Genomic reconstruction of the introduction and diversification of golden potato cyst nematode populations in Indonesia

2021 ◽  
Author(s):  
Nurul Dwi Handayani ◽  
Prabowo Lestari ◽  
Wouter Van As ◽  
Martijn Holterman ◽  
Sven Van den Elsen ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
18Th Century ◽  
Gene Families ◽  
Potato Production ◽  
Innate Immune ◽  
Sequencing Data ◽  
Cyst Nematodes ◽  
Selective Pressures ◽  
Production Areas ◽  
Venom Allergen

Potato cyst nematodes (PCN), the umbrella term for Globodera rostochiensis and G. pallida, co-evolved with their Solanaceous hosts in the Andeans. From there, PCN proliferated worldwide to virtually all potato production areas. PCN is a major factor limiting the potato production in Indonesia. In our survey, only G. rostochiensis was found. Fourteen field populations were collected on Java and Sumatra, and unique variants were called by mapping re-sequencing data on a G. rostochiensis reference genome. A phylogenetic tree based on 1.4 million unique variants showed a genotypic separation between the outgroup, a Scottish Ro1 population, and all Indonesian populations. This separation was comparable in size to the genotypic distinction between the Javanese and the Sumatran PCN populations. Next, variants within PCN effector gene families SPRYSEC, 1106, 4D06, and venom allergen-like protein (VAL) that all interfere with the host innate immune system were compared. Distinct selective pressures acted on these effector families; while SPRYSECs (4,341 SNPs/indels) behaved like neutral genes, the phylogenetic trees of 1106, 4D06 and VAL proteins (respectively 235, 790 and 150 SNPs/indels) showed deviating topologies. Our data suggest that PCN was introduced on Java not too long after the introduction of potato in the middle of the 18th century. Soon thereafter, the pathogen established on Sumatra, and started to diversify independently. This scenario was corroborated by diversification patterns of the effector families 1106, 4D06 and VAL. Our data demonstrate how genome re-sequencing data from a non-indigenous pathogen can be used to reconstruct the introduction and diversification process.

scholarly journals Identification and prevalence of potato cyst nematodes and root-knot nematodes in the potato production areas of İzmir Province, Turkey

2020 ◽  
pp. 259-272 ◽  
Author(s):  
Hülya DEMİRBAŞ PEHLİVAN ◽  
Galip KAŞKAVALCI ◽  
Ece Börteçine KASAPOĞLU ULUDAMAR ◽  
Halil TOKTAY ◽  
Halil ELEKCİOĞLU
Keyword(s):  
Potato Production ◽  
Potato Cyst Nematodes ◽  
Cyst Nematodes ◽  
Root Knot Nematodes ◽  
Production Areas

scholarly journals Assessing evidence for adaptive evolution in two hearing-related genes important for high-frequency hearing in echolocating mammals

2021 ◽  
Author(s):  
Hui Wang ◽  
Hanbo Zhao ◽  
Yujia Chu ◽  
Jiang Feng ◽  
Keping Sun
Keyword(s):  
Adaptive Evolution ◽  
Hair Cells ◽  
High Frequency ◽  
Phylogenetic Trees ◽  
Outer Hair Cells ◽  
Functional Domain ◽  
Coding Region ◽  
Selective Pressures ◽  
Wide Range ◽  
Different Parts

Abstract High-frequency hearing is particularly important for echolocating bats and toothed whales. Previously, studies of the hearing-related genes Prestin, KCNQ4, and TMC1 documented that adaptive evolution of high-frequency hearing has taken place in echolocating bats and toothed whales. In this study, we present two additional candidate hearing-related genes, Shh and SK2, that may also have contributed to the evolution of echolocation in mammals. Shh is a member of the vertebrate Hedgehog gene family and is required in the specification of the mammalian cochlea. SK2 is expressed in both inner and outer hair cells, and it plays an important role in the auditory system. The coding region sequences of Shh and SK2 were obtained from a wide range of mammals with and without echolocating ability. The topologies of phylogenetic trees constructed using Shh and SK2 were different; however, multiple molecular evolutionary analyses showed that those two genes experienced different selective pressures in echolocating bats and toothed whales compared to non-echolocating mammals. In addition, several nominally significant positively selected sites were detected in the non-functional domain of the SK2 gene, indicating that different selective pressures were acting on different parts of the SK2 gene. This study has expanded our knowledge of the adaptive evolution of high-frequency hearing in echolocating mammals.

scholarly journals Whole genome sequencing reveals the genomic diversity, taxonomic classification, and evolutionary relationships of the genus Nocardia

2021 ◽  
Vol 15 (8) ◽  
pp. e0009665
Author(s):  
Shuai Xu ◽  
Zhenpeng Li ◽  
Yuanming Huang ◽  
Lichao Han ◽  
Yanlin Che ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Gene Families ◽  
Single Copy ◽  
Taxonomic Classification ◽  
Genomic Diversity ◽  
Evolutionary Relationships ◽  
Taxonomic Structure ◽  
Pan Genome ◽  
Dipeptidyl Aminopeptidase

Nocardia is a complex and diverse genus of aerobic actinomycetes that cause complex clinical presentations, which are difficult to diagnose due to being misunderstood. To date, the genetic diversity, evolution, and taxonomic structure of the genus Nocardia are still unclear. In this study, we investigated the pan-genome of 86 Nocardia type strains to clarify their genetic diversity. Our study revealed an open pan-genome for Nocardia containing 265,836 gene families, with about 99.7% of the pan-genome being variable. Horizontal gene transfer appears to have been an important evolutionary driver of genetic diversity shaping the Nocardia genome and may have caused historical taxonomic confusion from other taxa (primarily Rhodococcus, Skermania, Aldersonia, and Mycobacterium). Based on single-copy gene families, we established a high-accuracy phylogenomic approach for Nocardia using 229 genome sequences. Furthermore, we found 28 potentially new species and reclassified 16 strains. Finally, by comparing the topology between a phylogenomic tree and 384 phylogenetic trees (from 384 single-copy genes from the core genome), we identified a novel locus for inferring the phylogeny of this genus. The dapb1 gene, which encodes dipeptidyl aminopeptidase BI, was far superior to commonly used markers for Nocardia and yielded a topology almost identical to that of genome-based phylogeny. In conclusion, the present study provides insights into the genetic diversity, contributes a robust framework for the taxonomic classification, and elucidates the evolutionary relationships of Nocardia. This framework should facilitate the development of rapid tests for the species identification of highly variable species and has given new insight into the behavior of this genus.

scholarly journals Genome Assemblies of the Warthog and Kenyan Domestic Pig Provide Insights into Suidae Evolution and Candidate Genes for African Swine Fever Tolerance

2021 ◽  
Author(s):  
Wen Feng ◽  
Lei Zhou ◽  
Pengju Zhao ◽  
Heng Du ◽  
Chenguang Diao ◽  
...  
Keyword(s):  
Large Scale ◽  
Genetic Resistance ◽  
African Swine Fever ◽  
Gene Families ◽  
Specific Gene ◽  
Chromosome 2 ◽  
Sequencing Data ◽  
Domestic Pig ◽  
Phacochoerus Africanus ◽  
Contraction And Expansion

As warthog (Phacochoerus africanus) has innate immunity against African swine fever (ASF), it is critical to understanding the evolutionary novelty of warthog to explain its specific ASF resistance. Here, we present two completed new genomes of one warthog and one Kenyan domestic pig, as the fundamental genomic references to decode the genetic mechanism on ASF tolerance. Our results indicated, multiple genomic variations, including gene losses, independent contraction and expansion of specific gene families, likely moulded warthog's genome to adapt the environment. Importantly, the analysis of presence and absence of genomic sequences revealed that, the warthog genome had a DNA sequence absence of the lactate dehydrogenase B (LDHB) gene on chromosome 2 compared to the reference genome. The overexpression and siRNA of LDHB indicated that its inhibition on the replication of ASFV. The Combining with large scale sequencing data of 123 pigs from all over world, contraction and expansion of TRIM genes families revealed that TRIM family genes in the warthog genome were potentially responsible for its tolerance to ASF. Our results will help further improve the understanding of genetic resistance ASF in pigs.

scholarly journals GeneRax: A tool for species tree-aware maximum likelihood based gene family tree inference under gene duplication, transfer, and loss

2019 ◽  
Author(s):  
Benoit Morel ◽  
Alexey M. Kozlov ◽  
Alexandros Stamatakis ◽  
Gergely J. Szöllősi
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Large Scale ◽  
Simulated Data ◽  
Gene Families ◽  
Species Tree ◽  
Homologous Gene ◽  
Sequence Alignments ◽  
Full Likelihood ◽  
True Tree

AbstractInferring phylogenetic trees for individual homologous gene families is difficult because alignments are often too short, and thus contain insufficient signal, while substitution models inevitably fail to capture the complexity of the evolutionary processes. To overcome these challenges species tree-aware methods also leverage information from a putative species tree. However, only few methods are available that implement a full likelihood framework or account for horizontal gene transfers. Furthermore, these methods often require expensive data pre-processing (e.g., computing bootstrap trees), and rely on approximations and heuristics that limit the degree of tree space exploration. Here we present GeneRax, the first maximum likelihood species tree-aware phylogenetic inference software. It simultaneously accounts for substitutions at the sequence level as well as gene level events, such as duplication, transfer, and loss relying on established maximum likelihood optimization algorithms. GeneRax can infer rooted phylogenetic trees for multiple gene families, directly from the per-gene sequence alignments and a rooted, yet undated, species tree. We show that compared to competing tools, on simulated data GeneRax infers trees that are the closest to the true tree in 90% of the simulations in terms of relative Robinson-Foulds distance. On empirical datasets, GeneRax is the fastest among all tested methods when starting from aligned sequences, and it infers trees with the highest likelihood score, based on our model. GeneRax completed tree inferences and reconciliations for 1099 Cyanobacteria families in eight minutes on 512 CPU cores. Thus, its parallelization scheme enables large-scale analyses. GeneRax is available under GNU GPL at https://github.com/BenoitMorel/GeneRax.

scholarly journals treeWidget: a BioJS component to visualise phylogenetic trees

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 49 ◽  
Author(s):  
Fabian Schreiber
Keyword(s):  
Phylogenetic Trees ◽  
Protein Domains ◽  
Gene Families ◽  
Sequence Information ◽  
Gene Duplications ◽  
Link Type ◽  
History Of ◽  
Conservation Patterns ◽  
Evolution Of Gene Families ◽  
The Web

Summary: Phylogenetic trees are widely used to represent the evolution of gene families. As the history of gene families can be complex (including lots of gene duplications), its visualisation can become a difficult task. A good/accurate visualisation of phylogenetic trees - especially on the web - allows easier understanding and interpretation of trees to help to reveal the mechanisms that shape the evolution of a specific set of gene/species. Here, I present treeWidget, a modular BioJS component to visualise phylogenetic trees on the web. Through its modularity, treeWidget can be easily customized to allow the display of sequence information, e.g. protein domains and alignment conservation patterns.Availability: http://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.7707

Prevalence and strain composition of potato virus Y circulating in potato fields in China’s north-central province Shanxi

Plant Disease ◽  
2021 ◽  
Author(s):  
Pengcheng Ding ◽  
Dexin Chen ◽  
Haixu Feng ◽  
Jiao Li ◽  
Hui Cao ◽  
...  
Keyword(s):  
Potato Virus ◽  
Potato Virus Y ◽  
Potato Production ◽  
Central China ◽  
Shanxi Province ◽  
Rt Pcr ◽  
Potato Leaf ◽  
Single Strain ◽  
North Central ◽  
Production Areas

Potato is an important crop in Shanxi province located in north-central China. During 2019-2020, 319 potato leaf samples were collected from eight locations distributed in three major potato production areas in Shanxi. Bio-chip detection kit revealed the presence of several potato viruses, and among them potato virus Y (PVY) was the most common one, reaching the incidence of 87.8% of all symptomatic samples. The immuno-captured multiplex reverse transcription (RT)-PCR was used to identify strains for all 280 PVY-positive samples, unveiling 242 samples infected with a single strain of PVY (86.4%) and 38 (13.6%) with a mixed infection. Of samples with a single-strain infection, PVY -SYR-II accounted for 102 (42.1%), followed by PVYN-Wi (33, 13.6%) , PVY -SYR-I (28, 11.6%), 261-4 (22, 9.1%), PVYNTNa (20, 8.3%), PVYNTNb (19, 7.9%), and PVY -SYR-III (18, 7.4%). Seven isolates representing different recombinants were selected for whole genome sequencing. Phylogenetic and recombination analyses confirmed the RT-PCR based strain typing for all seven strains of PVY found in Shanxi. SXKL-12 is the first SYR-III strain from potato reported from China. However, unlike that in other known SYR-III isolates, the region positioned from 1,764 to1,902 nt in SXKL-12 shared the highest sequence identity of 82.2% with an uncharacterized PVY isolate, JL-23, from China. Interestingly, the PVYN-Wi isolate SXZY-40 also possessed a more divergent sequence for the region positioned from 6,156 to 6,276 nt than other N-Wi isolates known to date, sharing the highest identity of 86.6% with an uncharacterized Chinese PVY isolate, JL-11. Pathogenicity analysis of dominant strains PVY -SYR-II and PVYN-Wi in six local popular potato cultivars revealed that Kexin 13, Helan 15 and Jizhangshu 12 were susceptible to these two strains with mild mottling or mosaic symptoms expression, while three cultivars, Jinshu 16, Qingshu 9, Xisen 6 were found fully resistant.

Phylogenomics of orchids and their mycorrhizal fungi : trees, diversity, and the pursuit of symbiosis

2019 ◽  
Author(s):  
◽  
Sarah Unruh
Keyword(s):  
Mycorrhizal Fungi ◽  
Phylogenetic Trees ◽  
High Throughput Sequencing ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Mycorrhizal Symbiosis ◽  
Sequencing Data ◽  
Phylogenetic Structure ◽  
University Of Missouri ◽  
Fungal Symbiosis

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT REQUEST OF AUTHOR.] Phylogenetic trees show us how organisms are related and provide frameworks for studying and testing evolutionary hypotheses. To better understand the evolution of orchids and their mycorrhizal fungi, I used high-throughput sequencing data and bioinformatic analyses, to build phylogenetic hypotheses. In Chapter 2, I used transcriptome sequences to both build a phylogeny of the slipper orchid genera and to confirm the placement of a polyploidy event at the base of the orchid family. Polyploidy is hypothesized to be a strong driver of evolution and a source of unique traits so confirming this event leads us closer to explaining extant orchid diversity. The list of orthologous genes generated from this study will provide a less expensive and more powerful method for researchers examining the evolutionary relationships in Orchidaceae. In Chapter 3, I generated genomic sequence data for 32 fungal isolates that were collected from orchids across North America. I inferred the first multi-locus nuclear phylogenetic tree for these fungal clades. The phylogenetic structure of these fungi will improve the taxonomy of these clades by providing evidence for new species and for revising problematic species designations. A robust taxonomy is necessary for studying the role of fungi in the orchid mycorrhizal symbiosis. In chapter 4 I summarize my work and outline the future directions of my lab at Illinois College including addressing the remaining aims of my Community Sequencing Proposal with the Joint Genome Institute by analyzing the 15 fungal reference genomes I generated during my PhD. Together these chapters are the start of a life-long research project into the evolution and function of the orchid/fungal symbiosis.

scholarly journals Identification, Evolutionary and Expression Analysis of PYL-PP2C-SnRK2s Gene Families in Soybean

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1356
Author(s):  
Zhaohan Zhang ◽  
Shahid Ali ◽  
Tianxu Zhang ◽  
Wanpeng Wang ◽  
Linan Xie
Keyword(s):  
Gene Family ◽  
Higher Plants ◽  
Expression Patterns ◽  
Family Members ◽  
Evolutionary Relationship ◽  
Gene Families ◽  
Class Iii ◽  
Sequencing Data ◽  
Entire Genome ◽  
Core Components

Abscisic acid (ABA) plays a crucial role in various aspects of plant growth and development, including fruit development and ripening, seed dormancy, and involvement in response to various environmental stresses. In almost all higher plants, ABA signal transduction requires three core components; namely, PYR/PYL/RCAR ABA receptors (PYLs), type 2C protein phosphatases (PP2Cs), and class III SNF-1-related protein kinase 2 (SnRK2s). The exploration of these three core components is not comprehensive in soybean. This study identified the GmPYL-PP2C-SnRK2s gene family members by using the JGI Phytozome and NCBI database. The gene family composition, conservation, gene structure, evolutionary relationship, cis-acting elements of promoter regions, and its coding protein domains were analyzed. In the entire genome of the soybean, there are 21 PYLs, 36 PP2Cs, and 21 SnRK2s genes; further, by phylogenetic and conservation analysis, 21 PYLs genes are classified into 3 groups, 36 PP2Cs genes are classified into seven groups, and 21 SnRK2s genes are classified into 3 groups. The conserved motifs and domain analysis showed that all the GmPYLs gene family members contain START-like domains, the GmPP2Cs gene family contains PP2Cc domains, and the GmSnRK2s gene family contains S_TK domains, respectively. Furthermore, based on the high-throughput transcriptome sequencing data, the results showed differences in the expression patterns of GmPYL-PP2C-SnRK2s gene families in different tissue parts of the same variety, and the same tissue part of different varieties. Our study provides a basis for further elucidation of the identification of GmPYL-PP2C-SnRK2s gene family members and analysis of their evolution and expression patterns, which helps to understand the molecular mechanism of soybean response to abiotic stress. In addition, this provides a conceptual basis for future studies of the soybean ABA core signal pathway.

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