Short tandem repeats (
Transposable elements (
This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at
- NSF-PAR ID:
- Publisher / Repository:
- Date Published:
- Journal Name:
- The Plant Journal
- Page Range / eLocation ID:
- p. 1052-1065
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Short tandem repeats (
STRs), also known as microsatellites, are commonly used to noninvasively genotype wild‐living endangered species, including African apes. Until recently, capillary electrophoresis has been the method of choice to determine the length of polymorphic STRloci. However, this technique is labor intensive, difficult to compare across platforms, and notoriously imprecise. Here we developed a MiSeq‐based approach and tested its performance using previously genotyped fecal samples from long‐term studied chimpanzees in Gombe National Park, Tanzania. Using data from eight microsatellite loci as a reference, we designed a bioinformatics platform that converts raw MiSeq reads into locus‐specific files and automatically calls alleles after filtering stutter sequences and other PCRartifacts. Applying this method to the entire Gombe population, we confirmed previously reported genotypes, but also identified 31 new alleles that had been missed due to sequence differences and size homoplasy. The new genotypes, which increased the allelic diversity and heterozygosity in Gombe by 61% and 8%, respectively, were validated by replicate amplification and pedigree analyses. This demonstrated inheritance and resolved one case of an ambiguous paternity. Using both singleplex and multiplex locus amplification, we also genotyped fecal samples from chimpanzees in the Greater Mahale Ecosystem in Tanzania, demonstrating the utility of the MiSeq‐based approach for genotyping nonhabituated populations and performing comparative analyses across field sites. The new automated high‐throughput analysis platform (available at https://github.com/ShawHahnLab/chiimp) will allow biologists to more accurately and effectively determine wildlife population size and structure, and thus obtain information critical for conservation efforts.
Contents Summary I. Introduction II. MT arrays in plant cells III. γ‐Tubulin and MT nucleation IV. MT nucleation sites or flexible MTOCs in plant cells V. MT‐dependent MT nucleation VI. Generating new MTs for spindle assembly VII. Generation of MTs for phragmoplast expansion during cytokinesis VIII. MT generation for the cortical MT array IX. MT nucleation: looking forward Acknowledgements References Summary
Cytoskeletal microtubules (
MTs) have a multitude of functions including intracellular distribution of molecules and organelles, cell morphogenesis, as well as segregation of the genetic material and separation of the cytoplasm during cell division among eukaryotic organisms. In response to internal and external cues, eukaryotic cells remodel their MTnetwork in a regulated manner in order to assemble physiologically important arrays for cell growth, cell proliferation, or for cells to cope with biotic or abiotic stresses. Nucleation of new MTs is a critical step for MTremodeling. Although many key factors contributing to MTnucleation and organization are well conserved in different kingdoms, the centrosome, representing the most prominent microtubule organizing centers ( MTOCs), disappeared during plant evolution as angiosperms lack the structure. Instead, flexible MTOCs may emerge on the plasma membrane, the nuclear envelope, and even organelles depending on types of cells and organisms and/or physiological conditions. MT‐dependent MTnucleation is particularly noticeable in plant cells because it accounts for the primary source of MTgeneration for assembling spindle, phragmoplast, and cortical arrays when the γ‐tubulin ring complex is anchored and activated by the augmin complex. It is intriguing what proteins are associated with plant‐specific MTOCs and how plant cells activate or inactivate MTnucleation activities in spatiotemporally regulated manners.
Morphometric analysis is a common approach for comparing and categorizing botanical samples; however, completing a suite of analyses using existing tools may require a multi‐stage, multi‐program process. To facilitate streamlined analysis within a single program, Morphological Analysis of Size and Shape (
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