2015 年 2 月 28 日
井上 潤 

- Current approaches of othorlogy assignment can be classified into
graph-based and tree-based methods (Trachana et al. 2011).

- The graph-based methods cluster
orthologs based on sequence similarity of proteins.

- The tree-based methods reconcile
the protein familhy tree with a species tree and infer orthology.

- The annotation of newly sequenced genome, comparative and functional genomics, and phylogenetics depend on
reliable descriptions of the evolutionary relationships of protein families.

- big protein families require
an increased resolution of rothologous-paralogous relationships within the same taxonomic level (Trachana et al. 2011).

- The comprehensive detection of gene loss, which should be supported by an elaborate orthology/paralogy assessment, requires different approaches (Kuraku and Kuratani, 2012).

taxon sampling が影響を及ぼす
- The phylogenetic distribution of the compared species influences
the orthology/paralogy assignment.

- Analyzing the orthogroups at different taxonimc levels sheds light on
the evolutionary history of the family (Trachana et al. 2011);

It would be intriguing to examine
whether gene losses were more frequent during the advent of mammals
during other periods of the vertebrate evolution (Kuraku and Kuratani, 2011).

- These fates may occur
through either neutral loss, selection, or via random mechanism (e.g., subfunctionalization/ DDC model) (Edger and Pires, 2009).


遺伝子のペアが syntenic であるとは.
A pair of genes that are syntenic are on the same chromosome in one species (Braasch and Postlethwait, 2012).

Conserved synteny とは
Conserved syntenies are situations in which a pair of genes that are syntenic in one species have orthologs that are sytenic in another species (B&P 12).

DCS block are defined
as runs of genes in the non-duplicated species that are found on two other chromosomes in the species that underwern a WGD (Howe et al. 2013, SI).

ヒト 16 番染色体に乗っている遺伝子.
Genes on human chromosome 16 (B&P 12)

- The content of other human chromosomes appears to have involved more rearrangements than Hsa16 (B&P 12),

Hsa17 の遺伝的内容は,Dre3上にある 7 染色体断片の重複を占める
- the genetic content on Hsa17 occupies duplicates of seven chromosome segments on Dre3 (B&P 12)

ohnologons は Dre3 にある
- Zebrafish ohnologons for Hsa17 are mainly on Dre3 (B&P 12)
- about half of the human orthologs of Dre12 genes are located on Hsa17 (B&P 12)

Dre12 のヒトオーソログは Hsa16 上に散らばっている
Human orthologs of Dre12 are widely scattered on Hsa 16 (B&P 12)

Synteny に乗っている遺伝子を判定
Kasahara et al. (2007) identified 6994 out of 20,352 human protein coding genes, which were located in a block of doubly conserved synteny (DCS) derived from the 3R-WGD.

the gene distribution and genome structure of northern pike (Rondeau et al .2014)

the algorithm plots
orthologs and paralogs along chromosomes (B&P 12).

human の染色体断片が,zebrafish の paralogon 内部に ohnologs を持つ
segments of human chromosomes have
orthologs and coorthologs in paralogons on two zenbrafish chromosomes (B&P 12).

配列類似性を組み合わせた Synteny 情報によって WGD で生じた ohnolog を判定
Synteny information combined with sequnece similarity identifies
accurately the paralogs that have arisen through WGD (Byrne and Wolfe, 2005).

They (chromonome) enable
large-scale conserved synteny analyses that inform orthology detection (Braach et al, 2014).

Chromosome 16 and 19 in zebrafish are syntenic with the same regions of human chromosomes, 1, 7, 8 and 19 (Howe et al. 2013).

Comparisons in the other direction, zebrafish to human (B&P 12),


gene arramgenets
- many gene arramgenets have been conserved from a common ancestor (Amemiya et al. 2013).
- Other gene arrangements can be seen in this example (Iberra-Laclette et al, 2013).
- gene order in these plots reflects gene arrangements in the human genome, not the fish genome (Braasch and Postlethwait, 2012).

- While conservation of gene order is limited to smaller syntenic blocks,
the wilder conservation of genome organization implies the northern pike exibits a suitable approximation of a non-duplicated genome (Rondeau et al. 2014).

- Although gene order is highly variable, chromosomal synteny remains
high between the northern pike and the Neoteleostei representatives (Rondeau et al. 2014).

Materials and Methods
WGD 前に分岐した種
- a related yeast species that diverged before the duplication (Kellis et al. 2004).

- the Esociformes diverged from the salmonid lineage prior to the WGD, supporting the use of northern pike as pre-duplication outgroup (Rondeau et al. 2014).

- a representative pre-duplication genome (Rondeau et al., 2014).
- a non-dupicated Protacanthopterygiian genome (Rondeau et al. 2014).

- 21,553 Human genes were subjected to
a comparative genomic analysis with other animal genomes.

- Automated genome-wide phylogenetic screening was implemented
based on this pilot analysis (Kuraku and Kuratani, 2012).

An automated procedure was developed to
single-copy orthologous genes from complete fungal genomes using Markov Clustering Algorithm (Aguileta et al. 2008).

Sensitivity analysis
In order to analyze the performance of our automated pipeline,
we assessed the quality of orthogroups at the resolution for the number of identified 3R/ 1to1 categories using 130 manually curated orthogroups in Sato et al. (2009).

We constructed a database, Genome Composition Database (Kryukov et al. 2012).

- BlastP searches were run toward peptide sequences for both the in-group and the outgroup (Kuraku and Kuratani, 2011).

Orthogroup の判定
系統解析によって ohnolog が判定された
Systematic analysis of the gene phylogenies described above successfully identifies
the duplicated genes derived from the 3R-WGD.

Duplicated daughter clades derived from the 3R-WGD were identified in
1040 out of 7019 orthogroups.

Synteny によって確認
the identifications for 910 orthogroups were ascertained
based on previously published information related to doubly conserved synteny in the medaka genome.

VGD 由来のより遠縁のパラログ.
are more distantly related paralogs resulting from the VGDs.

四足類と真骨類の間で XXX orthogroups を見いだした.
we identified a total of xxx orthogroups between tetrapods and teleosts, corresponding to all human and medaka genes examined.

xxx 遺伝子がオーソログを持っていた.
As a result, 15,472 of 21,553 human genes were found to have orthologs in teleost genomes (Table 1),

xxx 遺伝子ではオーソログを判定できなかった.
while no clear orthologs were identified for the remaining 6091 genes.

・xxxx orthogroups のうち
Among the 7685 orthogroups,

we counted
the number of 3R-WGD-derived genes.

-- の頻度を数える.その結果を〜と比較する.
Frequencies of all possible one to ten oligonucleotide were counted for each genome,
and these observed values were compared with expected values (Kryukov et al. 2012).

xxx はダブっていた.
666 were duplicated
specifically between query sequence and ortholog.

Human をオーソログとしない orthogroup を XXX に加えた.
We added Medaka-centered 710 orthogroups, for which human ortholog sequence could no be identified, to human centered 6975 orthogroups.

5909 loci present in a teleost genome, 1101 remain duplicated from the 3R-WGD.

GO 解析
・ 〜を支配する遺伝子.
Our inventory contained
a group of regulatory genes governing early embryonic axis formation, such as Noggins,
and multiple members of the opsin and prolactin-releasing hormone receptor gene familis.

A phylogenetic analysis supported
the exclusion of mammalian genes from the group
or vertebrate Wnt11b genes (Kuraku and Kuratani, 2012).

Our inventory has underestimated
the number of gene loss (Kuraku and Kuratani, 2011).

・それぞれの種が 1 遺伝子づつ持っている遺伝子グループ
To maximize orthology, we eventually retained
the 373 groups for which exactly one copy had been identified in each of the 17 species (Amemiya et al., 2013).


Our results might be affected by
incompleteness of the draft genome data of teleost, especially that of zebrafish (Sato et al. 2009).

- As the genome attempts to revert to
stable diploid state (Rondeau et al. 2014),

- all WGD duplicates will ave resolved to singletons (B&P 12),


### Data が主語
The advent of next generation sequencing techniques are promising for
the acceleration of research opportunities (B&P 12).

The analysis of fully sequenced genomes offers
valuable insight into the function and evolution of biological systems (Koonin and Galperin, 2003).

the recent availability of
multiple avian genome sequence assemblies allows us to
consider the role of chromosomal change in the evolution of Aves from their dinosaur ancestors (Romanov et al. 2014 ).

The availability of
anchored whole genome seuqneces for aminiote species has increased
the evolutionary depth of ancestral reconstruction from those made solely from chromosome painting data (Deakina and Ezaz, 2014).

As further higher quality sauropsid genoms become available,
it should become possible to further refine the evolutionary history of gene losses (Lovell et al. 2014).

### 結果が主語
More definitive answeres to these possibilities await
further completion and annotation of crocodilian genomes.

Extrapolating our model should be verified
in further studies
with an increased number of sample genes and genomes (Sato et al. 2009).

These issues should be addressed within
the broader context based on the emerging genome sequence data (Sato et al. 2009).

若い WGD の知見が古い WGD の研究に役立つ
the multitude and distribution of piscine GD events over evolutionary time will contribute to
studies of the gradual evolution of vertebrate animals after different types of GD (B&P 12).