A New Mitochondrial Genome of Sogatella furcifera (Horváth) (Hemiptera: Delphacidae) and Mitogenome-Wide Investigation on Polymorphisms

White-backed planthopper (WBPH), Sogatella furcifera (Horváth), is one of the major sap-sucking rice pests in East Asia. We have determined a new complete mitochondrial genome of WBPH collected in the Korean peninsula using NGS technology. Its length and GC percentages are 16,613 bp and 23.8%, respectively. We observed one polymorphic site, a non-synonymous change, in the COX3 gene with confirmation heteroplasmy phenomenon within individuals of WBPH by PCR amplification and Sanger sequencing, the first report in this species. In addition, this heteroplasmy was not observed in wild WBPH populations, suggesting that it may be uncommon in fields. We analyzed single nucleotide polymorphisms, insertion, and deletions, and simple sequence repeats among the three WBPH mitogenomes from Korea and China and found diverse intraspecific variations, which could be potential candidates for developing markers to distinguish geographical populations. Phylogenetic analysis of 32 mitogenomes of Delphacidae including the three WBPH mitogenomes suggested that Delphacinae seems to be monophyletic and Sogatella species including WBPH are clearly formed as one clade. In the future, it is expected that complete mitogenomes of individuals of geographically dispersed WBPH populations will be used for further population genetic studies to understand the migration pathway of WBPH.

Drought Stress Influences the Growth and Physiological Characteristics of Solanum rostratum Dunal Seedlings From Different Geographical Populations in China

Extensive studies have shown that the success of invasive plants in large environmental gradients can be partly attributed to related factors, including phenotypic plasticity and rapid evolution. To enhance their ability to compete and invade, invasive plants often show higher morphological and physiological plasticity to adapt to different habitat conditions. In the past two decades, invasive species have expanded to some new habitats in North and Northwest China, including arid oasis agricultural zones, which are disturbed by human activities, and the ecosystem itself is very fragile. To evaluate the ecological adaptability of invasive plants widely distributed in North and Northwest China, we studied the physiological response and tolerance mechanism of different geographical populations of Solanum rostratum Dunal to different drought-stress gradients in extremely arid regions (Xinjiang population) and semi-arid regions (Inner Mongolia population). The results showed that with the aggravation of drought stress, S. rostratum from different geographical populations adopted different physiological mechanisms to drought stress. Xinjiang population was mostly affected by root/shoot ratio and chlorophyll fluorescence characteristics, showing higher plasticity in the net and total photosynthetic rates, while the Inner Mongolia population mainly relied on the accumulation of osmotic adjustment substances, higher leaf dry matter content, and increased malondialdehyde to cope with drought stress. Based on these results, we concluded that the physiological responses of S. rostratum invading different habitats in northern China to drought stress were significantly different. The drought resistance of the Xinjiang population was higher than that of the Inner Mongolia population. In general, S. rostratum can be widely adapted to both harsh and mild habitats through phenotypic plasticity, threatening agricultural production and ecological environment security in northern China.

Global diversity of the gene encoding the Pfs25 protein—a Plasmodium falciparum transmission-blocking vaccine candidate

Background Vaccines against the sexual stages of the malarial parasite Plasmodium falciparum are indispensable for controlling malaria and abrogating the spread of drug-resistant parasites. Pfs25, a surface antigen of the sexual stage of P. falciparum, is a leading candidate for transmission-blocking vaccine development. While clinical trials have reported that Pfs25-based vaccines are safe and effective in inducing transmission-blocking antibodies, the extent of the genetic diversity of Pfs25 in malaria endemic populations has rarely been studied. Thus, this study aimed to investigate the global diversity of Pfs25 in P. falciparum populations. Methods A database of 307 Pfs25 sequences of P. falciparum was established. Population genetic analyses were performed to evaluate haplotype and nucleotide diversity, analyze haplotypic distribution patterns of Pfs25 in different geographical populations, and construct a haplotype network. Neutrality tests were conducted to determine evidence of natural selection. Homology models of the Pfs25 haplotypes were constructed, subjected to molecular dynamics (MD), and analyzed in terms of flexibility and percentages of secondary structures. Results The Pfs25 gene of P. falciparum was found to have 11 unique haplotypes. Of these, haplotype 1 (H1) and H2, the major haplotypes, represented 70% and 22% of the population, respectively, and were dominant in Asia, whereas only H1 was dominant in Africa, Central America, and South America. Other haplotypes were rare and region-specific, resulting in unique distribution patterns in different geographical populations. The diversity in Pfs25 originated from ten single-nucleotide polymorphism (SNP) loci located in the epidermal growth factor (EGF)-like domains and anchor domain. Of these, an SNP at position 392 (GGA/GCA), resulting in amino acid substitution 131 (Gly/Ala), defined the two major haplotypes. The MD results showed that the structures of H1 and H2 variants were relatively similar. Limited polymorphism in Pfs25 could likely be due to negative selection. Conclusions The study successfully established a Pfs25 sequence database that can become an essential tool for monitoring vaccine efficacy, designing assays for detecting malaria carriers, and conducting epidemiological studies of P. falciparum. The discovery of the two major haplotypes, H1 and H2, and their conserved structures suggests that the current Pfs25-based vaccines could be used globally for malaria control. Graphical Abstract

Mapping of population disparities in the cholangiocarcinoma urinary metabolome

Phenotypic diversity in urinary metabolomes of different geographical populations has been recognized recently. In this study, urinary metabolic signatures from Western (United Kingdom) and South-East Asian (Thai) cholangiocarcinoma patients were characterized to understand spectral variability due to host carcinogenic processes and/or exogenous differences (nutritional, environmental and pharmaceutical). Urinary liquid chromatography mass spectroscopy (LC–MS) spectral profiles from Thai (healthy = 20 and cholangiocarcinoma = 14) and UK cohorts (healthy = 22 and cholangiocarcinoma = 10) were obtained and modelled using chemometric data analysis. Healthy metabolome disparities between the two distinct populations were primarily related to differences in dietary practices and body composition. Metabolites excreted due to drug treatment were dominant in urine specimens from cholangiocarcinoma patients, particularly in Western individuals. Urine from participants with sporadic (UK) cholangiocarcinoma contained greater levels of a nucleotide metabolite (uridine/pseudouridine). Higher relative concentrations of 7-methylguanine were observed in urine specimens from Thai cholangiocarcinoma patients. The urinary excretion of hippurate and methyladenine (gut microbial-host co-metabolites) showed a similar pattern of lower levels in patients with malignant biliary tumours from both countries. Intrinsic (body weight and body composition) and extrinsic (xenobiotic metabolism) factors were the main causes of disparities between the two populations. Regardless of the underlying aetiology, biological perturbations associated with cholangiocarcinoma urine metabolome signatures appeared to be influenced by gut microbial community metabolism. Dysregulation in nucleotide metabolism was associated with sporadic cholangiocarcinoma, possibly indicating differences in mitochondrial energy production pathways between cholangiocarcinoma tumour subtypes. Mapping population-specific metabolic disparities may aid in interpretation of disease processes and identification of candidate biomarkers.

A clade of telosma mosaic virus from Thailand is undergoing geographical expansion and genetic differentiation in passionfruit of Vietnam and China

Passionfruit (Passiflora edulis) is widely cultivated in tropical and subtropical regions around the world. Several viruses of the genus Potyvirus pose serious threat to passion fruit production. The origin, dispersal and evolution of these potyviruses, however, are poorly understood. Here, we investigated the genetic structure of telosma mosaic virus (TelMV), a potyvirus that infects passionfruit in East and Southeast Asia, after a survey of its incidence in passionfruit plants of China. The phylogeny inferred from 140 nucleotide sequences of the coat protein (CP) gene of TelMV, including 96 determined in this study, separated this virus into 4 clades. TelMV isolates from passionfruit were placed into Clade 1–3, while those from other plant species into Clade 4. Interestingly, TelMV isolates of passionfruit from Thailand were found in all the three clades of Clade 1–3, but those from China and Vietnam were found exclusively in Clade 1. Nevertheless, TelMV isolates within Clade 1 tended to cluster according to their geographical origin. Geographical populations from Thailand, Taiwan and Hainan islands of China showed significant genetic differences with one another and with those from Guangxi, Fujian, Guangdong, Yunnan and Jiangsu provinces of China. Altogether, these data suggest that several distinct TelMV clades had arisen from the passionfruit of Thailand, but only one of which was dispersed. In expanding its distribution, this clade of TelMV has undergone geography-associated evolution. Further studies on this hypothesis may shed new insights into mechanisms underlying the emergence of potyviral diseases in passionfruit plants.

Geography-Driven Evolution of Potato Virus A Revealed by Genetic Diversity Analysis of the Complete Genome

Potato virus A (PVA), a member of the genus Potyvirus, is an important potato pathogen that causes 30%–40% yield reduction to global potato production. Knowledge on the genetic structure and the evolutionary forces shaping the structure of this pathogen is limited but vital in developing effective management strategies. In this study, we investigated the population structure and molecular evolution of PVA by analyzing novel complete genomic sequences from Chinese isolates combined with available sequences from Europe, South America, Oceania, and North America. High nucleotide diversity was discovered among the populations studied. Pairwise FST values between geographical populations of PVA ranged from 0.22 to 0.46, indicating a significant spatial structure for this pathogen. Although purifying selection was detected at the majority of polymorphic sites, significant positive selection was identified in the P1, NIa, and NIb proteins, pointing to adaptive evolution of PVA. Further phylogeny–trait association analysis showed that the clustering of PVA isolates was significantly correlated with geographic regions, suggesting that geography-driven adaptation may be an important determinant of PVA diversification.

Diverse Host Immune Responses of Different Geographical Populations of the Coconut Rhinoceros Beetle to Oryctes Rhinoceros Nudivirus (OrNV) Infection

Oryctes rhinoceros nudivirus (OrNV) is a double-stranded DNA (dsDNA) virus which has been used as a biocontrol agent to suppress coconut rhinoceros beetle (CRB) in the Pacific Islands. Recently a new wave of CRB incursions in Oceania is thought to be related to the presence of low-virulence isolates of OrNV or virus-tolerant haplotypes of beetles (CRB-G).

Significance of the suture line in cephalopod taxonomy revealed by 3D morphometrics in the modern nautilids Nautilus and Allonautilus

Assessing the taxonomic importance of the suture line in shelled cephalopods is a key to better understanding the diversity of this group in Earth history. Because fossils are subject to taphonomic artifacts, an in-depth knowledge of well-preserved modern organisms is needed as an important reference. Here, we examine the suture line morphology of all known species of the modern cephalopods Nautilus and Allonautilus. We applied computed tomography and geometric morphometrics to quantify the suture line morphology as well as the conch geometry and septal spacing. Results reveal that the suture line and conch geometry are useful in distinguishing species, while septal spacing is less useful. We also constructed cluster trees to illustrate the similarity among species. The tree based on conch geometry in middle ontogeny is nearly congruent with those previously reconstructed based on molecular data. In addition, different geographical populations of the same species of Nautilus separate out in this tree. This suggests that genetically distinct (i.e., geographically isolated) populations of Nautilus can also be distinguished using conch geometry. Our results are applicable to closely related fossil cephalopods (nautilids), but may not apply to more distantly related forms (ammonoids).

Genome-Wide SNP Discovery and Population Genetic Analysis of Mesocentrotus nudus in China Seas

Mesocentrotus nudus is an important commercially aquatic species because of its high edible and medicinal values. However, wild stocks have dramatically decreased in recent decades. Understanding the population structure and genetic diversity can provide vital information for genetic conservation and improvement. In the present study, the genotyping-by-sequencing (GBS) approach was adopted to identify the genome-wide single-nucleotide polymorphisms (SNPs) from a collection of 80 individuals consisting of five geographical populations (16 individuals from each population), covering the natural habitats of M. nudus in China seas. An average of 0.96-Gb clean reads per sample were sequenced, and a total of 51,738 biallelic SNPs were identified. Based on these SNPs, diversity index analysis showed that all populations have a similar pattern with positive Fis (0.136) and low Ne (724.3). Low genetic differentiation and high genetic connectivity among five geographical populations were detected by pairwise Fst, principal component analysis (PCA), admixture, and phylogenetic analysis. Besides, two YWL individuals originating from an isolated ancestor may imply that there is a genetically differentiated population in the adjacent sea. Overall, the results showed that GBS is an effective method to detect genome-wide SNPs for M. nudus and suggested that the protective measures and the investigation with larger spatial scale and sample size for M. nudus should be carried out in the future.