Journal of Genetics and Genomics

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

Qi Zhou, Wen Wang

2008, 35(11): 639-648. doi: 10.1016/S1673-8527(08)60085-5

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Abstract:
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 indispensible steps are involved in this process: origin of new gene copies through various mutational mechanisms and evolution of novel functions, which further more leads to fixation of the new copies within populations. The theoretical framework for the former step formed in 1970s. Ohno proposed gene duplication as the most important mechanism producing new gene copies. He also believed that the most common fate for new gene copies is to become pseudogenes. This classical view was validated and was also challenged by the characterization of the first functional young gene jingwei in Drosophila. Recent genome-wide comparison on young genes of Drosophila has elucidated a comprehensive picture addressing remarkable roles of various mechanisms besides gene duplication during origin of new genes. Case surveys revealed it is not rare that new genes would evolve novel structures and functions to contribute to the adaptive evolution of organisms. Here, we review recent advances in understanding how new genes originated and evolved on the basis of genome-wide results and experimental efforts on cases. We would finally discuss the future directions of this fast-growing research field in the context of functional genomics era.

Mitochondrial variants may influence the phenotypic manifestation of Leber's hereditary optic neuropathy-associated ND4 G11778A mutation

Wanshi Cai, Qun Fu, Xiangtian Zhou, Jia Qu, Yi Tong, Min-Xin Guan

2008, 35(11): 649-655. doi: 10.1016/S1673-8527(08)60086-7

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Abstract:
We report here the characterization of a five-generation Han Chinese family with Leber's hereditary optic neuropathy (LHON). Strikingly, this Chinese family displayed high penetrance and expressivity of visual loss. The average age-of-onset of vision loss was 18 years in this family. Nineteen (11 males/8 females) of 29 matrilineal relatives in this family developed visual loss with a wide range of severity, ranging from blindness to normal vision. Sequence analysis of mitochondrial genome in this pedigree revealed the presence of the ND4 G11778A mutation and 44 other variants belonging to Asian haplogroup M7b. The G11778A mutation is present at homoplasmy in matrilineal relatives of this Chinese family. Of other variants, the CO1 G6480A, ND5 T12811C and Cytb A15395G located at highly conserved residues of corresponding polypeptides. In fact, these variants were implicated to be involved in other clinical abnormalities. Here, these variants may act in synergy with the primary LHON-associated G11778A mutation. Thus, the mitochondrial dysfunction caused by the primary ND4 G11778A mutation may be worsened by these mitochondrial variants. The results imply that the G6480A, T12811C and A15395G variants might have a potential modifier role in increasing the penetrance and expressivity of the primary LHON-associated G11778A mutation in this Chinese family.

Genotypic analysis on the ORF-K1 gene of human herpesvirus 8 from patients with Kaposi's sarcoma in Xinjiang, China

Dezhi Zhang, Xiongming Pu, Weidong Wu, Ying Jin, Mijiti Juhear, Xiujuan Wu

2008, 35(11): 657-663. doi: 10.1016/S1673-8527(08)60087-9

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Abstract:
Human herpesvirus 8 (HHV-8) is thought to be essential for the development of all forms of Kaposi's sarcoma (KS). HHV-8 DNA is present virtually in all KS tumor biopsy samples. Genes at both ends of the HHV-8 genome have been shown to vary considerably. Seven major molecular subtypes of HHV-8 were defined based on the amino acid sequence of the open reading frame K1 (ORF-K1), generally known as A, B, C, D, E, F, and Z. Most strains collected worldwide were clustered into two subtypes (A and C). Here, the K1/VR1 region of HHV-8 was amplified by nested PCR in 22 (81.48%) of 27 cases from Xinjiang Uygur Autonomous Region, a province in northwestern China. Phylogenetic analysis on the basis of the K1/VR1 amino acid sequence indicated that the majority of these KS patients were infected by subtype C HHV-8 (n = 18, including 15 belonging to the C2 group), and several by subtype A (n = 4, including 3 being the A1 group). This is the first report of subtype A HHV-8 in China. Furthermore, the correlations between different forms and lesions of KS and different subtypes of HHV-8 were analyzed. The findings showed that subtype A HHV-8 resulted in significantly more frequent mucosal KS lesions than subtype C. However, there was no obvious correlation between different forms of KS and different subtypes of HHV-8.

A murine model for human immune thrombocytopenic purpura and comparative analysis of multiple gene expression in bone marrow and spleen

Hong Wei, Xinchun Ding, Jiangong Ren, Ka Liu, Pingping Tan, Daquan Li, Runlin Z. Ma

2008, 35(11): 665-671. doi: 10.1016/S1673-8527(08)60088-0

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Abstract:
Homeostasis of platelet number in human and other mammals is well maintained for prevention of minor bleeding and for other immunological functions, but the exact molecular mechanism responsible for immune thrombocytopenic purpura (ITP) has not been fully understood. In an effort to identify genetic factors involved in initiation of platelet production in response to bleeding injury or platelet destruction, we have successfully generated an animal model of human ITP via intraperitoneal injection of anti-platelet antibody into the Balb/c mouse. Platelet counts were dropped dramatically in animals that received antibody injection within 4 h, maintained at the minimum level for a period of 44 h, started to rebound after 48 h, and reached to the maximum at 144 h (6 days). Final homeostasis reached at approximately 408 h (17 days), following a minor cycle of platelet number fluctuation. Using semi-quantitative RT-PCR, we assessed and compared mRNA level of CD41, c-myb, c-mpl, caspase-3, caspase-9, GATA-1, and Bcl-xl in bone marrow and spleen. Alteration of mRNA expression was correlated with the change of platelet level, and an inverse relationship was found for expression of the genes between bone marrow and spleen. No transcription was detectable for any of the seven genes in bone marrow at the time when platelet number reached the maximum (144 h). In contrast, mRNA transcripts of the seven genes were found to be at the highest level in spleen tissue. This is the first study of simultaneous detection of multiple platelet related genes in a highly reproducible ITP animal model. Our results provided the supportive evidence that expression of the above seven genes are more related to negative regulation of platelet number in spleen tissue, at least in the model animals.

Characterization of T. aestivum-H. californicum chromosome addition lines DA2H and MA5H

Fang Kong, Haiyan Wang, Aizhong Cao, Bi Qin, Jianhui Ji, Suling Wang, Xiu-E Wang

2008, 35(11): 673-678. doi: 10.1016/S1673-8527(08)60089-2

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Abstract:
In order to transfer useful genes of Hordeum californicum into common wheat (Triticum aestivum L.), the T. aestivum c.v. Chinese Spring (CS)-H. californicum amphiploid was crossed to CS, and its backcrossing and self-fertilized progenies were analyzed by morphological observation, cytological, biochemical and molecular marker techniques. Alien addition lines with two H. californicum chromosomes were identified and their genetic constitution was characterized. STS-PCR analysis using chromosome 2B specific markers indicated that chromosome H3 of H. californicum belongs to homoeologous group 2, and was thus designated 2H. SDS-PAGE showed that chromosome H2 of H. californicum belongs to homoeologous group 5, and was designated 5H. The CS-H. californicum amphiploid and the chromosome addition lines (DA2H and MA5H) identified were evaluated for powdery mildew (Erysiphe graminis f. sp. triticii) resistance in field. The preliminary results indicated that the amphiploid showed higher powdery mildew resistance than CS. However, chromosome addition lines DA2H and MA5H were highly susceptible to powdery mildew, indicating that major powdery mildew resistant genes of H. californicum should be located on chromosomes other than 2H and 5H.

Comparison of the Δ12 fatty acid desaturase gene between high-oleic and normal-oleic peanut genotypes

Shanlin Yu, Lijuan Pan, Qingli Yang, Ping Min, Zengkai Ren, Hongsheng Zhang

2008, 35(11): 679-685. doi: 10.1016/S1673-8527(08)60090-9

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Abstract:
Δ¹² fatty acid desaturase gene has been targeted as a logical candidate controlling the high oleate trait in peanut seeds. By RT-PCR method, the full-length cDNAs of Δ¹² fatty acid desaturase gene were isolated from peanut (Arachis hypogaea L.) genotypes with normal and high ratio of oleic to linoleic acid, which were designated AhFAD2B and AhFAD2B′, respectively. Sequence alignment of their coding regions revealed that an extra A was inserted at the position +442 bp of AhFAD2B′ sequence of high oleic acid genotypes, which resulted in the shift of open reading frame and a truncated protein AhFAD2B′, with the loss of one histidine box involved in metal ion complex required for the reduction of oxygen. Analysis of transcript level showed that the expression of Δ¹² fatty acid desaturase gene in high oleic acid genotype was slightly lower than that in normal genotype. The enzyme activity experiment of yeast (Saccharomyces cerevisiae) cell transformed with AhFAD2B or AhFAD2B′ proved that only AhFAD2B gene product showed significant Δ¹² fatty acid desaturase activity, but AhFAD2B′ gene product did not. These results suggested that the change of AhFAD2B′ gene sequence resulted in lower activity or deactivation of Δ¹² fatty acid desaturase in high oleic acid genotype.

Analysis of the meiosis in the F1 hybrids of Longiflorum × Asiatic (LA) of lilies (Lilium) using genomic in situ hybridization

Shujun Zhou, Munikote S. Ramanna, Richard G.F. Visser, Jaap M. van Tuyl

2008, 35(11): 687-695. doi: 10.1016/S1673-8527(08)60091-0

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Abstract:
Longiflorum and Asiatic lilies of the genus Lilium of the family Liliaceae are two important groups of modern lily cultivars. One of the main trends of lily breeding is to realize introgression between these groups. With cut style pollination and embryo rescue, distant hybrids between the two groups have been obtained. However, the F₁ hybrids are highly sterile or some of them could produce a small number of 2n gametes, and their BC₁ progenies are usually triploids. Dutch lily breeders have selected many cultivars from these BC₁ progenies based on their variation. It is presumably suggested that such variation could be caused by intergenomic recombination and abnormal meiosis during gamete formation in F₁ hybrids of Longiflorum × Asiatic (LA) hybrids in Lilium. Therefore, the meiotic process of ten F₁ LA hybrids was cytologically investigated using genomic in situ hybridization and traditional cytological methods in the present research. The results showed that: at metaphase I, the homoeologous chromosome pairing among different F₁ hybrids ranged from 2.0 to 11.4 bivalents formed by homoeologous chromosomes per pollen mother cell (PMC), and very few multivalents, and even very few bivalents were formed by two chromosomes within one genome rather than homoeologous chromosomes in some PMCs; at anaphase I, all bivalents were disjoined and most univalents were divided. Both the disjoined bivalents (half-bivalents) and the divided univalents (sister chromatids) moved to the opposite poles, and then formed two groups of chromosomes; because the two resulting half-bivalents retained their axes in the cell undisturbed, many crossover types, including single crossovers, three strand double crossovers, four strand double crossovers, four strand triple crossovers, and four strand multiple crossovers between the non-sister chromatids in the tetrads of bivalents, were clearly inferred by analyzing the breakpoints on the disjoined bivalents. The present investigation not only explained the reason for sterility of the F₁ LA hybrids and the variation of their BC₁ progenies, but also provided a new method to analyze crossover types in other F₁ interspecific hybrids as well.

Instructions for authors

2008, 35(11): 697-700. doi: 10.1016/S1673-8527(08)60092-2

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Abstract:

2008 Vol. 35, No. 11