RESUMEN

Within the family Fabaceae, the genus Glycine is composed of two subgenera annuals (2n=40) and perennials. This life strategy transition may have differentially affected the evolution of various gene families. Its cultivated species G. max has high level of susceptibility to major pathogens including viruses, bacteria and fungi. Understanding nucleotide-binding domain leucine-rich repeat (NLR) genes evolution in soybean is of paramount importance due to their central role in plant immunity and their potential in improving disease resistance in soybean cultivars. In this study, we investigated the significance of this annual-perennial transition on the macroevolution of NLR genes in the genus Glycine. Our results reveal a remarkable distinction between annual species such as Glycine max and Glycine soja, which exhibit an expanded NLRome compared to perennial species (G. cyrtoloba, G. stenophita, G. dolichocarpa, G. falcata, G. syndetika, G. latifolia and G. tomentella). Our evolutionary timescale analysis pinpoints recent accelerated gene duplication events for this expansion, which occurred between 0.1 and 0.5 million years ago, driven predominantly by lineage-specific and terminal duplications. In contrast, perennials initially experienced significant contraction during the diploidisation phase following the Glycine-specific whole-genome duplication event (~10 million years ago). Despite the reduction in the NLRome, perennial lineages exhibit a unique and highly diversified repertoire of NLR genes with limited interspecies synteny. The investigation of gene gain and loss ratios revealed that this diversification resulted from the birth of novel genes following individual speciation events. Among perennials, G. latifolia, a well-known resistance resource, has the highest ratio of these novel genes in the tertiary gene pool. Our study suggests evolutionary mechanisms, including recombination and transposition, as potential drivers for the emergence of these novel genes. This study also provides evidence for the unbalanced expansion of the NLRome in the Dt subgenome compared with the At subgenome in the young allopolyploid G. dolichocarpa. To the best of our knowledge, this is the first study to investigate the effect of annuality and perenniality life transition on the evolution of NLR genes in the genus Glycine to identify its genomics resources for improving the resistance of soybean crop with global importance on the economy and food security.

RESUMEN

Dalbergioid is a large group within the family Fabaceae that consists of diverse plant species distributed in distinct biogeographic realms. Here, we have performed a comprehensive study to understand the evolution of the nucleotide-binding leucine-rich repeats (NLRs) gene family in Dalbergioids. The evolution of gene families in this group is affected by a common whole genome duplication that occurred approximately 58 million years ago, followed by diploidization that often leads to contraction. Our study suggests that since diploidization, the NLRome of all groups of Dalbergioids is expanding in a clade-specific manner with fewer exceptions. Phylogenetic analysis and classification of NLRs revealed that they belong to seven subgroups. Specific subgroups have expanded in a species-specific manner, leading to divergent evolution. Among the Dalbergia clade, the expansion of NLRome in six species of the genus Dalbergia was observed, with the exception of Dalbergia odorifera, where a recent contraction of NLRome occurred. Similarly, members of the Pterocarpus clade genus Arachis revealed a large-scale expansion in the diploid species. In addition, the asymmetric expansion of NLRome was observed in wild and domesticated tetraploids after recent duplications in the genus Arachis. Our analysis strongly suggests that whole genome duplication followed by tandem duplication after divergence from a common ancestor of Dalbergioids is the major cause of NLRome expansion. To the best of our knowledge, this is the first ever study to provide insight toward the evolution of NLR genes in this important tribe. In addition, accurate identification and characterization of NLR genes is a substantial contribution to the repertoire of resistances among members of the Dalbergioids species.

Asunto(s)

RESUMEN

One of the most important and critical factors in software projects is the proper cost estimation. This activity, which has to be done prior to the beginning of a project in the initial stage, always encounters several challenges and problems. However, due to the high significance and impact of the proper cost estimation, several approaches and methods have been proposed regarding how to perform cost estimation, in which the analogy-based approach is one of the most popular ones. In recent years, many attempts have been made to employ suitable techniques and methods in this approach in order to improve estimation accuracy. However, achieving improved estimation accuracy in these techniques is still an appropriate research topic. To improve software development cost estimation, the current study has investigated the effect of the LEM algorithm on optimization of features weighting and proposed a new method as well. In this research, the effectiveness of this algorithm has been examined on two datasets, Desharnais and Maxwell. Then, MMRE, PRED (0.25), and MdMRE criteria have been used to evaluate and compare the proposed method against other evolutionary algorithms. Employing the proposed method showed considerable improvement in estimating software cost estimation.

RESUMEN

Despite the benefits of standardization, the customization of Software as a Service (SaaS) application is also essential because of the many unique requirements of customers. This study, therefore, focuses on the development of a valid and reliable software customization model for SaaS quality that consists of (1) generic software customization types and a list of common practices for each customization type in the SaaS multi-tenant context, and (2) key quality attributes of SaaS applications associated with customization. The study was divided into three phases: the conceptualization of the model, analysis of its validity using SaaS academic-derived expertise, and evaluation of its reliability by submitting it to an internal consistency reliability test conducted by software-engineer researchers. The model was initially devised based on six customization approaches, 46 customization practices, and 13 quality attributes in the SaaS multi-tenant context. Subsequently, its content was validated over two rounds of testing after which one approach and 14 practices were removed and 20 practices were reformulated. The internal consistency reliability study was thereafter conducted by 34 software engineer researchers. All constructs of the content-validated model were found to be reliable in this study. The final version of the model consists of 6 constructs and 44 items. These six constructs and their associated items are as follows: (1) Configuration (eight items), (2) Composition (four items), (3) Extension (six items), 4) Integration (eight items), (5) Modification (five items), and (6) SaaS quality (13 items). The results of the study may contribute to enhancing the capability of empirically analyzing the impact of software customization on SaaS quality by benefiting from all resultant constructs and items.