Article
Clinical Neurology
Sanjiban Chakrabarty, Periyasamy Govindaraj, Bindu Parayil Sankaran, Madhu Nagappa, Shama Prasada Kabekkodu, Pradyumna Jayaram, Sandeep Mallya, Sekar Deepha, J. N. Jessiena Ponmalar, Hanumanthapura R. Arivinda, Angamuthu Kanikannan Meena, Rajan Kumar Jha, Sanjib Sinha, Narayanappa Gayathri, Arun B. Taly, Kumarasamy Thangaraj, Kapaettu Satyamoorthy
Summary: The study conducted comprehensive clinical, pathological, biochemical, and genetic analysis on 11 patients with MELAS syndrome, revealing the classical pathogenic mutation m.3243A > G and mutations in nuclear genes associated with MELAS clinical manifestations.
JOURNAL OF NEUROLOGY
(2021)
Article
Multidisciplinary Sciences
Charley Xia, Sarah J. Pickett, David C. M. Liewald, Alexander Weiss, Gavin Hudson, W. David Hill
Summary: Neuroticism is a heritable trait influenced by mitochondrial DNA, and associations between mitochondrial haplogroups and genetic variation have been found. The study reveals the links between neuroticism and various facets, as well as the relationships between mitochondrial genetic variation and overall health.
NATURE COMMUNICATIONS
(2023)
Review
Plant Sciences
Lu Shi, Jing Su, Myeong-Je Cho, Hao Song, Xiaoou Dong, Ying Liang, Zhiyong Zhang
Summary: Gene expression plays a crucial role in crop plant regulation. Genome editing of plant promoters offers the potential to modify gene expression patterns and create favorable traits. This can be done by precise generation of nucleotide sequences or by generating random mutations in the promoter region to select elite alleles based on phenotypic effects.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Yanlei Yue, Jiawen Li, Xuegang Sun, Zhen Li, Bingjun Jiang
Summary: By analyzing the polymorphisms of chloroplasts and mitochondria in 2580 soybean accessions, it was found that the chloroplast genome is more variable than the mitochondrial genome. There were 44 chloroplast haplotypes and 30 mitochondrial haplotypes. The distribution of these haplotypes was extremely uneven, with the top two haplotypes accounting for a large proportion of cultivated soybean accessions. Wild soybeans exhibited more diversity in organelle genomes, but only a small percentage of cultivated soybeans shared cytoplasm with wild soybeans. Evaluating the impact of cytoplasm on soybean performance is important for breeding.
Article
Oncology
Giulia Peduzzi, Manuel Gentiluomo, Francesca Tavano, Paolo Giorgio Arcidiacono, Stefano Ermini, Pavel Vodicka, Ugo Boggi, Giulia Martina Cavestro, Gabriele Capurso, Luca Morelli, Anna Caterina Milanetto, Raffaele Pezzilli, Rita T. Lawlor, Silvia Carrara, Martin Lovecek, Pavel Souc, Feng Guo, Thilo Hackert, Faik G. Uzunoglu, Maria Gazouli, Andrea Parniczky, Juozas Kupcinskas, Maarten F. Bijlsma, Bas Bueno-de-Mesquita, Roel Vermeulen, Casper H. J. van Eijck, Krzysztof Jamroziak, Renata Talar-Wojnarowska, William Greenhalf, Domenica Gioffreda, Maria C. Petrone, Stefano Landi, Livia Archibugi, Marta Puzzono, Niccola Funel, Cosimo Sperti, Maria L. Piredda, Beatrice Mohelnikova-Duchonova, Ye Lu, Viktor Hlavac, Xin Gao, Martin Schneider, Jakob R. Izbicki, George Theodoropoulos, Stefania Bunduc, Edita Kreivenaite, Olivier R. Busch, Ewa Malecka-Panas, Eithne Costello, Francesco Perri, Sabrina Gloria Giulia Testoni, Giuseppe Vanella, Claudio Pasquali, Martin Oliverius, Hermann Brenner, Martin Loos, Mara Gotz, Konstantinos Georgiou, Alint Eross, Evaristo Maiello, Andrea Szentesi, Francesca Bazzocchi, Daniela Basso, John P. Neoptolemos, P. Eter Hegyi, Vytautas Kiudelis, Federico Canzian, Daniele Campa
Summary: Mitochondrial metabolism has been linked to PDAC risk, with genetic variability potentially playing a role. However, this study did not find significant associations between mtSNPs or n-mtSNPs and PDAC risk. Gene-level analysis highlighted three genes (TERT, SUGCT, and SURF1) that showed some association with PDAC, but not at a statistically significant level.
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2021)
Review
Plant Sciences
Martina Ghidoli, Elena Ponzoni, Fabrizio Araniti, Daniela Miglio, Roberto Pilu
Summary: In recent years, there has been a growing interest in novel crops due to environmental issues in agriculture. One such crop, Camelina sativa (L.) Crantz, is attracting attention for its desirable features. It can grow in marginal lands with little inputs and is resistant to important pathogens. This review summarizes the main works on genetic improvement of Camelina, particularly in terms of yield, seed oil content and quality, and reduction in anti-nutritional substances.
Review
Biochemistry & Molecular Biology
Amir Hameed, Pawel Poznanski, Anna Nadolska-Orczyk, Waclaw Orczyk
Summary: Global climate change and the need for genetically modified crops require a comprehensive genetic evaluation. However, the complexity of polyploid genomes in food crops makes it challenging to identify candidate genes with confirmed heritability. While genome-wide association studies have been successful in identifying genetic variants associated with complex traits, limitations such as incomplete detection of structural variants and genetic heterogeneity result in a biased estimation of agronomically complex traits. The graph pangenome approach resolves these limitations and provides important insights for crop improvement through genome-linked fast breeding.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Liying Xue, Jesse D. Moreira, Karan K. Smith, Jessica L. Fetterman
Summary: Nuclear-mitochondrial DNA segments (NUMTs) are fragments of mtDNA that have been inserted into the nuclear genome. They can contaminate mtDNA sequencing results and introduce false positive variants. This review discusses their prevalence, mechanisms of de novo insertion, and approaches for minimizing contamination. Both wet lab-based and computational methods can be used to filter NUMTs, and multiple approaches should be applied for effective identification.
Article
Agronomy
Yong Huang, Huirong Dong, Meiqi Shang, Kejian Wang
Summary: With the increasing human population and deteriorating environment, there is a need to breed environmentally friendly and resource-conserving rice cultivars for sustainable agricultural development and food security. CRISPR/Cas technology allows efficient genome modification, promising higher yield, improved quality, and resistance in rice plants.
Article
Plant Sciences
Mengting Wang, Wenhui Yu, Jiapeng Yang, Zhenyu Hou, Chao Li, Zhitao Niu, Benhou Zhang, Qingyun Xue, Wei Liu, Xiaoyu Ding
Summary: Our study focuses on the Dendrobium orchids, which have large morphological divergence and difficulties in species taxonomy. We assembled the complete mitogenomes of two Dendrobium species and compared them with other orchids. The results reveal extensive variations in repetitive and chloroplast-derived sequences in Dendrobium mitogenomes, and the intergenic content has undergone expansion during evolution. We also sequenced the mitogenomes of 26 Dendrobium species and reconstructed their phylogenetic relationships based on mitochondrial and plastid data. The mitochondrial phylogeny shows partial characteristics of the plastid phylogeny and provides new insights into the phylogenetic relationships of Dendrobium species.
Review
Fisheries
Zituo Yang, Yepin Yu, Yi Xuan Tay, Gen Hua Yue
Summary: Selective breeding has significantly increased aquaculture production, and the use of CRISPR/Cas9 technology for gene/genome editing is faster and more precise, rapidly emerging as a tool for genetic improvement in over 20 aquaculture species.
REVIEWS IN AQUACULTURE
(2022)
Article
Biochemistry & Molecular Biology
Shi-Jie Ke, Ding-Kun Liu, Xiong-De Tu, Xin He, Meng-Meng Zhang, Meng-Jia Zhu, Di-Yang Zhang, Cui-Li Zhang, Si-Ren Lan, Zhong-Jian Liu
Summary: In this study, the complete mitochondrial genome of Apostasia shenzhenica was sequenced and assembled, revealing its genetic diversity and phylogenetic relationships among monocotyledons. The mitochondrial genome was 672,872 bp in length and contained 36 protein-coding genes, 16 tRNAs, two rRNAs, and two copies of nad4L. Repeat sequence analysis showed the presence of medium and small repeats, accounting for 1.28% of the mitogenome sequence. Selection pressure analysis indicated high conservation of the mitogenome in related species. RNA editing identified 416 sites in the protein-coding region. Additionally, 44 chloroplast genomic DNA fragments were transferred to the mitogenome, with five plastid-derived genes remaining intact. Phylogenetic analysis showed well-determined evolution and classification of most monocots. These findings contribute to the genetic resources of orchids and provide valuable insights into the taxonomy and molecular evolution of monocots.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Melinda R. Grosser, Samantha K. Sites, Mayara M. Murata, Yolanda Lopez, Karen C. Chamusco, Kyra Love Harriage, Jude W. Grosser, James H. Graham, Fred G. Gmitter, Christine D. Chase
Summary: Plant genomes contain nuclear, plastid, and mitochondrial components which have different inheritance and evolutionary patterns. Genetic markers from these three genomes can be used to study inheritance, genetic relationships, and phenotypic contributions. Developing mitochondrial markers is challenging due to their high variability in size, gene order, and non-coding sequences, as well as their conservation in protein-coding sequences. PCR amplification of introns using conserved flanking exons is an effective method for developing polymorphic nuclear genome markers.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biology
Darren J. Walsh, David J. Bernard, Faith Pangilinan, Madison Esposito, Denise Harold, Anne Parle-McDermott, Lawrence C. Brody
Summary: The analysis of somatic variation in the mitochondrial genome requires deep sequencing of mitochondrial DNA. This study presents a PCR-free method for ultra-deep sequencing coverage of the mitochondrial genome, using isolated intact mitochondria and a sequence-independent approach. The method avoids false-heteroplasmy calls caused by long-range PCR amplification and enables researchers to identify low frequency heteroplasmy without introducing PCR biases or NUMT contamination.
COMMUNICATIONS BIOLOGY
(2022)
Article
Plant Sciences
Jeffrey P. Mower, Lilly Hanley, Kirsten Wolff, Natalia Pabon-Mora, Favio Gonzalez
Summary: Aragoa, a genus of North Andean plants, is closely related to Littorella and Plantago within the Plantagineae family. Analysis of mitochondrial genomes revealed the sister relationship between Aragoa and Littorella + Plantago. However, conflicting results were found in the placement of P. nubicola within the Plantago genus based on mitochondrial and nuclear data. Extensive substitution rate variation among lineages hindered the resolution of phylogenetic relationships using mitochondrial data.
