We present a combined mean-field and simulation approach to different models describing the dynamics of classes formed by elements that can appear, disappear or copy themselves. These models, related to a paradigm duplication-innovation model known as Chinese Restaurant Process, are devised to reproduce the scaling behavior observed in the genome-wide repertoire of protein domains of all known species. In view of these data, we discuss the qualitative and quantitative differences of the alternative model formulations, focusing in particular on the roles of element loss and of the specificity of empirical domain classes.
The famous 2R hypothesis was first proposed by Susumu Ohno in 1970. It states that the two whole genome duplications had shaped the genome of early vertebrates. The most convincing evidence for 2R hypothesis comes from the 4:1 ratio chromosomal regions that have preserved both gene content and order in vertebrates compared with closely related. However, due to the shortage of such strict evidence, the 2R hypothesis is still under debates. Here, we present a combined perspective of phylogenetic and genomic homology to revisit the hypothesis of 2R whole genome duplications. Ancestral vertebrate …
Tandem-duplication-random-loss (TDRL) is an important genome rearrangement operation studied in evolutionary biology. This paper investigates some of the formal properties of TDRL operations on the symmetric group (the space of permutations over an $ n $-set). In particular, the cardinality of `balls' of radius one in the TDRL metric, as well as the cardinality of the maximum intersection of two such balls, are determined. The corresponding problems for the so-called mirror (or palindromic) TDRL rearrangement operations are also solved. The results represent an initial step in the study of err…
Segmental duplications (SDs), or low-copy repeats (LCR), are segments of DNA greater than 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a common cause of genomic structural variation, and several are associated with diseases of genomic origin. Despite their functional importance, SDs present one of the major hurdles for de novo genome assembly due to the ambiguity they cause in building and traversing both state-of-the-art overlap-layout-consensus and de Bruijn graphs. This causes SD regions to be misass…
As organisms are faced with intense rapidly changing selective pressures, new genetic material is required to facilitate adaptation. Among sources of genetic novelty, gene duplications and transposable elements (TEs) offer new genes or new regulatory patterns that can facilitate evolutionary change. With advances in genome sequencing it is possible to gain a broader view of how gene family proliferation and TE content evolve in non-model species when populations become threatened. Freshwater bivalves (Unionidae) currently face severe anthropogenic challenges. Over 70% of species in the United …
Increasing biological complexity is positively correlated with the relative genome-wide expansion of non-protein-coding DNA sequences
背景资料：在当前的基因组时代之前，有人认为生物体所使用的蛋白质编码基因的数量是衡量其复杂性的有效指标。然而，现在很清楚的是，主要的不一致性存在，生物复杂性和蛋白质编码基因的数量之间只有微弱的关系。例如，使用蛋白质编码基因数量作为评估生物复杂性的基础，将使尾索动物和昆虫的复杂性低于线虫，而人类的复杂性低于水稻。结果如下：我们分析了85个测序物种的非编码基因组DNA与总基因组DNA的比率（ncDNA/tgDNA），发现这个比率与生物学复杂性的增加密切相关。对于原核生物，ncDNA/tgDNA比率通常包含在0.05-0.24的带宽内，但在单细胞真核生物中上升到0.26-0.52，并且对于发育复杂的多细胞生物体上升到0.62-0.985。值得注意的是，原核生物物种的物种分布不均匀，接近平均值0.1177 ncDNA/tgDNA（p=1.58 x 10^-13），ncDNA/tgDNA与基因组大小呈非线性关系（r=0.15）。重要的是，ncDNA/tgDNA比率校正倍性，并且基本上不受重复序列的可变负荷的影响。结论：我们认为，所观察到的非编码DNA的增加和组成模式主要是增加的信息含量的函数。因此，内含子、基因间序列、重复元件和基因组DNA可能对复杂生物的进化和功能库比以前认识到的要重要得多。
This thesis is focused in the study of the evolution of the metabolic repertoire of Streptomyces, which are renowned as proficient producers of bioactive Natural Products (NPs). The main goal of my work was to contribute into the understanding of the evolutionary mechanisms behind the evolution of NP biosynthetic pathways. Specifically, the development of a bioinformatic method that helps into the discovery of new NP biosynthetic pathways from actinobacterial genome sequences with emphasis on members of the genus Streptomyces. I developed this method using a comparative and functional genomics…
Transposable Elements (TEs) or jumping genes are the DNA sequences that have an intrinsic capability to move within a host genome from one genomic location to another. Studies show that the presence of a TE within or adjacent to a functional gene may alter its expression. TEs can also cause an increase in the rate of mutation and can even mediate duplications and large insertions and deletions in the genome, promoting gross genetic rearrangements. Thus, the proper classification of the identified jumping genes is essential to understand their genetic and evolutionary effects in the genome. Whi…
Protein-protein interaction (PPI) networks are the backbone of all processes in living cells. In this work we relate conservation, essentiality and functional repertoire of a gene to the connectivity $k$ (i.e., the number of interaction links) of the corresponding protein in the PPI network. On a set of 42 bacterial genomes of different sizes, and with reasonably separated evolutionary trajectories, we investigate three issues: i) whether the distribution of connectivities changes between PPI subnetworks of essential and nonessential genes; ii) how gene conservation, measured both by the evolu…
