scholarly journals First annotated draft genomes of non-marine ostracods (Ostracoda, Crustacea) with different reproductive modes

2021 ◽  
Author(s):  
Patrick Tran Van ◽  
Yoann Anselmetti ◽  
Jens Bast ◽  
Zoé Dumas ◽  
Nicolas Galtier ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Genomic Research ◽  
Ecological Research ◽  
Linkage Maps ◽  
Transcriptome Data ◽  
Sequencing Technology ◽  
Gene Annotations ◽  
Ancient Asexual ◽  
Bac Libraries ◽  
Reference Genomes

Abstract Ostracods are one of the oldest crustacean groups with an excellent fossil record and high importance for phylogenetic analyses but genome resources for this class are still lacking. We have successfully assembled and annotated the first reference genomes for three species of non-marine ostracods; two with obligate sexual reproduction (Cyprideis torosa and Notodromas monacha) and the putative ancient asexual Darwinula stevensoni. This kind of genomic research has so far been impeded by the small size of most ostracods and the absence of genetic resources such as linkage maps or BAC libraries that were available for other crustaceans. For genome assembly, we used an Illumina-based sequencing technology, resulting in assemblies of similar sizes for the three species (335-382Mb) and with scaffold numbers and their N50 (19-56 kb) in the same orders of magnitude. Gene annotations were guided by transcriptome data from each species. The three assemblies are relatively complete with BUSCO scores of 92-96. The number of predicted genes (13,771-17,776) is in the same range as Branchiopoda genomes but lower than in most malacostracan genomes. These three reference genomes from non-marine ostracods provide the urgently needed basis to further develop ostracods as models for evolutionary and ecological research.

scholarly journals First annotated draft genomes of non-marine ostracods (Ostracoda, Crustacea) with different reproductive modes

2020 ◽  
Author(s):  
Patrick Tran Van ◽  
Yoann Anselmetti ◽  
Jens Bast ◽  
Zoé Dumas ◽  
Nicolas Galtier ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Genomic Research ◽  
Linkage Maps ◽  
Transcriptome Data ◽  
Sequencing Technology ◽  
Gene Annotations ◽  
Ancient Asexual ◽  
Bac Libraries ◽  
Reference Genomes

ABSTRACTSOstracods are one of the oldest crustacean groups with an excellent fossil record and high importance for phylogenetic analyses but genome resources for this class are still lacking. We have successfully assembled and annotated the first reference genomes for three species of non-marine ostracods; two with obligate sexual reproduction (Cyprideis torosa and Notodromas monacha) and the putative ancient asexual Darwinula stevensoni. This kind of genomic research has so far been impeded by the small size of most ostracods and the absence of genetic resources such as linkage maps or BAC libraries that were available for other crustaceans. For genome assembly, we used an Illumina-based sequencing technology, resulting in assemblies of similar sizes for the three species (335-382Mb) and with scaffold numbers and their N50 (19-56 kb) in the same orders of magnitude. Gene annotations were guided by transcriptome data from each species. The three assemblies are relatively complete with BUSCO scores of 92-96%, and thus exceed the quality of several other published crustacean genomes obtained with similar techniques. The number of predicted genes (13,771-17,776) is in the same range as Branchiopoda genomes but lower than in most malacostracan genomes. These three reference genomes from non-marine ostracods provide the urgently needed basis to further develop ostracods as models for evolutionary and ecological research.

scholarly journals Two highly representative rice BAC libraries of japonica cv Tainung 67 suitable for rice structural and functional genomic research

Plant Science ◽  
2006 ◽  
Vol 170 (4) ◽  
pp. 889-896
Author(s):  
Yann-Rong Lin ◽  
Teh-Yuan Chow ◽  
Meizhong Luo ◽  
Dave Kudrna ◽  
Chih-Chi Lin ◽  
...  
Keyword(s):  
Genomic Research ◽  
Functional Genomic ◽  
Bac Libraries

scholarly journals The Power of Using Novel Nanopore Sequencing Technology for Diagnosis, Genomic and Pathological Studies of Covid-19

2021 ◽  
Vol 2 (3) ◽  
pp. 4014-4028
Author(s):  
Chenghao Du
Keyword(s):  
Analytical Methods ◽  
Diagnostic Methods ◽  
Public Access ◽  
Genomic Research ◽  
Metagenomic Sequencing ◽  
Nanopore Sequencing ◽  
The Novel ◽  
Sequencing Technology ◽  
Different Types ◽  
Sequencing Platforms

The novel coronavirus disease 2019 (COVID‐19), originally identified in December 2019 Wuhan, China, has propagated to worldwide pandemic, causing many cases of death and morbidity. Since the development of COVID-19 vaccines is still under experimental stages without public access, different types of testing and detection ensuring rapid and accurate results are urgently required to prevent delaying isolation of infected patients. The traditional diagnostic and analytical methods of COVID-19 relied heavily on nucleic acid and antibody-antigen methods but are subject to assembly bias, restricted by reading length, showed some false positive/negative results and had a long turnaround time. Hence, three styles of nanopore sequencing techniques as complementary tools for COVID-19 diagnosis and analysis are introduced. The long-read nanopore sequencing technology has been adopted in metagenomic and pathological studies of virosphere including SARS-CoV-2 recently by either metagenomically, directly or indirectly sequencing the viral genomic RNA of SARS-CoV-2 in real-time to detect infected specimens for early isolation and treatment, to investigate the transmission and evolutionary routes of SARS-CoV-2 as well as its pathogenicity and epidemiology. In this article, the Nanopore-Based Metagenomic Sequencing, Direct RNA Nanopore Sequencing (DRS), and Nanopore Targeted Sequencing (NTS) become the main focus of the novel COVID-19 detecting analytical methods in sequencing platforms, which are discussed in comparison with other traditional and popular diagnostic methods. Finally, different types of nanopore sequencing platforms that are developed by Oxford Nanopore Technologies (ONT) due to various purposes and demands in viral genomic research are briefly discussed.

scholarly journals Enhanced genome annotation strategy provides novel insights on the phylogeny of Flaviviridae

2019 ◽  
Author(s):  
Adriano de Bernardi Schneider ◽  
Denis Jacob Machado ◽  
Daniel Janies
Keyword(s):  
Phylogenetic Relationship ◽  
Soybean Cyst Nematode ◽  
Phylogenetic Analyses ◽  
Optimality Criteria ◽  
Entire Family ◽  
Close Phylogenetic Relationship ◽  
The Family ◽  
Relationship Of ◽  
Reference Genomes ◽  
Annotation Strategy

The ongoing and severe public health threat of viruses of the family Flaviviridae, including dengue, hepatitis C, West Nile, yellow fever, and zika, demand a greater understanding of how these viruses evolve, emerge and spread in order to respond. Central to this understanding is an updated phylogeny of the entire family. Unfortunately, most cladograms of Flaviviridae focus on specific lineages, ignore outgroups, and rely on midpoint rooting, hampering their ability to test ingroup monophyly and estimate ingroup relationships. This problem is partly due to the lack of fully annotated genomes of Flaviviridae, which has genera with slightly different gene content, hindering genome analysis without partitioning. To tackle these problems, we developed an annotation pipeline for Flaviviridae that uses a combination of ab initio and homology-based strategies. The pipeline recovered 100% of the genes in reference genomes and annotated over 97% of the expected genes in the remaining non curated sequences. We further demonstrate that the combined analysis of genomes of all genera of Flaviviridae (Flavivirus, Hepacivirus, Pegivirus, and Pestivirus), as made possible by our annotation strategy, enhances the phylogenetic analyses of these viruses for all optimality criteria that we tested (parsimony, maximum likelihood, and posterior probability). The final tree sheds light on the phylogenetic relationship of viruses that are divergent from most Flaviviridae and should be reclassified, especially the soybean cyst nematode virus 5 (SbCNV-5) and the Tamana bat virus. We also corroborate the close phylogenetic relationship of dengue and zika viruses with an unprecedented degree of support.

scholarly journals The aphelid-like phagotrophic origins of fungi

2017 ◽  
Author(s):  
Guifre Torruella ◽  
Xavier Grau-Bove ◽  
David Moreira ◽  
Sergey A Karpov ◽  
John Burns ◽  
...  
Keyword(s):  
Cell Wall ◽  
Metabolic Pathways ◽  
Phylogenetic Analyses ◽  
Algal Cell ◽  
Rrna Genes ◽  
Transcriptome Data ◽  
Free Living ◽  
Statistical Support ◽  
Phylogenomic Analyses ◽  
Protein Datasets

Aphelids are poorly known phagotrophic parasites of algae whose life cycle and morphology resemble those of the widely diverse parasitic rozellids (Cryptomycota, Rozellomycota). In previous phylogenetic analyses of RNA polymerase and rRNA genes, aphelids and rozellids formed a monophyletic group together with the extremely reduced parasitic Microsporidia, named Opisthosporidia, which was sister to Fungi. However, the statistical support for that group was always moderate. We generated the first transcriptome data for one aphelid species, Paraphelidium tribonemae. In-depth multi-gene phylogenomic analyses using various protein datasets place aphelids as the closest relatives of Fungi to the exclusion of rozellids and Microsporidia. In contrast with the comparatively reduced Rozella allomycis genome, we infer a rich, free-living-like aphelid proteome, including cellulases likely involved in algal cell-wall penetration, enzymes involved in chitin biosynthesis and several metabolic pathways. Our results suggest that Fungi evolved from a complex aphelid-like ancestor that lost phagotrophy and became osmotrophic.

scholarly journals The evolutionary history of Shigella flexneri serotype 6 in Asia

2021 ◽  
Vol 7 (12) ◽  
Author(s):  
Si-Nguyen T. Mai ◽  
Ladaporn Bodhidatta ◽  
Paul Turner ◽  
Sonam Wangchuk ◽  
Tuyen Ha Thanh ◽  
...  
Keyword(s):  
Type Species ◽  
Evolutionary History ◽  
Vaccine Development ◽  
Phylogenetic Analyses ◽  
Shigella Flexneri ◽  
Epidemiological Studies ◽  
Genomic Research ◽  
Phylogenetic Groups ◽  
Content Type ◽  
Link Type

Shigella flexneri serotype 6 is an understudied cause of diarrhoeal diseases in developing countries, and has been proposed as one of the major targets for vaccine development against shigellosis. Despite being named as S. flexneri , Shigella flexneri serotype 6 is phylogenetically distinct from other S. flexneri serotypes and more closely related to S. boydii . This unique phylogenetic relationship and its low sampling frequency have hampered genomic research on this pathogen. Herein, by utilizing whole genome sequencing (WGS) and analyses of Shigella flexneri serotype 6 collected from epidemiological studies (1987–2013) in four Asian countries, we revealed its population structure and evolutionary history in the region. Phylogenetic analyses supported the delineation of Asian Shigella flexneri serotype 6 into two phylogenetic groups (PG-1 and −2). Notably, temporal phylogenetic approaches showed that extant Asian S. flexneri serotype 6 could be traced back to an inferred common ancestor arising in the 18th century. The dominant lineage PG-1 likely emerged in the 1970s, which coincided with the times to most recent common ancestors (tMRCAs) inferred from other major Southeast Asian S. flexneri serotypes. Similar to other S. flexneri serotypes in the same period in Asia, genomic analyses showed that resistance to first-generation antimicrobials was widespread, while resistance to more recent first-line antimicrobials was rare. These data also showed a number of gene inactivation and gene loss events, particularly on genes related to metabolism and synthesis of cellular appendages, emphasizing the continuing role of reductive evolution in the adaptation of the pathogen to an intracellular lifestyle. Together, our findings reveal insights into the genomic evolution of the understudied Shigella flexneri serotype 6, providing a new piece in the puzzle of Shigella epidemiology and evolution.

scholarly journals Investigation of Thermomorphogenesis-Related Genes for a Multi-Silique Trait in Brassica napus by Comparative Transcriptome Analysis

2021 ◽  
Vol 12 ◽  
Author(s):  
Liang Chai ◽  
Jinfang Zhang ◽  
Haojie Li ◽  
Cheng Cui ◽  
Jun Jiang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Higher Plants ◽  
Trna Synthetase ◽  
Isogenic Line ◽  
Transcriptome Data ◽  
Comparative Transcriptome ◽  
Fruit Morphology ◽  
Gene Annotations ◽  
New Perspective ◽  
Lower Temperature

In higher plants, the structure of a flower is precisely controlled by a series of genes. An aberrance flower results in abnormal fruit morphology. Previously, we reported multi-silique rapeseed (Brassica napus) line zws-ms. We identified two associated regions and investigated differentially expressed genes (DEGs); thus, some candidate genes underlying the multi-silique phenotype in warm area Xindu were selected. However, this phenotype was switched off by lower temperature, and the responsive genes, known as thermomorphogenesis-related genes, remained elusive. So, based on that, in this study, we further investigated the transcriptome data from buds of zws-ms and its near-isogenic line zws-217 grown in colder area Ma’erkang, where both lines showed normal siliques only, and the DEGs between them analyzed. We compared the 129 DEGs from Xindu to the 117 ones from Ma’erkang and found that 33 of them represented the same or similar expression trends, whereas the other 96 DEGs showed different expression trends, which were defined as environment-specific. Furthermore, we combined this with the gene annotations and ortholog information and then selected BnaA09g45320D (chaperonin gene CPN10-homologous) and BnaC08g41780D [Seryl-tRNA synthetase gene OVULE ABORTION 7 (OVA7)-homologous] the possible thermomorphogenesis-related genes, which probably switched off the multi-silique under lower temperature. This study paves a way to a new perspective into flower/fruit development in Brassica plants.

What Does DNA Tell Us about Past Connections and the Settlement of Sahul?

2021 ◽  
Author(s):  
Elizabeth Matisoo-Smith ◽  
Anna L. Gosling
Keyword(s):  
Indigenous Peoples ◽  
Large Scale ◽  
Human Impacts ◽  
Genomic Research ◽  
Community Consultation ◽  
Sequencing Technology ◽  
Local Fauna ◽  
Population Replacement ◽  
Scale Population ◽  
Early Human

Archaeological evidence indicates that the continent of Sahul has been continuously settled for almost as long as modern humans have lived outside of Africa. The relative isolation of the continent, and the difficulty involved in getting there, have meant that the populations have not been subject to the large-scale population replacement seen in other parts of the world. Recent advances in DNA sequencing technology, including the ability to sequence full genomes in both ancient and modern populations, have revealed that the genomes of the Indigenous peoples of Australia and New Guinea, and the local fauna, can contribute significantly to our understanding of early human migrations from Africa, human impacts on environments, as well as human evolution more broadly. Given the power of genomic data, it is of the utmost importance that genomic research of ancient and modern samples is conducted ethically, with full community consultation and engagement at all stages.

scholarly journals Two New Aspergillus flavus Reference Genomes Reveal a Large Insertion Potentially Contributing to Isolate Stress Tolerance and Aflatoxin Production

2020 ◽  
Vol 10 (10) ◽  
pp. 3515-3531 ◽  
Author(s):  
Jake C. Fountain ◽  
Josh P. Clevenger ◽  
Brian Nadon ◽  
Ramey C. Youngblood ◽  
Walid Korani ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Phylogenetic Analyses ◽  
Aflatoxin Production ◽  
Genome Project ◽  
Fungal Genome ◽  
Bzip Transcription Factor ◽  
Important Species ◽  
Long Read ◽  
Phylogenomic Analyses ◽  
Reference Genomes

Efforts in genome sequencing in the Aspergillus genus have led to the development of quality reference genomes for several important species including A. nidulans, A. fumigatus, and A. oryzae. However, less progress has been made for A. flavus. As part of the effort of the USDA-ARS Annual Aflatoxin Workshop Fungal Genome Project, the isolate NRRL3357 was sequenced and resulted in a scaffold-level genome released in 2005. Our goal has been biologically driven, focusing on two areas: isolate variation in aflatoxin production and drought stress exacerbating aflatoxin production by A. flavus. Therefore, we developed two reference pseudomolecule genome assemblies derived from chromosome arms for two isolates: AF13, a MAT1-2, highly stress tolerant, and highly aflatoxigenic isolate; and NRRL3357, a MAT1-1, less stress tolerant, and moderate aflatoxin producer in comparison to AF13. Here, we report these two reference-grade assemblies for these isolates through a combination of PacBio long-read sequencing and optical mapping, and coupled them with comparative, functional, and phylogenetic analyses. This analysis resulted in the identification of 153 and 45 unique genes in AF13 and NRRL3357, respectively. We also confirmed the presence of a unique 310 Kb insertion in AF13 containing 60 genes. Analysis of this insertion revealed the presence of a bZIP transcription factor, named atfC, which may contribute to isolate pathogenicity and stress tolerance. Phylogenomic analyses comparing these and other available assemblies also suggest that the species complex of A. flavus is polyphyletic.

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