The Baboon Kidney Transcriptome: Analysis of Transcript Sequence, Splice Variants, and Abundance

Spradling, Kimberly D.; Glenn, Jeremy P.; Garcia, Roy; Shade, Robert E.; Cox, Laura A.

doi:10.1371/journal.pone.0057563

Cited by 23 publications

(26 citation statements)

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“…hirta ( Table 2 ). The number of genes expressed in the kidney and sequenced via transcriptome analysis for the baboon [ 31 ] and three heteromyid rodents [ 3 ], [ 32 ] are similar to our reconstructions.…”

Section: Discussionsupporting

confidence: 59%

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Characterization of the Kidney Transcriptome of the Long-Haired Mouse Abrothrix hirta (Rodentia, Sigmodontinae) and Comparison with That of the Olive Mouse A. olivacea

et al. 2015

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To understand how small mammals cope with the challenge of water homeostasis is a matter of interest for ecologists and evolutionary biologists. Here we take a step towards the understanding of the transcriptomic functional response of kidney using as a model the long–haired mouse (Abrothrix hirta) a species that distributes across Patagonian steppes and Austral temperate rainforests in Argentina and Chile. Specifically, we i) characterize the renal transcriptome of A. hirta, and ii) compare it with that—already available—of the co-generic and co-distributed A. olivacea. Renal mRNA transcripts from 16 specimens of A. hirta from natural populations were analyzed. Over 500 million Illumina paired-end reads were assembled de novo under two approaches, an individual assembly for each specimen, and a single in-silico normalized joint assembly including all reads from all specimens. The total number of annotated genes was similar with both strategies: an average of 14,956 in individual assemblies and 14,410 in the joint assembly. Overall, 15,463 distinct genes express in the kidney of A. hirta. Transcriptomes of A. hirta and A. olivacea were similar in terms of gene abundance and composition: 95.6% of the genes of A. hirta were also found in A. olivacea making their functional profiles also similar. However, differences in the transcriptome of these two species were observed in the set of highly expressed genes, in terms of private genes for each species and the functional profiles of highly expressed genes. As part of the novel transcriptome characterization, we provide distinct gene lists with their functional annotation that would constitute the basis for further research on these or any other species of the subfamily Sigmodontinae, which includes about 400 living species distributed from Tierra del Fuego to southern United States.

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Section: Discussionsupporting

confidence: 59%

“… Gene abundance for Gene Ontology terms at the higher level, using DAVID [ 31 ] tools and databases, are shown for biological process (BP_FAT), cellular component (CC_FAT) and molecular function (MF_FAT). …”

Section: Supporting Informationmentioning

confidence: 99%

Characterization of the Kidney Transcriptome of the Long-Haired Mouse Abrothrix hirta (Rodentia, Sigmodontinae) and Comparison with That of the Olive Mouse A. olivacea

et al. 2015

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“…For example, Myo1d redistributes along the length of intestinal microvilli in Myo1a-null mice[ 68 ]. Myo1c and Myo1d are found in renal brush borders of PTs by proteomic analyses [ 69 ], and all class I myosins are identified in kidney by transcriptomic analyses [ 70 , 71 ].…”

Section: Discussionmentioning

confidence: 99%

Myosin 1b Regulates Amino Acid Transport by Associating Transporters with the Apical Plasma Membrane of Kidney Cells

Komaba

Coluccio

2015

PLoS ONE

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Amino acid transporters (AATers) in the brush border of the apical plasma membrane (APM) of renal proximal tubule (PT) cells mediate amino acid transport (AAT). We found that the membrane-associated class I myosin myosin 1b (Myo1b) localized at the apical brush border membrane of PTs. In opossum kidney (OK) 3B/2 epithelial cells, which are derived from PTs, expressed rat Myo1b-GFP colocalized in patched microvilli with expressed mouse V5-tagged SIT1 (SIT1-V5), which mediates neutral amino acid transport in OK cells. Lentivirus-mediated delivery of opossum Myo1b-specific shRNA resulted in knockdown (kd) of Myo1b expression, less SIT1-V5 at the APM as determined by localization studies, and a decrease in neutral AAT as determined by radioactive uptake assays. Myo1b kd had no effect on Pi transport or noticeable change in microvilli structure as determined by rhodamine phalloidin staining. The studies are the first to define a physiological role for Myo1b, that of regulating renal AAT by modulating the association of AATers with the APM.

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“…Regardless of the strategy, a large number of homologous mouse genes were obtained in our study. According to microarray studies [ 33 ] , about 7600 genes are expressed in the kidneys of adult humans; meanwhile, recent HTS transcriptome studies found 15,369 for the baboon kidneys [ 34 ]. Clearly, in this study we were able to find almost the same number of genes (15,077 through TrinityNorm) that Spradling et al [ 34 ] even though we used a very stringent e-value for the BLASTX analysis.…”

Section: Discussionmentioning

confidence: 99%

Characterization of the kidney transcriptome of the South American olive mouse Abrothrix olivacea

et al. 2014

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BackgroundThe olive mouse Abrothrix olivacea is a cricetid rodent of the subfamily Sigmodontinae that inhabits a wide range of contrasting environments in southern South America, from aridlands to temperate rainforests. Along its distribution, it presents different geographic forms that make the olive mouse a good focal case for the study of geographical variation in response to environmental variation. We chose to characterize the kidney transcriptome because this organ has been shown to be associated with multiple physiological processes, including water reabsorption.ResultsTranscriptomes of thirteen kidneys from individuals from Argentina and Chile were sequenced using Illumina technology in order to obtain a kidney reference transcriptome. After combining the reads produced for each sample, we explored three assembly strategies to obtain the best reconstruction of transcripts, TrinityNorm and DigiNorm, which include its own normalization algorithms for redundant reads removal, and Multireads, which simply consist on the assembly of the joined reads. We found that Multireads strategy produces a less fragmented assembly than normalization algorithms but recovers fewer number of genes. In general, about 15000 genes were annotated, of which almost half had at least one coding sequence reconstructed at 99% of its length. We also built a list of highly expressed genes, of which several are involved in water conservation under laboratory conditions using mouse models.ConclusionBased on our assembly results, Trinity's in silico normalization is the best algorithm in terms of cost-benefit returns; however, our results also indicate that normalization should be avoided if complete or nearly complete coding sequences of genes are desired. Given that this work is the first to characterize the transcriptome of any member of Sigmodontinae, a subfamily of cricetid rodents with about 400 living species, it will provide valuable resources for future ecological and evolutionary genomic analyses.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-446) contains supplementary material, which is available to authorized users.

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The Baboon Kidney Transcriptome: Analysis of Transcript Sequence, Splice Variants, and Abundance

Cited by 23 publications

References 100 publications

Characterization of the Kidney Transcriptome of the Long-Haired Mouse Abrothrix hirta (Rodentia, Sigmodontinae) and Comparison with That of the Olive Mouse A. olivacea

Characterization of the Kidney Transcriptome of the Long-Haired Mouse Abrothrix hirta (Rodentia, Sigmodontinae) and Comparison with That of the Olive Mouse A. olivacea

Myosin 1b Regulates Amino Acid Transport by Associating Transporters with the Apical Plasma Membrane of Kidney Cells

Characterization of the kidney transcriptome of the South American olive mouse Abrothrix olivacea

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