Genome-wide identification and expression analysis of the cucumber PYL gene family

Abscisic acid (ABA) is a very important hormone in plants. It regulates growth and development of plants and plays an important role in biotic and abiotic stresses. The Pyrabactin resistance 1-like (PYR/PYL) proteins play a central role in ABA signal transduction pathways. The working system of PYL genes in cucumber, an important economical vegetable (Cucumis sativus L.), has not been fully studied yet. Through bioinformatics, a total of 14 individual PYL genes were identified in Chinese long ‘9930’ cucumber. Fourteen PYL genes were distributed on six chromosomes of cucumber, and their encoded proteins predicted to be distributed in cytoplasm and nucleus. Based on the phylogenetic analysis, the PYL genes of cucumber, Arabidopsis, rice, apple, Brachypodium distachyon and soybeancould be classified into three groups. Genetic structures and conserved domains analysis revealed that CsPYL genes in the same group have similar exons and conserved domains. By predicting cis-elements in the promoters, we found that all CsPYL members contained hormone and stress-related elements. Additionally, the expression patterns of CsPYL genes were specific in tissues. Finally, we further examined the expression of 14 CsPYL genes under ABA, PEG, salt stress. The qRT-PCR results showed that most PYL gene expression levels were up-regulated. Furthermore, with different treatments about 3h, the relative expression of PYL8 was up-regulated and more than 20 times higher than 0h. It indicated that this gene may play an important role in abiotic stress.

Patterns of convergence and divergence between bipolar disorder type I and type II: evidence from integrative genomic analyses

Genome-wide association studies (GWAS) analyses have revealed genetic evidence of bipolar disorder (BD), but little is known about genetic structure of BD subtypes. We aimed to investigate genetic overlap and distinction of bipolar type I (BDI) & type II (BDII) by conducting integrative post-GWAS analyses. This study utilized single nucleotide polymorphism (SNP)-level approaches to uncover correlated and distinct genetic loci. Transcriptome-wide association analyses (TWAS) were then approached to pinpoint functional genes expressed in specific brain tissues and blood. Next, we performed cross-phenotype analysis including exploring the potential causal associations between BDI & II and drug responses and comparing the difference of genetic structures among four different psychiatric traits. Our results find SNP-level evidence revealed three genomic loci, SLC25A17, ZNF184 and RPL10AP3 shared by BDI & II, while one locus (i.e., MAD1L1) and significant gene sets involved in calcium channel activity, neural and synapsed signals that distinguished two subtypes. TWAS data implicated different genes effecting BDI & II through expression in specific brain regions (e.g., nucleus accumbens for BDI). Cross-phenotype analyses indicated that BDI & II have different drug response, but share continuous genetic structures with schizophrenia (SCZ) and major depression disorder (MDD), which help fill the gaps left by the dichotomy of mental disorder. These combined evidences illustrate genetic convergence and divergence between BDI & II and provide an underlying biological and trans-diagnostic insight into major psychiatric disorders.

GENETIC BASIS OF ALGEBRAIC BIOLOGY, GESTALT GENETICS AND TETRA-EIDOSES BY Yu. I. KULAKOV

The article is devoted to the universal algebraic rules of nucleotide sequences in the DNA of genomes of higher and lower organisms. The patterns identified by the author are related to the known binary nature of genetic structures and are expressed in genomic gestalt phenomena, which are similar to genetically inherited phenomena of gestalt psychology. This allows the author to develop the ideas of gestalt genetics and algebraic biology. Many genetic phenomena of tetrastructurization evoke associations with Kulakov’s concept of tetra-eidoses.

Long read sequencing reveals sequential complex rearrangements driven by Hepatitis B virus integration

Integration of Hepatitis B (HBV) virus into human genome disrupts genetic structures and cellular functions. Here, we conducted multiplatform long read sequencing on two cell lines and five clinical samples of HBV-induced hepatocellular carcinomas (HCC). We resolved two types of complex viral integration induced genome rearrangements and established a Time-phased Integration and Rearrangement Model (TIRM) to depict their formation progress by differentiating inserted HBV copies with HiFi long reads. We showed that the two complex types were initialized from focal replacements and the fragile virus-human junctions triggered subsequent rearrangements. We further revealed that these rearrangements promoted a prevalent loss-of-heterozygosity at chr4q, accounting for 19.5% of HCC samples in ICGC cohort and contributing to immune and metabolic dysfunction. Overall, our long read based analysis reveals a novel sequential rearrangement progress driven by HBV integration, hinting the structural and functional implications on human genomes.

Genetic Evaluation of Ancient Platycladus orientalis L. (Cupressaceae) in the Middle Reaches of the Yellow River Using Nuclear Microsatellite Markers

As a precious and rare genetic resource, ancient Platycladus orientalis L. (Cupressaceae) has important scientific, cultural and historical value. The ancient temples and royal cemeteries in the middle reaches of the Yellow River contain the most concentrated and abundant distributions of ancient P. orientalis. Due to unfavorable conditions, the genetic resources of ancient trees are facing great threats and challenges; thus, it is urgent to strengthen the evaluation of the genetic resources of ancient P. orientalis. In this study, we used nine polymorphic nuclear simple sequence repeats (nSSRs) to evaluate the genetic resources of 221 individuals in 19 ancient P. orientalis populations in the middle reaches of the Yellow River. These selected polymorphic nSSR loci can be used reliably and rapidly in P. orientalis genetic studies. Our study showed that the 19 ancient P. orientalis populations have high genetic diversity (mean H = 0.562, He = 0.377). High historical gene flow (mean Nm = 1.179) and high genetic differentiation (mean Fst = 0.184) were observed in the ancient P. orientalis population. The analysis of molecular variance (AMOVA) showed that higher genetic variation existed within populations (93%) rather than among populations (7%). The genetic structures showed that the 19 populations were divided into two groups. The Mantel test and neighbor-joining (NJ) tree analysis showed no geographical distribution characteristics among populations, which may indicate a history of transplanting by ancient humans. Our research provides a theoretical basis for the protection and utilization of ancient P. orientalis germplasm resources and exploration of the historical origin and genetic relationships among the populations of P. orientalis on a large scale in the future.

The Genealogical Divergence Index Across a Speciation Continuum in Hercules Beetles

The genealogical divergence index (gdi) was developed to aid in molecular species delimitation under the multispecies coalescent model, which has been shown to delimit genetic structures but not necessarily species. Although previous studies have used meta-analyses to show that gdi could be informative for distinguishing taxonomically good species, the biological and evolutionary implications of divergences showing different gdi values have yet to be studied. I showed that an increase in gdi value was correlated with later stages of divergence further along a speciation continuum in an Amazonian Hercules beetle system. Specifically, a gdi value of 0.7 or higher was associated with diverge between biological species that can coexist in geographic proximity while maintaining their evolutionary independence. Divergences between allopatric species that were conventionally given subspecific status, such as geographic taxa that may or may not be morphologically divergent, had gdi values that fell within the species delimitation ambiguous zone (0.2 < gdi < 0.7). However, the results could be drastically affected by the sampling design, i.e., the choice of different geographic populations and the lumping of distinct genetic groups when running the analyses. Different gdi values may prove to be biologically and evolutionarily informative should additional speciation continua from different empirical systems be investigated, and the results obtained may help with objectively delimiting species in the era of integrative taxonomy.

Population Genetic Structures of Puccinia striiformis f. sp. tritici in the Gansu-Ningxia Region and Hubei Province, China

Wheat stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst), is a destructive wheat disease in China. The Gansu–Ningxia region (GN) is a key area for pathogen over-summering in China, and northwestern Hubei (HB) is an important region for pathogen over-wintering, serving as a source of inoculum in spring epidemic regions. The spatiotemporal population genetic structure of Pst in HB and the pathogen population exchanges between GN and HB are important for estimating the risk of interregional epidemics. Here, 567 isolates from GN and HB were sampled from fall 2016 to spring 2018 and were genotyped using simple sequence repeat markers. The genotypic and genetic diversity of Pst subpopulations in HB varied among seasons and locations. Greater genetic diversification levels were found in the spring compared with fall populations using principal coordinate analysis and Bayesian assignments. In total, there were 17 common genotypes among the 208 determined, as shown by a small overlap of genotypes in the principal coordinate analysis and dissimilar Bayesian assignments in both regions, which revealed the limited genotype exchange between the populations of GN and HB.

Structural Analysis and Spatiotemporal Expression of Atxn1 Genes in Zebrafish Embryos and Larvae

Zebrafish have come into focus to model cerebellar diseases such as spinocerebellar ataxias (SCAs), which is caused by an expansion of translated CAG repeats in several unrelated genes. In spinocerebellar ataxia type 1 (SCA1), gain-of-function in the mutant ATXN1 contributes to SCA1’s neuropathy. Human ATXN1 and its paralog ATXN1L are chromatin-binding factors, act as transcriptional repressors, and have similar expression patterns. However, little is known about atxn1 genes in zebrafish. Recently, two family members, atxn1a and atxn1b, were identified as duplicate orthologs of ATXN1, as was atxn1l, the ortholog of ATXN1L. In this study, we analyzed the phylogenetic relationship of the atxn1 family members in zebrafish, compared their genetic structures, and verified the predicted transcripts by both RT-PCR and whole-mount in situ hybridization. All three genes, atxn1a, atxn1b, and atxn1l, show overlapping, but also distinct, expression domains during embryonic and larval development. While atxn1a and atxn1l display similar spatiotemporal embryonic expression, atxn1b expression is initiated during the onset of brain development and is predominantly expressed in the cerebellum throughout zebrafish development. These results provide new insights into atxn1 genes and their expression patterns in zebrafish during embryonic and late-larval development and may contribute importantly to future experiments in disease modeling of SCAs.

Stock Assessment of Hatchery-Released Clam Meretrix meretrix in an Estuary of China From the Perspectives of Population Ecology and Genetic Diversity

In this study, the release effects of the buried clam Meretrix meretrix in a northern estuary of China (Shuangtaizi Estuary) was assessed in terms of population ecology and genetic variability by using longer-term monitoring data from 2011 (used as the baseline data) to 2018. A total of 2.4 × 108 hatchery juveniles were released from 2012 to 2014, and follow-up monitoring survey of the growth, distribution, density, and biomass of M. meretrix population was carried out. Results showed a temporary spike in the population of M. meretrix, and the population underwent considerable year-to-year fluctuations in total abundance and biomass. Meanwhile, the age structure of the populations from 2011 to 2018 is still an unstable expanding type. Genetic analysis based on 10 polymorphic microsatellite markers revealed no significant genetic differentiation and weak genetic structures between years but higher genetic diversities in 2014–2018 than in the initial period (2013) of stock restoration. Our study suggests that effective policies for management and conservation to restore M. meretrix population by local governments are still needed in the long run.