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Comparative Genomics of Closely Related Species - Uncovering the Evolutionary Process of Shaping the Characteristics Representing the Species
https://ir.soken.ac.jp/records/4106
https://ir.soken.ac.jp/records/41067aae51fb-f6bb-4c7c-99ba-3fc0081c0bde
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要旨・審査要旨 (496.5 kB)
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本文 (5.4 MB)
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| Item type | 学位論文 / Thesis or Dissertation(1) | |||||
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| 公開日 | 2013-11-28 | |||||
| タイトル | ||||||
| タイトル | Comparative Genomics of Closely Related Species - Uncovering the Evolutionary Process of Shaping the Characteristics Representing the Species | |||||
| タイトル | ||||||
| タイトル | Comparative Genomics of Closely Related Species - Uncovering the Evolutionary Process of Shaping the Characteristics Representing the Species | |||||
| 言語 | en | |||||
| 言語 | ||||||
| 言語 | eng | |||||
| 資源タイプ | ||||||
| 資源タイプ識別子 | http://purl.org/coar/resource_type/c_46ec | |||||
| 資源タイプ | thesis | |||||
| 著者名 |
原, 雄一郎
× 原, 雄一郎 |
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| フリガナ |
ハラ, ユウイチロウ
× ハラ, ユウイチロウ |
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| 著者 |
HARA, Yuichiro
× HARA, Yuichiro |
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| 学位授与機関 | ||||||
| 学位授与機関名 | 総合研究大学院大学 | |||||
| 学位名 | ||||||
| 学位名 | 博士（学術） | |||||
| 学位記番号 | ||||||
| 内容記述タイプ | Other | |||||
| 内容記述 | 総研大乙第225号 | |||||
| 研究科 | ||||||
| 値 | 先導科学研究科 | |||||
| 専攻 | ||||||
| 値 | 23 生命共生体進化学専攻 | |||||
| 学位授与年月日 | ||||||
| 学位授与年月日 | 2013-03-22 | |||||
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| 値 | 2012 | |||||
| 要旨 | ||||||
| 内容記述タイプ | Other | |||||
| 内容記述 | A huge amount of species living on the earth display extensively diversified phenotypes. During the long period of evolution from their common an cestors, characteristic shaping each species, i.e. "species-ness", has been acquired over time. One of the biggest issues in biology, since the age of Darwin, is to unveil the processes of acquiring species-ness in the course of evolution. Several approaches have been developed to infer the states of ancestral species by comparing morphological and ecological characteristics and/or the genomic contents of extant species. Despite that much evidence has been accumulated, the processes of the evolution of shaping species-specific characteristics are still limitedly understood. This would be because each inferred state at the ancestor only illustrates a point of time in the ancestral lineage, which would be hard to reconstruct a whole picture of evolutionary processes from ancestors to extant species. Today, it becomes easier to infer the ancestral genomes from those of extant species, and much more information can be extracted because of the rapid increase of number of species whose whole genome has been sequenced and rapid accumulation of knowledge on biological function of genes, which enable the inference of phenotype to genotype. If the whole pictures of ancestral genomes are provided with high resolution in timeline of evolution, the continuous process of evolution could be reconstructed. This can be most easily attained for the group of closely related species whose genomes are available and the genomes of common ancestors are almost wholly inferred with high accuracy. My aim in this study is to uncover the process of acquisition of "species-ness", the specific characteristics of species, comparing the whole genomes of closely related extant species as well as inference of ancestors. To achieve it, I designed an approach consisting of three integrative and sequential analyses based on the reconstruction of the genomes of ancestral species. The first is to distinguish different processes of genomic changes such as single point mutation, indels, and inversion to reveal the detail of structural evolution of genomes with finer precision. The second is to reconstruct the history of species based on refined genomic comparison attained by the first procedure. The third is to identify the species-specific genomic content that provides species to have each own species-ness. This can be carried out once the evolutionary history of species is firmly established by the second procedure. In order to examine feasibility of above approaches, I conducted comparative genomic analyses of closely related species by selecting specific examples, some of which are currently controversial and much debated, as follows: (i) Identification of ultramicro inversions within local alignments between closely related species, (ii) Reconstruction of the demographic histories of the human lineage using whole genome alignments, and (iii) Identification of the species-specific characteristics involved in the pathogenicity and adaptation to the host environments in Theileria parasites. (i) Identification of ultramicro inversions within local alignments between closely related species. Inversion is one of the major mechanisms for generating genomic diversity in evolution. While the inversions of large size have been well investigated since the early 20th century, little is understood about the minimal size of inversions, which would have useful information for clarifying the minute structural changes of genomes. I developed an efficient method for identifying minimal-sized inversions that I call "Ultramicro Inversions" of 5-125 bp buried in nucleotide alignments, and identified 3,330 ultramicro inversions within the human-chimpanzee genome alignments. Around 26% of the ultramicro inversions consisted of adenine (A) and thymine (T) only, and the ultramicro inversions were also frequently found in chromosome Y and regions close to transposable elements. These observations suggested that the ultramicro inversions are related to instability of the genomic structures. Ninety ultramicro inversions were found in gene regions, and 28 out of 90 were in the coding regions, indicating that some parts of the ultramicro inversions may contribute to gene evolution. At least 31% of the ultramicro inversions in the human-chimpanzee alignments were bounded by inverted repeats, suggesting that such ultramicro inversions involved in the chromosomal recombinations via DNA stem-loops. In addition, I identified ultramicro inversions in various lineages other than primates: 1,285, 40, and 62 ultramicro inversions in the fly, fungi, and rice genomes, respectively, and 20 on average in the genomes of four and two lineages of eubacteria and archaea, respectively. This observation indicates that ultramicro inversions are ubiquitous across the three domains of the living world. While frequencies of the ultramicro inversions were up to seven times different between the lineages, the mechanisms of ultramicro inversions seemed to be more various across the lineages. The fractions of AT-exclusive and stem-loop type ultramicro inversions were much more different across the lineages. Identification of ultramicro inversion hotspots in silico would be helpful for capturing the inversions in experiments and clarifying the mechanisms of minute genome structural evolution. Our inversion-identification method is also applicable in the fine-tuning of genome alignments by distinguishing ultramicro inversions from simple point mutations and indels. (ii) Reconstruction of the demographic histories of the human lineage using whole genome alignments. The demographic history of human would provide helpful information for identifying the evolutionary events that shaped the humanity but remains controversial even in the genomic era. In order to settle the controversies, I inferred the evolutionary history of human and great apes based on an estimation of the speciation times (T) and ancestral population sizes (N) in the lineage leading to human and great apes using the whole-genome alignments. A coalescence simulation determined the sizes of alignment blocks and intervals between them required to obtain recombination-free blocks with a high frequency. This simulation revealed that the size of the alignment block strongly affects the parameter inference, indicating that recombination is an important factor for achieving optimum parameter inference and that this simulation is helpful for the optimum data collection. From the whole genome alignments (1.9 giga-bases) of human (H), chimpanzee (C), gorilla (G), and orangutan, and the small-sized regions subject to the genomic changes by the other mechanisms than point mutations, such as CpG sites and ultramicro inversions, were excluded. 100-bp alignment blocks separated by ≥5-kb intervals were sampled from the alignments and subjected to estimate τ=μT and θ=4μgN using the MCMC method, where μ is the mutation rate and g is the generation time. Although the estimated τHC differed across chromosomes, τHC and τHCG were strongly correlated across chromosomes, indicating that variation in τ is subject to variation in μ across the lineages, rather than T, and thus, all chromosomes are likely to share a single speciation time. Subsequently, I estimated Ts of the human lineage from chimpanzee, gorilla, and orangutan to be 6.0-7.6, 7.6-9.7, and 15-19 MYA, respectively, assuming variable μ across lineages and chromosomes. These speciation times were consistent with the fossil records. I conclude that the speciation times in our recombination-free analysis would be conclusive and the speciation between human and chimpanzee was a single event. (iii) Identification of the species-specific characteristics involved in the pathogenicity and adaptation to the host environments in Theileria parasites. Theileria is a tick-born apicomplexan group causing parasitosis in livestock. Some theilerias are parasitic to cattle, but the relationship between the theileria and cattle seem to have evolved specifically in each lineage. While T. annulata and T. parva (transforming theileria) induce abnormal proliferation of infected cells of lymphocyte or macrophage/monocyte lineages and are severely pathogenic, T. orientalis does not induce such transformation and shows moderate pathogenicity. Here, in order to clarify the process of acquiring the high pathogenicity and diverged systems infecting the hosts, I reconstructed the evolutionary history of theileria based on the comparative genomics of the almost whole genomes. While synteny across the chromosomes of the three theilerias was well conserved, subtelomeric regions were largely different: T. orientalis lacks the large tandemly arrayed subtelomere-encoded variable secreted protein-encoding gene family. Through the orthologue clustering, in addition, I found that duplication and deletion rates in the transforming theileria lineage were 1.66 and 1.95 times faster than those in the T. orientalis lineages, respectively. Expansion of particular gene families by gene duplication was found specifically in the two transforming theileria species. One of the most notable families is the TashAT/TpHN gene family, which is considered to be involved in transformation and abnormal proliferation of host leukocytes. The transforming theileria possessed around 20 TashAT/TpHN members, while only one member was identified in T. orientalis, and no homologues were found in a babesia and plasmodiums. I also found the gene families expanded specifically in T. orientalis lineages such as ABC transporters, implying species-specific strategies against host systems. Differences between the genome sequences of theileria species illustrated different tempo and mode of gene duplication and deletion between transforming theilerias and T. orientalis. It is implied, moreover, that such differences in evolutionary modes resulted in the novel abilities to transform and immortalize bovine leukocytes. The genomic changes between close relatives will provide insight into proteins and mechanisms that have evolved to induce and regulate this process. In the above studies, I have examined and demonstrated effectiveness of the three steps of integrative and sequential approach for clarifying the evolutionary processes to attain "species-ness" at the genome level by reconstructing the genomes of ancestral species from closely related extant species. Even though the current approaches are based on the well-established fields of genomics, population genetics, and molecular phylogenetics, the integration of the approaches, as shown here, is innovative in the field of in silico genomic analysis and provides new insight on evolutionary biology. In the near future, comparative analysis of closely related species will be expanded for the genomes of species suitable to solve a particular biological issue. The integrative approach provided here would become one of de-facto standard for such analyses. |
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