Allotetraploid cotton is an economically important natural-fiber-producing crop worldwide. After polyploidization, Gossypium hirsutum L. evolved to produce a higher fiber yield and to better survive harsh environments than Gossypium barbadense, which produces superior-quality fibers. The global genetic and molecular bases for these interspecies divergences were unknown. Here we report high-quality de novo-assembled genomes for these two cultivated allotetraploid species with pronounced improvement in repetitive-DNA-enriched centromeric regions. Whole-genome comparative analyses revealed that speciesspecific alterations in gene expression, structural variations and expanded gene families were responsible for speciation and the evolutionary history of these species. These findings help to elucidate the evolution of cotton genomes and their domestication history. The information generated not only should enable breeders to improve fiber quality and resilience to ever-changing environmental conditions but also can be translated to other crops for better understanding of their domestication history and use in improvement.

to CLCD (Ali, 1999). Among those, a diverse genetic base of the cultivars grown in Pakistan was suggested Epidemics of cotton leaf curl virus disease (CLCD) was the compelas an important element in controlling the disease (Zhu ling factor in the decision to devise new strategies for cotton breeding programs of Pakistan. The genetic similarity among the elite cotton et al., 2000); a narrow genetic base may predispose the (Gossypium spp.) cultivars released before the advent of CLCD epi-crop to an epidemic (Holley and Goodman, 1989). demics was in the range of 81.5 to 93.41%. New cultivars were devel-Restriction fragment length polymorphisms (RFLPs) oped by crossing the exotic resistant germplasm (LRA-5166, CP-15/2, have been applied to cotton species to study genetic and Cedix) with adapted varieties highly susceptible to CLCD. A diversity, population genetics, evolutionary history, and study was designed to assess the genetic relatedness or diversity among genome mapping (Shappley et al., 1996; Wang et al., the newly released, extremely resistant and resistant cultivars. After 1995; Yu et al., 1997). For our purposes, this may not screening 27 cotton genotypes by different diagnostic methods such be a viable approach because the level of polymorphism as field evaluation, whitefly-transmission studies, grafting, dot-blotin cotton is quite low compared with other plant taxa hybridization, and multiplex PCR using conserved primers sequences, (Brubaker and Wendel, 2000). Moreover, the analysis 20 extremely resistant and resistant cultivars were selected for a random amplified polymorphic DNA (RAPD) analysis. The genetic simi-The plant material used in the study consisted of 27 cotton cultivars, varieties, or genotypes. These cultivars or varieties

Twenty‐two cotton varieties were screened for resistance to cotton leaf curl disease (CLCuD), a disease of viral origin, using three procedures: field evaluation, whitefly transmission assay and graft inoculation. Viral infection of cotton varieties was determined by visual symptom assessment as well as dot‐blot and multiplex PCR diagnostic techniques. Crosses were made between the most susceptible variety (S‐12) and highly resistant varieties (CP‐15/2, LRA‐5166 and CIM‐443). All F1 plants of these crosses were resistant, showing dominant expression of the resistance as well as the absence of extrachromosomal inheritance. The F2 plants of the crosses CP‐15/2 × S12, LRA‐5166 × S‐12 and CIM‐443 × S12 exhibited a ratio of 13 resistant (symptomless) to three susceptible (with symptoms). Screening of the F2 generation for virus infection by multiplex PCR further subdivided the resistant class into those exhibiting a high level of resistance (HR; PCR‐negative) and those exhibiting resistance (R; symptomless, yet showing virus replication by PCR analysis). Hence, the final ratio was 3:10:3 (HR:resistant:susceptible). The F3 progeny of susceptible F2 plants segregated for resistance, indicating the probable presence of a suppressor gene (S). These findings are consistent with three genes being involved in G. hirsutum resistance to CLCuD, two for resistance (R1CLCuDhir and R2CLCuDhir) and a suppressor of resistance (SCLCuDhir).

Background The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea–dwelling species will allow several pending evolutionary questions to be unlocked. Findings We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. Conclusions This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.

Increasing scarcity of irrigational water is a major threat to sustainable production of cotton (Gossypium hirsutum L.). It could be resolved by developing drought-tolerant cultivars. Osmotic adjustment and cellular membrane stability are well-documented traits that help to sustain yield under drought in cereals. However, their utility in cotton is not well established. Here, we studied genotypic variability and relationships among osmotic adjustment, cell membrane stability and productivity traits under field-induced water stress at the flowering stage. We evaluated a set of cotton germplasm comprising 32 cotton genotypes under contrasting water regimes for measurements of productivity including seedcotton yield, number of bolls per plant and boll weight, and physiological attributes such as osmotic adjustment and cell membrane stability in two field trials. The mean reduction in seedcotton yield due to water deficit was 20 and 43% in 2003 and 2004, respectively. Genotypes differed considerably for relative yield losses due to water stress ranging from 20 to 74%. Significant association between number of bolls and seedcotton yield under a water-limited regime suggests boll retention as the principal determinant of yield in a water-deficit-stress environment. Cell membrane stability varied significantly among the cotton genotypes; however, its association with productivity measurements was not significant in the water-limited regime. The significant positive correlation found between cell membrane stability and osmotic adjustment implicates the role of osmolytes in the protection of various cellular functions, including those associated with cellular membranes. Moderate but significant differences for osmotic adjustment were found among the genotypes in both years. Osmotic adjustment was positively associated with seedcotton yield under the water-limited regime and inversely correlated with the drought susceptibility index. These results demonstrated the contribution of osmotic adjustment in sustaining yield under water-deficit stress in cotton. Thus, like cereals, osmotic adjustment may be useful as a selection criterion in breeding programs with the objective of improving drought tolerance and yield in cotton under water-limited environments; however, the role of cell membrane stability as a drought-tolerant trait requires further investigation.