The Relationship between Gene Network Structure and Expression Variation among Individuals and Species

Sears, Karen E.; Maier, Jennifer; Rivas‐Astroza, Marcelo; Poe, Rachel; Zhong, Sheng; Kosog, Kari; Marcot, Jonathan D.; Behringer, Richard R.; Cretekos, Chris J.; Rasweiler, John J.; Rapti, Zoi

doi:10.1371/journal.pgen.1005398

Cited by 26 publications

(28 citation statements)

References 54 publications

(46 reference statements)

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“…1) were removed from each species and total RNA purified (see Materials and Methods and [53] for more details). We used the Illumina TruSeq RNA Sample Preparation Kit to generate libraries.…”

Section: Resultsmentioning

confidence: 99%

“…For bat, read alignment and gene expression were computed with RSEM [94] using as reference sequences the 88,930 gene isoforms previously described. RNA-Seq data has been deposited in the NCBI Gene Expression Omnibus (GEO) under accession number GSE71390 [53]. …”

Section: Methodsmentioning

confidence: 99%

“…These species include a generalized, pentadactyl mammal (mouse), a representative of the only mammalian group to evolve a wing capable of powered flight (bat), a marsupial whose hind limb development lags significantly behind forelimb development relative to eutherian mammals (opossum) [52], and a mammal that displays digit reduction (pig). We performed RNA-Seq on the developing fore- and hindlimbs of these four mammalian species [53]. We then quantified the transcriptomes of the fore- and hind limbs of these species at the ridge, bud, and paddle stages of development (Fig.…”

Section: Introductionmentioning

confidence: 99%

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Transcriptomic insights into the genetic basis of mammalian limb diversity

et al. 2017

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BackgroundFrom bat wings to whale flippers, limb diversification has been crucial to the evolutionary success of mammals. We performed the first transcriptome-wide study of limb development in multiple species to explore the hypothesis that mammalian limb diversification has proceeded through the differential expression of conserved shared genes, rather than by major changes to limb patterning. Specifically, we investigated the manner in which the expression of shared genes has evolved within and among mammalian species.ResultsWe assembled and compared transcriptomes of bat, mouse, opossum, and pig fore- and hind limbs at the ridge, bud, and paddle stages of development. Results suggest that gene expression patterns exhibit larger variation among species during later than earlier stages of limb development, while within species results are more mixed. Consistent with the former, results also suggest that genes expressed at later developmental stages tend to have a younger evolutionary age than genes expressed at earlier stages. A suite of key limb-patterning genes was identified as being differentially expressed among the homologous limbs of all species. However, only a small subset of shared genes is differentially expressed in the fore- and hind limbs of all examined species. Similarly, a small subset of shared genes is differentially expressed within the fore- and hind limb of a single species and among the forelimbs of different species.ConclusionsTaken together, results of this study do not support the existence of a phylotypic period of limb development ending at chondrogenesis, but do support the hypothesis that the hierarchical nature of development translates into increasing variation among species as development progresses.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-0902-6) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Transcriptomic insights into the genetic basis of mammalian limb diversity

et al. 2017

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“…In these studies, they compared the transcriptomes of bat, mouse, pig, and opossum limbs at the ridge, bud, and paddle stages of development (Maier et al, 2017;Sears et al, 2015). exist for the developmental evolution of mammalian limbs.…”

Section: S T U DI E S Th a T Cr Os S -Tr Ad I Ti On Al Or D Er Bou mentioning

confidence: 99%

Timing the developmental origins of mammalian limb diversity

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et al. 2017

Genesis

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Mammals have highly diverse limbs that have contributed to their occupation of almost every niche. Researchers have long been investigating the development of these diverse limbs, with the goals of identifying developmental processes and potential biases that shape mammalian limb diversity. To date, researchers have used techniques ranging from the genomic to the anatomic to investigate the developmental processes shaping the limb morphology of mammals from five orders (Marsupialia, Chiroptera, Rodentia, Cetartiodactyla, and Perissodactyla). Results of these studies suggest that the differential expression of genes controlling diverse cellular processes underlies mammalian limb diversity. Results also suggest that the earliest development of the limb tends to be conserved among mammalian species, while later limb development tends to be more variable. This research has established the mammalian limb as a model system for evolutionary developmental biology, and set the stage for more in-depth, cross-disciplinary research into the genetic controls, tissue-level cellular behaviors, and selective pressures that have driven the developmental evolution of mammalian limbs. Ideally, these studies will be performed in a diverse suite of mammalian species within a comparative, phylogenetic framework.

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“…Research into the relationship between innovation (necessary for evolution) and network robustness has found important clues to the mechanisms of evolution in both biological GRNs [4][5][6][7][8] and model GRNs [9][10][11][12][13][14].…”

Section: Introductionmentioning

confidence: 99%