RESUMO
With advanced sequencing technology, dozens of complex polyploid plant genomes have been characterized. However, for many polyploid species, their diploid ancestors are unknown or extinct, making it impossible to unravel the subgenomes and genome evolution directly. We developed a novel subgenome-phasing algorithm, SubPhaser, specifically designed for a neoallopolyploid or a homoploid hybrid. SubPhaser first searches for the subgenome-specific sequence (k-mer), then assigns homoeologous chromosomes into subgenomes, and further provides tools to annotate and investigate specific sequences. SubPhaser works well on neoallopolyploids and homoploid hybrids containing subgenome-specific sequences like wheat, but fails on autopolyploids lacking subgenome-specific sequences like alfalfa, indicating that SubPhaser can phase neoallopolyploid/homoploid hybrids with high accuracy, sensitivity and performance. This highly accurate, highly sensitive, ancestral data free chromosome phasing algorithm, SubPhaser, offers significant application value for subgenome phasing in neoallopolyploids and homoploid hybrids, and for the subsequent exploration of genome evolution and related genetic/epigenetic mechanisms.
Assuntos
Genoma de Planta , Poliploidia , Diploide , Epigênese Genética , Triticum/genéticaRESUMO
Two novel actinobacteria, designated YIM 121936T and YIM 121940T, were isolated from alkaline sediment in Yuanjiang, China. The cells of the novel strains were Gram-stain-positive, aerobic, motile, non-spore-forming and coccus-shaped. The two strains both contained meso-diaminopimelic acid as the diagnostic diamino acid. The whole-cell sugars were arabinose, galactose, glucose, mannose and ribose. The predominant menaquinone was MK-9(H2). The polar lipid profile of both strains comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, one unknown phosphoglycolipid and five unknown phospholipids. The predominant fatty acids of both strains were anteiso-C15â:â0. The genomic DNA G+C contents of strains YIM 121936T and YIM 121940T were 74.7 and 75.2â%, respectively. Strain YIM 121936T was closely related to Kineococcus aurantiacus IFO 15268T (97.19â%), Kineococcus gypseus YIM 121300T (97.00â%) and Kineococcus mangrovi NBRC 110933T (97.00â%). Strain YIM 121940T was closely related to K. aurantiacus IFO 15268T (97.41â%), Kineococcus endophytica KLBMP 1274T (97.18â%), Kineococcus rhizosphaerae RP-B16T (97.09â%), Kineococcus radiotolerans SRS 30216T (97.09â%), K. gypseus YIM 121300T (97.00â%) and K. mangrovi NBRC 110933T (97.00â%). Strain YIM 121936T shared high 16S rRNA gene sequence similarity (99â%) with YIM 121940T. Similarities of two strains with other species of the genus Kineococcus were <97â%. The DNA-DNA hybridization values were below 70â% among all the strains studied. YIM 121936T and YIM 121940T are representatives of two new species in the genus Kineococcus, for which names Kineococcus terreus sp. nov. (type strain YIM 121936T=KCTC 39738T=DSM 102155T) and Kineococcus aureolus sp. nov. (type strain YIM 121940T=KCTC 39739T=DSM 102158T) are proposed, respectively.