Chromosome-level genome assembly of a triploid poplar Populus alba ’Berolinensis’

Related studies have provided significant insights into polyploid breeding in recent years, but limited research was focused on trees. The genomic information for the growth and response to abiotic stress in polyploidy trees is still largely unknown. Populus alba ’Berolinensis’, also named “Yinzhong poplar”, is a triploid poplar in the northeast of China. This hybrid triploid poplar is widely used as landscape ornamentals in urban areas because of its fast growth and high tolerance to abiotic stress. As an artificially synthesized male allotriploid hybrid, the three monoploid genomes of P. alba ’Berolinensis’ originated from different poplar species, so it is the desired material for studying polyploidy genomic collaboration mechanisms. Therefore, we intensively studied the allelic genomic collaboration mechanism in P. alba ’Berolinensis’. This study generated a high-quality chromosome-level genome assembly for the P. alba ’Berolinensis’ consisting of 19 allelic chromosomes. Its three monoploid chromosomes are polymorphic with an average of 42.22 variant sites per allelic gene locus. Meanwhile, we found that stress related genes such as RD22 and LEA7 exhibited structure variations. The above information has all been deployed to our polyploid genome online analysis website TreeGenomes (https://www.treegenomes.com). These polyploid genomic related resources will provide critical foundations for the molecular breeding of P. alba ’Berolinensis’ and help us uncover the allopolyploidization effects on the resistance and traits of polyploidy species deeper in the future.

Epigenetic modifications potentially controlling the allelic expression of imprinted genes in sunflower endosperm

Background Genomic imprinting is an epigenetic phenomenon mainly occurs in endosperm of flowering plants. Genome-wide identification of imprinted genes have been completed in several dicot Cruciferous plant and monocot crops. Results Here, we analyzed global patterns of allelic gene expression in developing endosperm of sunflower which belongs to the composite family. Totally, 691 imprinted loci candidates were identified in 12 day-after-pollination sunflower endosperm including 79 maternally expressed genes (MEG) and 596 paternally expressed genes (PEG), 6 maternally expressed noncoding RNAs (MNC) and 10 paternally expressed noncoding RNAs (PNC). And a clear clustering of imprinted genes throughout the rapeseed genome was identified. Generally, imprinting in sunflower is conserved within a species, but intraspecific variation also was detected. Limited loci in sunflower are imprinted in other several different species. The DNA methylation pattern around imprinted genes were investigated in embryo and endosperm tissues. In CG context, the imprinted genes were significantly associated with differential methylated regions exhibiting hypomethylation in endosperm and hypermethylation in embryo, which indicated that the maternal demethylation in CG context potentially induce the genomic imprinting in endosperm. Conclusion Our study would be helpful for understanding of genomic imprinting in plants and provide potential basis for further research in imprinting in sunflower.

PAC: Highly accurate quantification of allelic gene expression for population and disease genetics

Analysis of allele-specific gene expression (ASE) is a powerful approach for studying gene regulation. However, detection of ASE events relies on accurate alignment of RNA-sequencing reads, where challenges still remain. We have developed PAC, a method that combines multiple steps to improve the quantification of allelic reads, including personalised (i.e. diploid) read alignment with improved allocation of multi-mapping reads. We show that PAC outperforms standard alignment approaches for ASE detection in both accuracy and in the number of sites it can reliably quantify.

Gene Conversion amongst Alu SINE Elements

The process of non-allelic gene conversion acts on homologous sequences during recombination, replacing parts of one with the other to make them uniform. Such concerted evolution is best described as paralogous ribosomal RNA gene unification that serves to preserve the essential house-keeping functions of the converted genes. Transposed elements (TE), especially Alu short interspersed elements (SINE) that have more than a million copies in primate genomes, are a significant source of homologous units and a verified target of gene conversion. The consequences of such a recombination-based process are diverse, including multiplications of functional TE internal binding domains and, for evolutionists, confusing divergent annotations of orthologous transposable elements in related species. We systematically extracted and compared 68,097 Alu insertions in various primates looking for potential events of TE gene conversion and discovered 98 clear cases of Alu–Alu gene conversion, including 64 cases for which the direction of conversion was identified (e.g., AluS conversion to AluY). Gene conversion also does not necessarily affect the entire homologous sequence, and we detected 69 cases of partial gene conversion that resulted in virtual hybrids of two elements. Phylogenetic screening of gene-converted Alus revealed three clear hotspots of the process in the ancestors of Catarrhini, Hominoidea, and gibbons. In general, our systematic screening of orthologous primate loci for gene-converted TEs provides a new strategy and view of a post-integrative process that changes the identities of such elements.

Grain Fe and Zn content, heterosis, combining ability and its association with grain yield in irrigated and aerobic rice

Genetic improvement of rice for grain micronutrients, viz., iron (Fe) and zinc (Zn) content is one of the important breeding objectives, in addition to yield improvement under the irrigated and aerobic ecosystems. In view of developing genetic resources for aerobic conditions, line (L) × tester (T) analysis was conducted with four restorers, four CMS lines and 16 hybrids. Both hybrids and parental lines were evaluated in irrigated and aerobic field conditions for grain yield, grain Fe and Zn content. General Combining Ability (GCA) effects of parents and Specific Combining Ability (SCA) effects of hybrids were observed to be contrasting for the micronutrient content in both the growing environments. The grain Fe and Zn content for parental lines were negatively correlated with grain yield in both the contrasting growing conditions. However, hybrids exhibited positive correlation for grain Fe and Zn with grain yield under limited water conditions. The magnitude of SCA mean squares was much higher than GCA mean squares implying preponderance of dominance gene action and also role of complementary non-allelic gene(s) interaction of parents and suitability of hybrids to the aerobic system. The testers HHZ12-SAL8-Y1-SAL1 (T1) and HHZ17-Y16-Y3-Y2 (T2) were identified as good combiners for grain Zn content under irrigated and aerobic conditions respectively.

Gene action and Combining Ability Studies Using line x Tester Analysis in Sunflower (Helianthus annuus L.)

The present investigation was aimed to study the combining ability and gene action in parents and hybrids of sunflower for seed yield and components traits. Six female lines were crossed with four male lines by Line x Tester method, to obtain 24 F1s. Data were recorded on ten characters. Among the female parents CMS-108A, CMS-250A and CMS-207A were good general combiners for seed yield and other contributing traits. Among the male parents, IB-22, EC-178178, EC-601957 were identified as the best general combiners for seed yield and other yield contributing traits. The crosses showing high desirable SCA effect have involved one of the parents of high GCA effect and in turn, had high per se performance. The SCA effect of hybrids viz., CMS-207A x IB-22 and CMS-108A x GP-6-116 were highly significant for seed yield/plant (g) and other component traits in a desirable direction, indicating that the high performance of these crosses is due to non-allelic gene action.Non-additive gene action is predominant for all the studied characters except days to 50% flowering, plant height (cm) and hull content (%).

Association of Serotonin Transporter Gene (5-HTTLPR/rs25531) Polymorphism with Comorbidities of Panic Disorder

<b><i>Introduction:</i></b> Panic disorder (PD) has many comorbidities such as depression, bipolar disorder (BPD), and agoraphobia (AG). PD is a moderately heritable anxiety disorder whose pathogenesis is not well understood. Recently, a tri-allelic serotonin transporter (5-HTTLPR/rs25531) polymorphism was reported to be more sensitive to personality traits compared to the bi-allelic 5-HTTLPR polymorphism. We hypothesized that the 5-HTTLPR/rs25531 polymorphism may lead to a pathological anxious state depending on the presence or absence of a comorbidity in PD. <b><i>Methods:</i></b> In this study, we investigated the relationship between comorbidities in PD and tri-allelic 5-HTTLPR polymorphisms. A total of 515 patients with PD (148 males, 367 females) were genotyped, and the Revised NEO Personality Inventory as well as anxiety-related psychological tests were administered. Depression, BPD, and AG were diagnosed as comorbidities. <b><i>Results:</i></b> For the tri-allele 5-HTTLPR genotype, a significant interaction effect was found between openness to experience and comorbid depression. Examination of the interaction between AG and the tri-allelic 5-HTTLPR genotype revealed that L’ allele carriers are associated with higher trait anxiety than the S’S’ genotype group in PD without AG. <b><i>Conclusion:</i></b> Some anxiety and personality traits can be characterized by the tri-allelic gene effect of 5-HTTLPR. These results suggest that tri-allelic 5-HTTLPR genotypes have genetic effects on the presence of comorbidities of PD.

Genetic identification and restriction fragment length polymorphism (RFLP) based analysis of Myxovirus resistant gene (Mx) of chicken in Bangladesh

The Myxovirus resistant gene (Mx) codes for Mx protein with antiviral activity. Mx gene has been found in yeast and vertebrates ranging from fish to humans. In the present study Mx gene and its diversity in chicken is reported. A total of 42 blood samples were collected from different groups of chicken and were analyzed by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP). The diversity of Mx gene was enumerated by RFLP of PCR product with RsaI and SspI restriction enzyme. Mx gene was amplified from all the tested samples (100%) with the primers used. The primers amplified specific 100bp and 300bp DNA fragments from Mx gene. RFLP analysis of PCR product obtained with mismatched primers revealed that three types of Mx gene allele are prevailing in the tested samples; these are homozygous resistant Mx allelic gene (R/R), heterozygous Mx allelic gene (R/S) and homozygous sensitive Mx allelic gene (S/S). The proportions of each gene allele in the sampled chicken were 42.86% R/R, 42.86% S/S and 14.29% R/S. Interestingly, variation in Mx gene was observed within and between the groups of chicken. Present study has limitations like number of sample, species of bird sampled, etc. However, the study provides the genetic basis to some extent of chicken about resistance or sensitivity to avian influenza. To the best of our knowledge this is the first report of Mx gene related study in chicken in Bangladesh. Bangladesh J. of Livestock Res. 20(1-2): 18-25, Jan-Dec 2013

Large X-Linked Palindromes Undergo Arm-to-Arm Gene Conversion across Mus Lineages

Large (&gt;10 kb), nearly identical (&gt;99% nucleotide identity), palindromic sequences are enriched on mammalian sex chromosomes. Primate Y-palindromes undergo high rates of arm-to-arm gene conversion, a proposed mechanism for maintaining their sequence integrity in the absence of X–Y recombination. It is unclear whether X-palindromes, which can freely recombine in females, undergo arm-to-arm gene conversion and, if so, at what rate. We generated high-quality sequence assemblies of Mus molossinus and M. spretus X-palindromic regions and compared them with orthologous M. musculus X-palindromes. Our evolutionary sequence comparisons find evidence of X-palindrome arm-to-arm gene conversion at rates comparable to autosomal allelic gene conversion rates in mice. Mus X-palindromes also carry more derived than ancestral variants between species, suggesting that their sequence is rapidly diverging. We speculate that in addition to maintaining genes’ sequence integrity via sequence homogenization, palindrome arm-to-arm gene conversion may also facilitate rapid sequence divergence.