PubMed · 14414273
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K LARSEN. 1959-10-08. [Something on experimental polyploids].. https://pubmed.ncbi.nlm.nih.gov/14414273/
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Chaetoceros socialis is a cosmopolitan diatom species that is crucial for maintaining marine ecosystem structure and driving elemental cycles. C. socialis can form harmful algal blooms (HABs) that may cause a negative impact on the marine ecosystems. Whole-genome information for C. socialis is still unavailable, which may hinder more targeted studies on its ecological adaptive responses and evolutionary drivers. To address this gap, we employed cutting-edge genomic technologies including PacBio single-molecule real-time (SMRT) sequencing and high-throughput chromatin conformation capture (Hi-C) to achieve the first chromosome-level genome assembly of C. socialis. The assembled genome is 60.22 Mb in size with a scaffold N50 of 7.81 Mb and has been anchored to eight pseudochromosomes. A total of 13,378 protein-coding genes were predicted, of which 12,069 (90.22%) were functionally annotated. This high-quality genomic resource provides a fundamental data platform for systematically elucidating the ecological adaptation mechanisms of C. socialis.
Vermilion Snapper (Rhomboplites aurorubens, Lutjanidae) inhabits deep waters (20-300 m) from North America to Brazil and supports significant commercial and recreational fisheries. Despite its economic importance, the understanding of its basic biology remains limited. Classified as Vulnerable on the Red List due to overfishing, populations have declined by over 30% in recent generations. We assembled and annotated the first chromosome-scale genome of this species by combining PacBio long reads, Illumina short reads, and Hi-C data. The resulting assembly is 987.5 Mbp, with a scaffold N50 size of 41.3 Mbp, and includes 135 contigs clustered and ordered onto 24 chromosomes with 34,496 predicted genes. The high-quality assembly and annotation contained about 98% complete and single-copy BUSCO genes. It is the most complete, chromosome-level genome assembly of an Atlantic snapper to date. The genome assembly and supporting data are valuable tools for ecological and comparative genomics studies of snappers and other valuable commercial species within the family.
Mantle cell lymphoma (MCL) is an aggressive non-Hodgkin's lymphoma with median patient survival times of approximately 3 years. Although the characteristic t(11;14)(q13;q32) is found in virtually all cases, experimental evidence suggests that this event alone is insufficient to result in lymphoma and secondary genomic alterations are required. Using a newly developed DNA microarray of 32 433 overlapping genomic segments spanning the entire human genome, we can for the first time move beyond marker based analysis and comprehensively search for secondary genomic alterations concomitant with the t(11;14) in eight commonly used cell models of MCL (Granta-519, HBL-2, NCEB-1, Rec-1, SP49, UPN-1, Z138C and JVM-2). Examining these genomes at tiling resolution identified an unexpected average of 35 genetic alterations per cell line, with equal numbers of amplifications and deletions. Recurrent high-level amplifications were identified at 18q21 containing BCL2, and at 13q31 containing GPC5. In addition, a recurrent homozygous deletion was identified at 9p21 containing p15 and p16. Alignment of these profiles revealed 14 recurrent losses and 21 recurrent gains as small as 130 kb. Remarkably, even the intra immunoglobulin gene deletions at 2p11 and 22q11 were detected, demonstrating the power of combining the detection sensitivity of array comparative genomic hybridization (CGH) with the resolution of an overlapping whole genome tiling-set. These alterations not only coincided with previously described aberrations in MCL, but also defined 13 novel regions. Further characterization of such minimally altered genomic regions identified using whole genome array CGH will define novel dominant oncogenes and tumor suppressor genes that play important roles in the pathogenesis of MCL.