Dataset Information

MRatBN7.2: familiar and unfamiliar features of a new rat genome reference assembly.

ABSTRACT: Rat genomic tools have been slower to emerge than for those of humans and mice and have remained less thorough and comprehensive. The arrival of a new and improved rat reference genome, mRatBN7.2, in late 2020 is a welcome event. This assembly, like predecessor rat reference assemblies, is derived from an inbred Brown Norway rat. In this "user" survey we hope to provide other users of this assembly some insight into its characteristics and some assessment of its improvements as well as a few caveats that arise from the unique aspects of this assembly. mRatBN7.2 was generated by the Wellcome Sanger Institute as part of the large Vertebrate Genomes Project. This rat assembly has now joined human, mouse, chicken, and zebrafish in the National Center for Biotechnology Information (NCBI)'s Genome Reference Consortium, which provides ongoing curation of the assembly. Here we examine the technical procedures by which the assembly was created and assess how this assembly constitutes an improvement over its predecessor. We also indicate the technical limitations affecting the assembly, providing illustrations of how these limitations arise and the impact that results for this reference assembly.

SUBMITTER: de Jong TV

PROVIDER: S-EPMC9236863 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature

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mRatBN7.2: familiar and unfamiliar features of a new rat genome reference assembly.

de Jong Tristan V TV Chen Hao H Brashear Wesley A WA Kochan Kelli J KJ Hillhouse Andrew E AE Zhu Yaming Y Dhande Isha S IS Hudson Elizabeth A EA Sumlut Mary H MH Smith Melissa L ML Kalbfleisch Theodore S TS Doris Peter A PA

Physiological genomics 20220511 7

Rat genomic tools have been slower to emerge than for those of humans and mice and have remained less thorough and comprehensive. The arrival of a new and improved rat reference genome, mRatBN7.2, in late 2020 is a welcome event. This assembly, like predecessor rat reference assemblies, is derived from an inbred Brown Norway rat. In this "user" survey we hope to provide other users of this assembly some insight into its characteristics and some assessment of its improvements as well as a few cav ...[more]

PMID: 35543507

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Project description:To study individual recognition in animals, discrimination tasks are often conducted by presenting 2D images of real conspecifics. However, animals may discriminate the images merely as visual stimulus combinations without establishing referential relationships to the individuals depicted. In the current study, we investigated whether goats are able to discriminate photos of familiar and unfamiliar conspecifics, whether they not only process the photos as visual stimuli, but also understand them as virtual copies of real conspecifics and whether they grasp the concept of familiarity. Using a computer-controlled learning device, in three tests, goats of two experimental groups (A and B) had to discriminate portrait (Te1), profile (Te2) or headless body photos (Te3) of conspecifics. Tests were presented as 4-choice tasks, with one photo from Group A (rewarded) plus three photos from Group B (distractors). That is, the rewarded photo was familiar to Group A, but unfamiliar to Group B. Finally, in a reversal test (Te4) we reversed this principle. The goats learned the discriminations in Te1 to Te3 within two (Te1 and Te2) and three training days (Te3), respectively, and they needed between 91 [CL (66, 126)] and 174 [CL (126, 241)] trials to reach the learning criterion, with no statistically significant differences between the groups. In Te4, in contrast, the animals took 403 [Group A; CL (291, 557)] and 385 [Group B; CL (286, 519)] trials, respectively, to learn the task. The lack of spontaneous preferences for the photo of the familiar conspecific in the pretests of Te1 to Te3 in Group A, as well as the lack of differences in the number of trials to learn the discriminations between both groups, do not at first glance suggest that the goats established a correspondence between real conspecifics and their 2D representations. However, the higher number of trials in Te4 suggests that both groups formed the learning rule of choosing either the known (Group A) or the unknown goat (Group B) over the course of Te1 to Te3 and then failed after the rule was reversed, providing evidence that goats can associate 2D photos of conspecifics with real animals.

Dataset Information

MRatBN7.2: familiar and unfamiliar features of a new rat genome reference assembly.

Publications

mRatBN7.2: familiar and unfamiliar features of a new rat genome reference assembly.

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