Segmental duplications and their variation in a complete human genome

Despite their importance in disease and evolution, highly identical segmental duplications (SDs) have been among the last regions of the human reference genome (GRCh38) to be finished. Based on a complete telomere-to-telomere human genome (T2T CHM13), we present the first comprehensive view of human SD organization. SDs account for nearly one-third of the additional sequence increasing the genome-wide estimate from 5.4% to 7.0% (218 Mbp). An analysis of 266 human genomes shows that 91% of the new T2T CHM13 SD sequence (68.3 Mbp) better represents human copy number. We find that SDs show increased single-nucleotide variation diversity when compared to unique regions; we characterize methylation signatures that correlate with duplicate gene transcription and predict 182 novel protein-coding gene candidates. We find that 63% (35.11/55.7 Mbp) of acrocentric chromosomes consist of SDs distinct from rDNA and satellite sequences. Acrocentric SDs are 1.75-fold longer (p=0.00034) than other SDs, are frequently shared with autosomal pericentromeric regions, and are heteromorphic among human chromosomes. Comparing long-read assemblies from other human (n=12) and nonhuman primate (n=5) genomes, we use the T2T CHM13 genome to systematically reconstruct the evolution and structural haplotype diversity of biomedically relevant (LPA, SMN) and duplicated genes (TBC1D3, SRGAP2C, ARHGAP11B) important in the expansion of the human frontal cortex. The analysis reveals unprecedented patterns of structural heterozygosity and massive evolutionary differences in SD organization between humans and their closest living relatives.

Chromosome count, meiotic abnormalities and pollen sterility in Lahaul sweetvetch (Hedysarum astragaloides Benth. ex Baker, Fabaceae), an endemic and threatened species from India

Male meiotic studies were carried out on eight different accessions of Hedysarum astragaloides Benth. ex Baker (Fabaceae), an endemic and threatened species of northwest Himalaya, India. Although genetic factors such as meiosis, chromosome number, and ploidy level may be causative for the evolution, endemism, rare distribution or even extinction of the species, no detailed information exists. Keeping this in mind H. astragaloides has been studied cytologically. Male meiotic investigations revealed diploid level (2n=2x=14) for species and normal meiotic course in the accessions from the Manali Hills resulting in nearly 100% pollen fertility. However, the accessions scored from the Manimahesh Hills and Pangi Valley depicted inter-pollen mother cell transfer of chromatin material and structural heterozygosity for reciprocal translocations. Consequent upon these meiotic anomalies, some pollen sterility (21%) resulted. On account of this sweeping genetic outcome, the incidence of anomalies such as this in an endemic and threatened species warrants grave consideration. It is sensible to conclude that conservation measures should include the collection of germplasm from the localities where plants are meiotically stable with high gametic fertility, to ensure good germination and healthy plants for future use. Seeds from meiotically normal individuals should be given priority for inclusion in seed banks.