scholarly journals How to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research

2014 ◽  
Vol 39 (3) ◽  
pp. 400-411 ◽  
Author(s):  
STEPHEN L. CAMERON
2021 ◽  
Author(s):  
Yu Zhang ◽  
Xizhi Luo ◽  
Shiyu Chen

Abstract We re-annotated repeats sequence of 459 plant genomes and release a new resource of plant repeats: PlantRep (http://www.plantrep.cn/). We compared the structural and evolutionary characteristics of repeat sequences in different plant taxonomic group. The contribution of repeat sequences to the genes was examined systematically. PlantRep sheds lights of evolution of plant repeats and provides a free-resource for deep annotation of genome and comparative genomics research of repeat elements in plants.


2005 ◽  
Vol 23 (2) ◽  
pp. 246-256 ◽  
Author(s):  
Simon N. Twigger ◽  
Dean Pasko ◽  
Jeff Nie ◽  
Mary Shimoyama ◽  
Susan Bromberg ◽  
...  

The broad goal of physiological genomics research is to link genes to their functions using appropriate experimental and computational techniques. Modern genomics experiments enable the generation of vast quantities of data, and interpretation of this data requires the integration of information derived from many diverse sources. Computational biology and bioinformatics offer the ability to manage and channel this information torrent. The Rat Genome Database (RGD; http://rgd.mcw.edu ) has developed computational tools and strategies specifically supporting the goal of linking genes to their functional roles in rat and, using comparative genomics, to human and mouse. We present an overview of the database with a focus on these unique computational tools and describe strategies for the use of these resources in the area of physiological genomics.


2019 ◽  
Vol 70 (22) ◽  
pp. 6539-6547 ◽  
Author(s):  
Xiaohan Yang ◽  
Degao Liu ◽  
Timothy J Tschaplinski ◽  
Gerald A Tuskan

Abstract Crassulacean acid metabolism (CAM) photosynthesis is an important biological innovation enabling plant adaptation to hot and dry environments. CAM plants feature high water-use efficiency, with potential for sustainable crop production under water-limited conditions. A deep understanding of CAM-related gene function and molecular evolution of CAM plants is critical for exploiting the potential of engineering CAM into C3 crops to enhance crop production on semi-arid or marginal agricultural lands. With the newly emerging genomics resources for multiple CAM species, progress has been made in comparative genomics studies on the molecular basis and subsequently on the evolution of CAM. Here, recent advances in CAM comparative genomics research in constitutive and facultative CAM plants are reviewed, with a focus on the analyses of DNA/protein sequences and gene expression to provide new insights into the path and driving force of CAM evolution and to identify candidate genes involved in CAM-related biological processes. Potential applications of new computational and experimental technologies (e.g. CRISPR/Cas-mediated genome-editing technology) to the comparative and evolutionary genomics research on CAM plants are offered.


2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Jenny Makkonen ◽  
Arto Vesterbacka ◽  
Frank Martin ◽  
Japo Jussila ◽  
Javier Diéguez-Uribeondo ◽  
...  

2006 ◽  
Vol 361 (1467) ◽  
pp. 403-412 ◽  
Author(s):  
Kenneth H Wolfe

Yeasts provide a powerful model system for comparative genomics research. The availability of multiple complete genome sequences from different fungal groups—currently 18 hemiascomycetes, 8 euascomycetes and 4 basidiomycetes—enables us to gain a broad perspective on genome evolution. The sequenced genomes span a continuum of divergence levels ranging from multiple individuals within a species to species pairs with low levels of protein sequence identity and no conservation of gene order. One of the most interesting emerging areas is the growing number of events such as gene losses, gene displacements and gene relocations that can be attributed to the action of natural selection.


2016 ◽  
Vol 16 (1) ◽  
pp. 71-75 ◽  
Author(s):  
M. S. Makarenko ◽  
A. V. Usatov ◽  
N. V. Markin ◽  
K. V. Azarin ◽  
O. F. Gorbachenko ◽  
...  

BMC Genomics ◽  
2009 ◽  
Vol 10 (1) ◽  
pp. 148 ◽  
Author(s):  
Wonhoon Lee ◽  
Jongsun Park ◽  
Jaeyoung Choi ◽  
Kyongyong Jung ◽  
Bongsoo Park ◽  
...  

2017 ◽  
Vol 8 ◽  
Author(s):  
Sangrong Sun ◽  
Jinpeng Wang ◽  
Jigao Yu ◽  
Fanbo Meng ◽  
Ruiyan Xia ◽  
...  

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