On the origin and evolution of new genes-a genomic and experimental perspective

The inherent interest on the origin of genetic novelties can be traced back to Darwin. But it was not until recently that we were allowed to investigate the fundamental process of origin of new genes by the studies on newly evolved Young genes. Two indisp

Sex chromosomes in the black muntjac recapitulate incipient evolution of mammalian sex chromosomes

Background: The regular mammalian X and Y chromosomes diverged from each other at least 166 to 148 million years ago, leaving few traces of their early evolution, including degeneration of the Y chromosome and evolution of dosage compensation. Results: We

Origin and evolution of ubiquitin-conjugating enzymes from Guillardia theta nucleomorph to hominoid

The origin of eukaryotic ubiquitin-conjugating enzymes (E2s) can be traced back to the Guillardia theta nucleomorph about 2500 million years ago (Mya). E2s are largely vertically inherited over eukaryotic evolution [Lespinet, O., Wolf, Y.I., Koonin, E.V.,

Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication

Background: Various evolutionary models have been proposed to interpret the fate of paralogous duplicates, which provides substrates on which evolution selection could act. In particular, domestication, as a special selection, has played important role in crop cultivation with divergence of many genes controlling important agronomic traits. Recent studies have indicated that a pair of duplicate genes was often sub-functionalized from their ancestral functions held by the parental genes. We previously demonstrated that the rice cell-wall invertase (CWI) gene GIF1 that plays an important role in the grain-filling process was most likely subjected to domestication selection in the promoter region. Here, we report that GIF1 and another CWI gene OsCIN1 constitute a pair of duplicate genes with differentiated expression and function through independent selection. Results: Through synteny analysis, we show that GIF1 and another cell-wall invertase gene OsCIN1 were paralogues derived from a segmental duplication originated during genome duplication of grasses. Results based on analyses of population genetics and gene phylogenetic tree of 25 cultivars and 25 wild rice sequences demonstrated that OsCIN1 was also artificially selected during rice domestication with a fixed mutation in the coding region, in contrast to GIF1 that was selected in the promoter region. GIF1 and OsCIN1 have evolved into different expression patterns and probable different kinetics parameters of enzymatic activity with the latter displaying less enzymatic activity. Overexpression of GIF1 and OsCIN1 also resulted in different phenotypes, suggesting that OsCIN1 might regulate other unrecognized biological process. Conclusion: How gene duplication and divergence contribute to genetic novelty and morphological adaptation has been an interesting issue to geneticists and biologists. Our discovery that the duplicated pair of GIF1 and OsCIN1 has experiencedsub-functionalization implies that selection could act independently on each duplicate towards different functional specificity, which provides a vivid example for evolution of genetic novelties in a model crop. Our results also further support the established hypothesis that gene duplication with sub-functionalization could be one solution for genetic adaptive conflict.

Large Gene Family Expansions and Adaptive Evolution for Odorant and Gustatory Receptors in the Pea Aphid, Acyrthosiphon pisum

Gaining insight into the mechanisms of chemoreception in aphids is of primary importance for both integrative studies on the evolution of host plant specialization and applied research in pest control management because aphids rely on their sense of smell

The nuclear matrix of Euglena gracilis (Euglenophyta): A stage of nuclear matrix evolution?

Euglena gracilis cell was extracted sequentially with CSK-Triton buffer, RSB-Magik solution and DNase-As solution. DGD embedment-free electron microscopy showed that in the extracted nucleus there was a residual non-chromatin fibrous network. That it could not be removed by hot trichloroacetic acid further supported the idea that it was a non-histone, non-chromatin fibrous protein network, and should be the internal network of the nuclear matrix. After the sequential extraction, the nuclear membrane was removed, leaving behind a layer of lamina; the chromatin was digested and eluted from the dense chromosomes and residual chromosomal structures that should be chromosomal scaffold were revealed. Western blot analysis with antiserum against rat lamins showed that nuclear lamina of the cell possessed two positive polypeptides, a major one and a minor one, which had molecular masses similar to lamin B and lamin A, respectively. Comparing these data with those of the most primitive eukaryote Archezoa and of higher eukaryotes, it was suggested that the lower unicellular eukaryote E. gracillis already had the nuclear matrix structure, and its nuclear matrix (especially the lamina) might represent a stage of evolutionary history of the nuclear matrix. (C) 2000 Editions scientifiques et medicales Elsevier SAS.

The evolution of YidC/Oxa/Alb3 family in the three domains of life: a phylogenomic analysis

Background: YidC/Oxa/Alb3 family includes a group of conserved translocases that are essential for protein insertion into inner membranes of bacteria and mitochondria, and thylakoid membranes of chloroplasts. Because mitochondria and chloroplasts are of b

KARYOTYPE EVOLUTION OF SHREW MOLES (SORICOMORPHA: TALPIDAE)

The Chinese long-tailed mole (Scaptonyx fusicaudus) closely resembles American (Neurotrichus gibbsii) and Japanese (Dymecodon pilirostris and Urotrichus talpoides) shrew moles in size, appearance, and ecological habits, yet it has traditionally been classified either together with (viz subfamily Urotrichinae) or separately (tribe Scaptonychini) from the latter genera (tribe Urotrichini sensu lato). We explored the merit of these competing hypotheses by comparing the differentially stained karyotypes of S.fusicaudus and N. gibbsii with those previously reported for both Japanese taxa. With few exceptions, diploid chromosome number (2n = 34), fundamental autosomal number (FNa = 64), relative size, and G-banding pattern of S. fusicaudus were indistinguishable from those of D. pilirostris and U. talpoides. In fact, only chromosome 15 differed significantly between these species, being acrocentric in D. pilirostris, subtelocentric in U. talpoides, and metacentric in S. fusicaudus. This striking similarity is difficult to envisage except in light of a shared common ancestry, and is indicative of an exceptionally low rate of chromosomal evolution among these genera. Conversely, the karyotype of N. gibbsii deviates markedly in diploid chromosome and fundamental autosomal number (2n = 38 and FNa = 72, respectively), morphology, and G-banding pattern from those of Scaptonyx and the Japanese shrew moles. These differences cannot be explained by simple chromosomal rearrangements, and Suggest that rapid chromosomal reorganization Occurred ill the karyotype evolution of this species, possibly due to founder or bottleneck events.

CLASSIFICATION AND EVOLUTION OF ASIAN COLOBINES

In order to study the differentiation of Asian colobines, 14 variables measured on 123 skulls, including Rhinopithecus, Presbytis, Presbytiscus (Rhinopithecus avunculus), Pygathrix and Nasalis were analyzed by one-way, cluster and discriminant function analyses. Information on paleoenvironmental changes in China and southeast Asia since the late Tertiary was used to examine the influences of migratory routes and range of distribution in Asian colobines. A cladogram for 6 genera of Asian colobines was constructed from the results of various analyses. Some new points or revisions were suggested: (1) Following one of two migratory routes, ancient species of Asian colobines perhaps passed through Xizang (Tibet) along the northern bank of the Tethys sea and through the Heng Duan Shan regions of Yunnan into Vietnam. An ancient landmass linking Yunnan and Xizang was already present on the east bank of the Tethys sea. Accordingly, Asian colobines would have two centers of evolutionary origin: Sundaland and the Heng Duan Shan regions of China. (2) Pygathrix shares more cranial features with Presbytiscus than with Rhinopithecus. This differs somewhat from the conclusion reached by Groves. (3) Nasalis (karyotype: 2n = 48) may be the most primitive genus among Asian colobines. Certain features shared with Rhinopithecus, e.g. large body size, terrestrial activity and limb proportions, can be interpreted as symple-siomorphic characters. (4) Rhinopithecus, with respect to craniofacial features, is a special case among Asian colobines. It combines a high degree of evolutionary specialization with retention of some primitive features thought to have been present in the ancestral Asian colobine.