusions Rare variant analysis of a large international consortium identified two new candidate genes—FBLN2 and PDGFD. The new genes have known functions in vasculogenesis and remodeling. Trio analysis predicted that ~ 15% of pediatric IPAH may be explained by de novo variants.

scholarly journals Targeted sequencing and integrative analysis to prioritize candidate genes in neurodevelopmental disorders

2021 ◽  
Author(s):  
Yi Zhang ◽  
Tao Wang ◽  
Yan Wang ◽  
Kun Xia ◽  
Jinchen Li ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Neurodevelopmental Disorders ◽  
De Novo ◽  
Genetic Data ◽  
Chinese Patients ◽  
The Novel ◽  
Mutational Spectrum ◽  
Functional Variants ◽  
Public Data ◽  
Chromosomal Genes

AbstractNeurodevelopmental disorders (NDDs) are a group of diseases characterized by high heterogeneity and frequently co-occurring symptoms. The mutational spectrum in patients with NDDs is largely incomplete. Here, we sequenced 547 genes from 1102 patients with NDDs and validated 1271 potential functional variants, including 108 de novo variants (DNVs) in 78 autosomal genes and seven inherited hemizygous variants in six X chromosomal genes. Notably, 36 of these 78 genes are the first to be reported in Chinese patients with NDDs. By integrating our genetic data with public data, we prioritized 212 NDD candidate genes with FDR < 0.1, including 17 novel genes. The novel candidate genes interacted or were co-expressed with known candidate genes, forming a functional network involved in known pathways. We highlighted MSL2, which carried two de novo protein-truncating variants (p.L192Vfs*3 and p.S486Ifs*11) and was frequently connected with known candidate genes. This study provides the mutational spectrum of NDDs in China and prioritizes 212 NDD candidate genes for further functional validation and genetic counseling.

Whole exome sequencing identifies FOXL2, FOXA2 and FOXA3 as candidate genes for monogenic congenital anomalies of the kidneys and urinary tract

2021 ◽  
Author(s):  
Bixia Zheng ◽  
Steve Seltzsam ◽  
Chunyan Wang ◽  
Luca Schierbaum ◽  
Sophia Schneider ◽  
...  
Keyword(s):  
Urinary Tract ◽  
Exome Sequencing ◽  
Candidate Genes ◽  
Whole Exome Sequencing ◽  
Congenital Anomalies ◽  
De Novo ◽  
Horseshoe Kidney ◽  
Missense Variant ◽  
Whole Exome ◽  
Fox Genes

Abstract Background Congenital anomalies of the kidneys and urinary tract (CAKUT) constitute the most common cause of chronic kidney disease in the first three decades of life. Variants in four Forkhead box (FOX) transcription factors have been associated with CAKUT. We hypothesized that other FOX genes, if highly expressed in developing kidney, may also represent monogenic causes of CAKUT. Methods We here performed whole exome sequencing (WES) in 541 families with CAKUT and generated 4 lists of CAKUT candidate genes: A) 36 FOX genes showing high expression during renal development, B) 4 FOX genes known to cause CAKUT to validate list A; C) 80 genes that we identified as unique potential novel CAKUT candidate genes when performing WES in 541 CAKUT families, and D) 175 genes identified from WES as multiple potential novel CAKUT candidate genes. Results To prioritize potential novel CAKUT candidates in FOX gene family, we overlapped 36 FOX genes (list A) with list C and D of WES-derived CAKUT candidates. Intersection with list C, identified a de novo FOXL2 in-frame deletion in a patient with eyelid abnormalities and ureteropelvic junction obstruction, and a homozygous FOXA2 missense variant in a patient with horseshoe kidney. Intersection with list D, identified a heterozygous FOXA3 missense variant in a CAKUT family with multiple affected individuals. Conclusion We hereby identified FOXL2, FOXA2 and FOXA3 as novel monogenic candidate genes of CAKUT, supporting the utility of a paralog-based approach to discover mutated genes associated with human disease.

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