Article
Biochemistry & Molecular Biology
Kadri Runnel, Kessy Abarenkov, Ovidiu Copot, Vladimir Mikryukov, Urmas Koljalg, Irja Saar, Leho Tedersoo
Summary: This study assessed the efficiency of long-read high throughput sequencing (HTS) for taxonomic identification of fungal specimens and found that PacBio HTS had a higher success rate and lower cost compared to Sanger sequencing. It also enabled the detection of gene polymorphism within the specimens, providing crucial information for species delimitation and population-level studies.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemistry & Molecular Biology
Yuanyuan Cheng, Catherine Grueber, Carolyn J. Hogg, Katherine Belov
Summary: The major histocompatibility complex (MHC) is crucial for the vertebrate immune system, but accurately characterizing MHC genetic diversity in non-model species is technically challenging due to gene duplication and diversification. A new long-read based MHC typing method has been developed to address these challenges and provide better solutions for high accuracy MHC typing in research. This approach allows for population-scale MHC typing in various species, revealing new insights into genetic diversity.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemistry & Molecular Biology
Daniela Polic, Yeserin Yildirim, Kyung Min Lee, Markus Franzen, Marko Mutanen, Roger Vila, Anders Forsman
Summary: This study investigated the genetic structure and its association with geographical and climatic factors in three butterfly species. The results showed differences between species in genetic structure and how it was associated with climate. Geographical proximity played a significant role in genetic structure and evolutionary relationships. Solar radiation and precipitation were associated with genetic structure on a regional scale, but the specific combinations of factors linked to variation within species were unique. The findings highlight the importance of comparative phylogeographical studies in sympatric sister species.
Article
Medical Laboratory Technology
Huijun Li, Xiangyu Zhu, Ying Yang, Wanjun Wang, Aiping Mao, Jiaqi Li, Shilai Bao, Jie Li
Summary: This study evaluated the clinical utility of long-read sequencing (LRS) in carrier screening and genetic diagnosis of congenital adrenal hyperplasia (CAH). The results showed that the LRS method can achieve a precise, comprehensive, and intuitive result in the genetic diagnosis of 21-hydroxylase deficiency (21-OHD), making it a promising tool for clinical application in CAH.
CLINICA CHIMICA ACTA
(2023)
Review
Biochemical Research Methods
Jiadong Lin, Peng Jia, Songbo Wang, Walter Kosters, Kai Ye
Summary: Structural variant (SV) detection is essential for genomic studies, and comparing read-based and assembly-based strategies is important. This study investigated the factors that influence the two strategies and assessed their performance using well-curated SVs. It was found that a majority of SVs could be detected by both strategies, but discordance was mainly caused by complex SVs and inversions.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Genetics & Heredity
Ludmila Kaplun, Greice Krautz-Peterson, Nir Neerman, Christine Stanley, Shane Hussey, Margo Folwick, Ava McGarry, Shirel Weiss, Alexander Kaplun
Summary: Technological advances in Next-Generation Sequencing have improved clinical efficiency of genetic testing by detecting various genetic variants. However, short read sequencing still has limitations that can only be addressed by orthogonal confirmation. Long read sequencing technology compensates for these limitations and improves the detection of variants. At Variantyx, a combined approach using short read WGS-based variant detection with ONT long read sequencing has been developed to provide reliable and efficient clinical genetic testing.
FRONTIERS IN GENETICS
(2023)
Article
Biology
Shanika L. Amarasinghe, Matthew E. Ritchie, Quentin Gouil
Summary: The long-read Tools database provides researchers with an essential resource to keep track of the expanding collection of long-read data analysis tools and choose the most relevant tool for their analysis needs.
Article
Biochemical Research Methods
Mengfei Liu, Linlin Hao, Sien Yang, Xiaohui Wu
Summary: Poly(A) tails play an essential role in regulating gene expression, and there is currently a lack of easy-to-use tools for measuring poly(A) tails in different sequencing protocols. In this study, we developed PolyAtailor, a unified and efficient framework for identifying and analyzing poly(A) tails, and compared its performance with other methods.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Environmental Sciences
Lili Li, Yawen Xiao, Rikke Heidemann Olsen, Chong Wang, Hecheng Meng, Lei Shi
Summary: This study investigates the antibiotic resistome context in Chinese swine farms using metagenomics sequencing and identifies a high abundance and diversity of antibiotic resistance genes. The study suggests that these genes are mainly carried by mobile genetic elements with a high transmission potential. Additionally, the study identifies the bacterial hosts of these genes and explores the genetic contexts of multiple resistant genes. The findings provide valuable insights into the mobile antibiotic resistome in Chinese swine farms.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biochemistry & Molecular Biology
Gabriele Bonetti, William Cozza, Andrea Bernini, Jurgen Kaftalli, Chiara Mareso, Francesca Cristofoli, Maria Chiara Medori, Leonardo Colombo, Salvatore Martella, Giovanni Staurenghi, Anna Paola Salvetti, Benedetto Falsini, Giorgio Placidi, Marcella Attanasio, Grazia Pertile, Mario Bengala, Francesca Bosello, Antonio Petracca, Fabiana D'Esposito, Benedetta Toschi, Paolo Lanzetta, Federico Ricci, Francesco Viola, Giuseppe Marceddu, Matteo Bertelli
Summary: This study investigates the use of PacBio sequencing to detect genetic variants in low-complexity regions, such as the ORF15 exon of RPGR, and interpret their pathogenicity through structural studies. The results show that PacBio sequencing is more accurate in detecting these variants and provides a way to predict their pathogenicity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Pei Xu, Ying Wang, Fengshuo Sun, Rongling Wu, Huilong Du, Yuhong Wang, Libo Jiang, Xiaohua Wu, Xinyi Wu, Liming Yang, Nailin Xing, Yaowen Hu, Baogen Wang, Yunping Huang, Ye Tao, Qiang Gao, Chengzhi Liang, Yanwei Li, Zhongfu Lu, Guojing Li
Summary: The bottle gourd is a horticultural crop with diverse fruit shapes. A high-quality reference genome was utilized to identify 11 quantitative trait loci (QTLs) related to fruit shape, revealing syntenic relationships with known fruit shape genes.
Review
Biochemical Research Methods
Tianjiao Zhang, Jie Zhou, Wentao Gao, Yuran Jia, Yanan Wei, Guohua Wang
Summary: High-quality genome chromosome-scale sequences are crucial for genomics downstream analysis, especially in the construction of haplotype-resolved and complete genomes. The emergence of long-read sequencing technology has greatly improved complex genome assembly. Among various computational methods, uncollapsed assembly is the most accurate and complete way to represent genomes. Genome assembly is closely related to haplotype reconstruction.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Genetics & Heredity
Laura K. Conlin, Erfan Aref-Eshghi, Deborah A. McEldrew, Minjie Luo, Ramakrishnan Rajagopalan
Summary: Long-read sequencing (LRS) technology shows potential in molecular diagnostics, offering significant advantages over short-read sequencing in areas such as structural variation, highly repetitive nonunique regions, long-range haplotype phasing, and base modifications detection. However, further validation is needed for the argument of increased diagnostic yield from LRS, potentially requiring larger cohort studies.
Review
Biochemistry & Molecular Biology
Ricardo De Paoli-Iseppi, Josie Gleeson, Michael B. Clark
Summary: Alternative splicing of RNA is a key mechanism leading to the expression of multiple transcript isoforms from a single gene, increasing the complexity of the transcriptome and proteome. Long-read sequencing technologies can address the limitations of short-read sequencing in resolving complex isoforms and distinguish changes that may impact RNA regulation or protein function. Integration of long-read sequencing with other technologies allows for detailed profiling of alternative splicing at the isoform level and determination of the impact of genetic variation on isoform expression.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Obstetrics & Gynecology
Yanfei Cheng, Qian Yu, Minyue Ma, Hui Wang, Shuang Tian, Wenling Zhang, Jinning Zhang, Yifan Liu, Qi Yang, Xiao Pan, Hongbin Liang, Li Wang, Don Leigh, David S. Cram, Yuanqing Yao
Summary: This study aimed to utilize long-read, third-generation sequencing as part of a general strategy for structural rearrangement and monogenic disease embryo testing. The results demonstrated successful achievement of high definition chromosome breakpoints in 15 couples undergoing PGT-SR, and identification of tightly linked informative markers for two couples undergoing PGT-M. The selection of informative markers around the target is crucial for couples considering clinical PGT.
FERTILITY AND STERILITY
(2021)
Article
Fisheries
Oscar Aramburu, Andres Blanco, Carmen Bouza, Paulino Martinez
Summary: Disease resilience is crucial for turbot aquaculture. Researchers have compiled genomic information to construct an atlas of candidate genes and genomic regions involved in pathogen resistance. This information can help develop effective breeding strategies to enhance turbot's resistance against pathogens.
Article
Environmental Sciences
Heidi Samantha Moraes Utsunomiya, Joao Victor Cassiel Ferraz, Gabriel Hiroshi Fujiwara, Davi Marques Gutierres, Isabela Ferreira Fernandes, Bruno Serra de Lacerda Valverde, Classius de Oliveira, Lilian Franco-Belussi, Marisa Narciso Fernandes, Cleoni dos Santos Carvalho
Summary: This study evaluated the effects of exposure to water from different sites of the Sorocaba River on genetic damage, oxidative stress, neurotoxicity, and energy metabolism in bullfrog tadpoles. The results indicated that exposure to water from different sites caused changes in various indicators, which may have effects on the development of tadpoles.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Natalia Lima Lira, Sandro Tonello, Roberto Laridondo Lui, Josiane Baccarin Traldi, Heleno Brandao, Claudio Oliveira, Daniel Rodrigues Blanco
Summary: Studies on fish eggs and larvae have been conducted since the late 19th century and have provided important information for understanding fish fauna and environmental inventory. The use of molecular identification techniques, particularly DNA barcoding, has greatly improved taxonomic precision in studying ichthyoplankton. Recent research shows a significant increase in the use of DNA barcoding, with high accuracy compared to traditional taxonomic identification methods.
MOLECULAR BIOLOGY REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Roberto de la Herran, Miguel Hermida, Juan Andres Rubiolo, Jessica Gomez-Garrido, Fernando Cruz, Francisca Robles, Rafael Navajas-Perez, Andres Blanco, Paula Rodriguez Villamayor, Dorinda Torres, Pablo Sanchez-Quinteiro, Daniel Ramirez, Maria Esther Rodriguez, Alberto Arias-Perez, Ismael Cross, Neil Duncan, Teresa Martinez-Pena, Ana Riaza, Adrian Millan, M. Cristina De Rosa, Davide Pirolli, Marta Gut, Carmen Bouza, Diego Robledo, Laureana Rebordinos, Tyler Alioto, Carmelo Ruiz-Rejon, Paulino Martinez
Summary: This study reports a novel molecular sexing tool, which identified 41 single nucleotide polymorphism variants in the follicle stimulating hormone receptor (fshr) gene through whole genome resequencing of six males and six females, and validated the sex association. The study also found differential expression of the fshr gene between male and female gonads at an early stage of gonadal differentiation, suggesting a mechanism hampering the action of the follicle stimulating hormone driving the undifferentiated gonad toward testis.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Veterinary Sciences
Lorena Elizabeth Chalco-Torres, Ana Elizabeth Guerrero-Lopez, Robert Gustavo Sanchez-Prado, Jhonny Edgar Perez, Claudio Oliveira, Juan Antonio Gomez, Fernando Lenin-Aguilar, Mauro Nirchio-Tursellino
Summary: The bond between dogs and humans is a complex and multidimensional phenomenon that poses a public health problem. A study conducted in Apizaco, Tlaxcala, Mexico found that there is a problem with handling dog excreta, which can lead to zoonosis. Dogs without guardians were more likely to be parasitized by Toxocara canis and Ancylostoma caninum, while dogs with guardians and access to public roads were more likely to be infected with T. canis and A. caninum. It highlights the need for a comprehensive public health program promoting responsible dog ownership.
REVISTA CIENTIFICA-FACULTAD DE CIENCIAS VETERINARIAS
(2023)
Article
Zoology
George M. T. Mattox, Ralf Britz, Camila S. Souza, Andre L. S. Casas, Flavio C. T. Lima, Claudio Oliveira
Summary: Two new species of the genus Priocharax are described from the Rio Jurua system in Brazil, bringing the total known species diversity to seven. These species can be distinguished from each other and from their congeners by a combination of morphological and genetic characteristics. Unfortunately, the localities where these species were found are facing significant degradation, posing a threat to their conservation status.
CANADIAN JOURNAL OF ZOOLOGY
(2023)
Article
Fisheries
Jefferson L. Crispim-Rodrigues, Maxwell J. Bernt, Brandon T. Waltz, Gabriel S. C. Silva, Ricardo C. Benine, Claudio Oliveira, Raphael Covain, Fabio F. Roxo
Summary: During a recent collection expedition in the Rio Negro, Brazil, eight individuals of an unknown species were discovered, which were classified as a new species in the genus Rhadinoloricaria based on their combination of characteristics, including elongated papillae on the lower lip and unbranched barbelets on the margin of the lower lip. Morphological and phylogenetic analyses, along with osteological computed tomography scans, confirmed that these specimens represent a new species of Rhadinoloricaria.
JOURNAL OF FISH BIOLOGY
(2023)
Article
Veterinary Sciences
Lorena Elizabeth Chalco-Torres, Ana Elizabeth Guerrero-Lopez, Robert Gustavo Sanchez-Prado, Jhonny Edgar Perez, Claudio Oliveira, Juan Antonio Gomez, Fernando Lenin-Aguilar, Mauro Nirchio-Tursellino
Summary: This study presented a case of a dog infected with Parvovirus and Ehrlichia canis, confirmed by immunochromatography tests and PCR. The detection of E. ewingii suggests its presence outside its natural distribution range and raises the possibility of colonization in local vectors. Molecular studies on local ticks are needed to investigate if this is an isolated case or if there is local transmission of E. ewingii.
REVISTA CIENTIFICA-FACULTAD DE CIENCIAS VETERINARIAS
(2023)
Article
Zoology
Camila S. Souza, George M. T. Mattox, George Vita, Luz E. Ochoa, Bruno F. Melo, Claudio Oliveira
Summary: Phenacogaster is a genus in South America that has the highest species richness in the subfamily Characinae. This study describes a previously undescribed species within the genus, based on molecular phylogeny and genetic diversity analyses of 73 specimens. The new species is found in various river basins and can be distinguished by specific morphological traits.
Article
Zoology
Henrique R. Varella, Sven O. Kullander, Naercio A. Menezes, Claudio Oliveira, Hernan Lopez-Fernandez
Summary: This study proposes a new classification for pike cichlids, elevating the clade to the rank of subtribe (Crenicichlina) and redefining the genus Crenicichla. Teleocichla is maintained as a valid genus, while four new genera are proposed. The results also suggest that resource partitioning in environments with fast-flowing water and rocky beds may have played a role in the evolution of pike cichlids.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2023)
Review
Agriculture, Dairy & Animal Science
Luis A. Quintela, Juan J. Becerra, Ana I. Pena, Uxia Yanez, Paula R. Villamayor, Pablo Sanchez-Quinteiro, Paulino Martinez, Pedro G. Herradon
Summary: The commercial use of AI in rabbit farming is relatively recent and has been evolving. This review article highlights two important milestones: the introduction of biostimulation and the addition of GnRH analogues to induce ovulation. Biostimulation practically eliminates the use of hormones to synchronize heat with AI, while the vaginal administration of GnRH offers advantages in terms of health, animal welfare, and workforce. It has been approved by the EMA and might become the most widely used method.
WORLD RABBIT SCIENCE
(2023)
Article
Genetics & Heredity
Mauro Nirchio Tursellino, Marcelo de Bello Cioffi, Francisco de Menezes Cavalcante Sassi, Geize Aparecida Deon, Claudio Oliveira, Mariana Kuranaka, Jonathan Valdiviezo-Rivera, Victor Hugo Gonzalez, Anna Rita Rossi
Summary: In this study, cytogenetic investigation on the Transancistrus santarosensis fish reveals a karyotype of 2n = 54 chromosomes, indicating an early stage of differentiation of the ZZ/ZW sex chromosome system. The fish has also accumulated heterochromatin and shows non-syntenic ribosomal genes localization, characteristics considered derived in the family.
Article
Zoology
George M. T. Mattox, Mauricio Cetra, Camila S. Souza, Osvaldo T. Oyakawa, Rodrigo M. M. Bento, Claudio Oliveira
Summary: Spintherobolus papilliferus is an endangered characid endemic to the Atlantic Rainforest. It has been found in the upper rio Tiete basin around Sao Paulo city and a coastal stream in Bertioga, Sao Paulo State. A new distributional record of S. papilliferus was discovered in the rio Ribeira de Iguape basin in Juquitiba, Sao Paulo State. Morphometric analysis revealed a significant difference in body shape and other features between this population and the other two populations. DNA-barcoding confirmed that the rio Ribeira de Iguape population belongs to S. papilliferus.
NEOTROPICAL ICHTHYOLOGY
(2023)
Article
Fisheries
Pauline Kamermans, Ainhoa Blanco, Pim van Dalen, Marc Engelsma, Nienke Bakker, Pascalle Jacobs, Marco Dubbeldam, Ines M. Sambade, Manuel Vera, Paulino Martinez
Summary: This study collected infected flat oysters (Ostrea edulis) with the pathogenic parasite Bonamia ostreae in the Dutch Delta area and successfully selected individuals with Bonamia resistance to produce Bonamia-free larvae. The results showed that it is possible to screen for individuals with resistance to Bonamia during the hatchery production of flat oysters. Evaluation: 8 points.
AQUATIC LIVING RESOURCES
(2023)
Article
Multidisciplinary Sciences
Rodrigo Zieri, Lilian Franco-Belussi, Classius De Oliveira
Summary: In this study, the researchers investigated the short-term effects of alpha-MSH on melanophores, melanocytes, and melanomacrophages in the South American frog Physalaemus nattereri. They found that these melanin-containing cells increased their pigmentation after receiving the hormone, but the response varied among different organs.
ANAIS DA ACADEMIA BRASILEIRA DE CIENCIAS
(2023)
Article
Fisheries
Miguel Petrere Jr, Davi Butturi-Gomes
Summary: This short communication aims to raise awareness about the misuse of confidence intervals in Ecology and Fisheries statistical models that ignore the lack of independence.
FISHERIES RESEARCH
(2024)
Article
Fisheries
Peter-John F. Hulson, Benjamin C. Williams
Summary: This study evaluates the impact of considering ageing error and growth variability on the determination of input sample size (ISS) in statistical catch-at-age assessment models. The results show that including these sources of uncertainty decreases the ISS determined through bootstrap methods. This indicates that there is more variability in age composition and conditional age-at-length data than previously accounted for. Including these sources of uncertainty improves the estimation of ISS and subsequently improves the quality of stock assessment models.
FISHERIES RESEARCH
(2024)
Article
Fisheries
Jason M. Cope
Summary: Fishery resource assessment is a complex and challenging task, but with the use of different analysis methods and tools, effective management guidance can be provided even with limited data and resources.
FISHERIES RESEARCH
(2024)
Article
Fisheries
Regina L. Cunha, Joana I. Robalo, Sara M. Francisco, Ines Farias, Rita Castilho, Ivone Figueiredo
Summary: Recent advances in genomics have greatly contributed to the assessment of fish stocks by providing precise identification of genetic boundaries. This study used a genotyping-by-sequencing approach to reveal the existence of an additional genetic cluster of blackspot seabream in the northeast Atlantic, which was not previously identified. Factors such as ocean circulation patterns and local upwelling may play a role in the genetic differentiation observed in this study.
FISHERIES RESEARCH
(2024)
Article
Fisheries
Huihua Lee, Mark N. Maunder, Kevin R. Piner
Summary: Estimating growth is important for fish population assessment. Integrated assessment models and the influence of misfitting size composition data have renewed interest in how growth is modeled. The available data types control how the length-at-age relationship is estimated. Estimating length-at-age is complex due to multiple sources of biological variability and difficulties in obtaining representative samples.
FISHERIES RESEARCH
(2024)
Article
Fisheries
A. Ladino, I. Perez-Arjona, V. Espinosa, M. Chillaron, V. Vidal, L. M. Godinho, G. Moreno, G. Boyra
Summary: This study examines the acoustic properties of skipjack tuna and Atlantic mackerel, both bladderless pelagic fish species, and explains the significant differences observed. The research shows that the differences in material properties of their tissues predict a more than 10 dB greater reduced target strength in skipjack compared to mackerel at certain frequencies.
FISHERIES RESEARCH
(2024)
Article
Fisheries
Nelly Pena-Cutimbo, Cristel Cordero-Maldonado, Clara Ortiz-Alvarez, Joanna Alfaro-Shigueto, Jeffrey C. Mangel
Summary: Bycatch is a global problem for marine megafauna. This study assessed the bycatch interactions of the Peruvian artisanal purse-seine fishery in 2019 and found that all taxa groups were affected by bycatch. Dusky dolphins, guanay cormorants, and eagle rays were the most frequently reported bycatch species.
FISHERIES RESEARCH
(2024)
Article
Fisheries
Jen-Ming Liu, Po-Yuk So
Summary: The set-net fishery is an environmentally friendly fishery posing little risk to the marine ecosystem. This study identified ocean temperature, sea surface factors, and climatic factors as the main factors affecting the installation of set-nets.
FISHERIES RESEARCH
(2024)
Article
Fisheries
Josie L. Palmer, Carina Armstrong, Hasan D. Akbora, Damla Beton, Cigdem Caglar, Brendan J. Godley, Kristian Metcalfe, Meryem Ozkan, Robin T. E. Snape, Annette C. Broderick
Summary: Small-scale fisheries are vital for global food security and cultural heritage, but the lack of information hampers effective management and mitigation of ecological impacts. This study provides the first comprehensive overview of the small-scale fishery fleet in Northern Cyprus. The fleet operates mainly over the continental shelf, using static and demersal gear types, and catches a diverse range of species, some of which are threatened. The findings can be used to improve fisheries management and conservation measures.
FISHERIES RESEARCH
(2024)
