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Evolutionary Genomics Lab
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A lab that uncovers the evolution of traits from vast amounts of genomic information.
AboutAbout the lab
Finding what makes organisms fascinating in vast amounts of biological information.
The Evolutionary Genomics Lab (Makino Lab) uses large-scale biological information to understand the genetic basis of organisms' traits and aims to elucidate their evolutionary processes.
As data such as genome sequences and gene expression accumulate rapidly with technological innovations like next-generation sequencing, it is becoming increasingly important to find what makes organisms fascinating in this vast amount of information.
In particular, the lab focuses on genes duplicated in the genome and studies their relationship to diseases and ecological characteristics.
In the graduate school, the lab corresponds to the Evolutionary Genomics group of the Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences.
Key terms
- whole-genome duplication
- A special event in which the entire genome is duplicated. When it occurs, every gene has a copy.
- ohnolog
- A duplicated gene that arose through whole-genome duplication.
NewsLab news
A paper by Prof. Makino and colleagues was published in American Journal of Botany
A paper by Prof. Makino and colleagues was published in BMC ecology and evolution
A paper by Prof. Makino and colleagues was published in Proceedings. Biological sciences
A paper by Prof. Makino and colleagues was published in Scientific Reports
A paper by Prof. Makino and colleagues was published in Genome biology and evolution
ResearchResearch themes
The lab investigates the evolution of duplicated genes through comparative genomic analysis and also works on applying the findings to medicine, such as predicting disease-causing genes.
*Illustrative imageIdentifying genes that resist duplication
To test from an evolutionary perspective that ohnologs, which arose through whole-genome duplication, are vulnerable to changes in gene dosage, the lab used comparative genomic analysis to examine gene duplication patterns during evolution in multiple animals. As a result, it found that ohnologs are a group of genes that rarely duplicate during evolution.
*Illustrative imageGene duplication deserts in the human genome
Focusing on the dosage balance of ohnologs, the lab showed that genes adjacent to ohnologs tend to lack copy number variation. Copy number variation is strongly suppressed in genomic regions where ohnologs are densely located, and the lab discovered that gene duplication deserts exist in the human genome.
*Illustrative imageApplying comparative genomic analysis to medicine
The lab has shown that ohnologs include many disease-causing genes. It found that 75% of the Down syndrome-related genes reported so far are ohnologs, and it has also predicted many causative genes for Klinefelter syndrome, Turner syndrome, psychiatric disorders, Alzheimer's disease, and other conditions. Currently, it also focuses on gene-dosage-sensitive genomic regions other than ohnologs, aiming to establish methods for predicting new disease-causing genes from genome analysis.
*Illustrative imageResearch areas by professor
Professor Takashi Makino studies the evolution of duplicated genes, the evolution of genes involved in regeneration, and genome analysis of endangered species and invasive alien species. Associate Professor Toshiharu Ichinose (concurrent appointment) studies Drosophila, neural circuits, behavioral science, and translational profiling, and Lecturer Ryusuke Yokoyama studies the mechanisms of plant cell wall construction using molecular genetics. Assistant Professor Kanako Bessho-Uehara works on molecular genetic analysis of rice domestication, elucidation of signaling pathways involved in plant morphogenesis, and elucidation of the molecular mechanisms of gall formation.
MembersFaculty
The members of the Evolutionary Genomics Lab are faculty and students. The news section of the lab's website lists presentations by doctoral, master's, and fourth-year undergraduate students.
- ProfessorTakashi Makino
- Associate Professor (Concurrent)Toshiharu Ichinose
- Associate Professor (Cross-Appointment)Atsuko Sato
- LecturerRyusuke Yokoyama
- Assistant ProfessorKanako Bessho-Uehara
- Assistant Professor (Concurrent)Manabu Bessho-Uehara
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Report an errorAbout the images
The top and research theme images are illustrative and were not taken at the lab. They are cropped from Wikimedia Commons images. Cropped CC BY-SA images are provided under the same CC BY-SA license as the original (version shown on each line).
- Top image: “Human karyotype with bands and sub-bands” Mikael Häggström, M.D. Author info - Reusing images- Conflicts of interest: None Mikael Häggström, M.D.- The work integrates Public Domain source images by Was A Bee, Kelvin Ma and Michał Komorniczak- Also, a special acknowledgement to everyone involved in the Human Genome Project for generating the source data.edit / CC0 (cropped)
- Identifying genes that resist duplication: “Gene-duplication” Courtesy: National Human Genome Research Institute / Public domain (cropped)
- Gene duplication deserts in the human genome: “Human karyotype diagram showing autosomes and sex chromosomes - NHGRI” National Human Genome Research Institute (NHGRI) / Public domain (cropped)
- Applying comparative genomic analysis to medicine: “Human karyotype (263 17) Karyotype Human, 45,XY t13-14” Doc. RNDr. Josef Reischig, CSc. / CC BY-SA 3.0 (cropped)
- Research areas by professor: “Ceropsylla sideroxyli leaf galls” Yann Kemper / CC0 (cropped)
- Related lab (Microbial Genetics and Evolution Lab): “Micrococcus riboflavin” GK Sims / Public domain (cropped)
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