www.aging-us.com AGING 2020, Vol. 12, No.

16
Research Paper
Genetic variation between long-lived versus short-lived bats
illuminates the molecular signatures of longevity
Zixia Huang1, Conor V. Whelan1, Dina Dechmann2,3,4, Emma C. Teeling1
1
School of Biology and Environmental Science, University College Dublin, Belfield, Dublin, Ireland
2
Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
3
Department of Biology, University of Konstanz, Konstanz, Germany
4
Smithsonian Tropical Research Institute, Panama

Correspondence to: Emma C. Teeling; email: [email protected]

Keywords: bats, longevity, comparative genomics, transcriptomics, autophagy
Received: June 6, 2020 Accepted: July 6, 2020 Published: July 16, 2020

Copyright: Huang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution
License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original
author and source are credited.

ABSTRACT

Bats are the longest-lived mammals given their body size with majority of species exhibiting exceptional
longevity. However, there are some short-lived species that do not exhibit extended lifespans. Here we
conducted a comparative genomic and transcriptomic study on long-lived Myotis myotis (maximum lifespan =
37.1 years) and short-lived Molossus molossus (maximum lifespan = 5.6 years) to ascertain the genetic
difference underlying their divergent longevities. Genome-wide selection tests on 12,467 single-copy genes
between M. myotis and M. molossus revealed only three genes (CCDC175, FATE1 and MLKL) that exhibited
significant positive selection. Although 97.96% of 12,467 genes underwent purifying selection, we observed a
significant heterogeneity in their expression patterns. Using a linear mixed model, we obtained expression of
2,086 genes that may truly represent the genetic difference between M. myotis and M. molossus. Expression
analysis indicated that long-lived M. myotis exhibited a transcriptomic profile of enhanced DNA repair and
autophagy pathways, compared to M. molossus. Further investigation of the longevity-associated genes
suggested that long-lived M. myotis have naturally evolved a diminished anti-longevity transcriptomic profile.
Together with observations from other long-lived species, our results suggest that heightened DNA repair and
autophagy activity may represent a universal mechanism to achieve longevity in long-lived mammals.

INTRODUCTION lifespan to predicted lifespan for a non-flying mammal

of the same body size [2, 3]. Using this approach bats
Natural selection has shaped a large variation of are the longevity extremists, with some species living
lifespan across mammals, with maximum lifespan up to ten times longer than expected given their body
ranging from a few months (e.g. short-lived shrews) to size [2]. The Brandt’s bat (Myotis brandtii) holds the
211 years (e.g. bowhead whale) [1]. Although the record for longevity [4], with a maximum lifespan of
bowhead whale is exceptionally long-lived, its lifespan >40 years, living 8~10 times longer than expected given
is arguably not as extreme as that of a 30 years old body size (~7 grams) [2, 4, 5]. This renders bats as one
naked mole-rat given their body sizes, as maximum of the most ideal taxa to explore the molecular basis of
lifespan (MLS) exhibits a positive correlation with body extraordinary longevity in mammals.
size within mammals [2, 3]. Thus, lifespan comparison
across mammals requires body size correction. To Although the majority of bat species are long-lived,
resolve this, the longevity quotient (LQ) was especially within the Myotis genus, there are a few
introduced, which is defined as the ratio of observed short-lived exceptions, such as the velvety free-tailed

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bat (Molossus molossus) and the evening bat transcriptomes of M. myotis and M. molossus. Although
(Nycticeius humeralis), living as long as would be the majority of genes underwent purifying selection, we
expected given their body size [5, 6]. A recent study has observed a significant transcriptional alteration between
suggested that the ancestral bat lived up to 2.6 times these two species. Among 2,086 genes that exhibited
longer than expected given body size, indicating that the large interspecific expression variation, the genes that
extreme longevity observed in the longest-lived bat showed higher expression in long-lived M. myotis were
genera may have evolved multiple times [7]. This also mainly enriched in DNA repair and autophagy. Further
suggests that short-lived bat species may have lost their pathway analysis suggested that six biological
longevity adaptations. Therefore, this wide range of processes, including autophagy, were differentially
lifespans observed in bats enables us to utilize expressed between M. myotis and M. molossus. We also
comparative evolutionary approaches to search for show that M. myotis had significantly lower expression
genetic differences within closely-related long- and levels of anti-longevity genes, suggestive of a
short-lived bat species. In contrast to comparative transcriptomic signature of longevity naturally evolved
studies on phylogenetically-distant species (e.g. bats in long-lived bats. Together with the previous findings
versus mice), this comparison could minimize the in other long-lived mammals, our study implies that
‘noise’ resulting from heterogenous physiology, and enhanced DNA repair and autophagy activity may
may reveal key anti-aging molecular adaptations that represent a universal mechanism to achieve longevity in
have evolved in long-lived bats, or were lost in their long-lived mammals.
short-lived counterparts.
RESULTS
Genome-wide comparative analyses have been carried
out on a few long- and short-lived species in primates The majority of genes undergo purifying selection
[8], rodents [9, 10], whales [11] and bats [12]. These
studies revealed a few genes that showed convergent To evaluate the natural selection acting on protein-
amino acid mutations, or exhibited positive selection, or coding genes between M. myotis and M. molossus, we
were differentially expressed in long-lived species calculated the ratio of Ka and Ks substitution rates for
compared with their short-lived counterparts. Although each pair of orthologous genes. We observed that most
there is little commonality across the gene candidates of the genes (97.96%) were under purifying selection
that are associated with longevity revealed by these (Ka/Ks ratio < 1, FDR < 0.05), with the median of
studies, they are mainly enriched in DNA repair and Ka/Ks ratios equal to 0.103 (Figure 1A). In total, 48
maintenance, autophagy, homeostasis, and nutrient genes had the ratios of Ka/Ks > 1, only three of which
sensing pathways [13]. In bats, our previous (FATE1, MLKL and CCDC175) exhibited significant
longitudinal studies showed that long-lived M. myotis positive selection (Fisher’s exact test, FDR < 0.05,
bats maintained their transcriptomic profiles [14] and Figure 1B). To determine if positive selection on these
telomere length [5], and did not exhibit an increased genes was the consequence of species-specific
level of mitochondrial damage with advancing age [15], selective pressures, we conducted pairwise analyses of
all of which likely contribute to their extraordinary orthologous genes across 6 bat species (See Methods).
longevity. However, a parallel comparison between We found that each comparison resulted in a unique
long- and short-lived bats is lacking. set of positively selected genes (PSGs)
(Supplementary Table 1). Interestingly, positive
In this study we performed a comparative genomic and selection on FATE1 and CCDC175 was also observed
transcriptomic analysis between long-lived Myotis between M. molossus, M. myotis and other bat species
myotis (MLS = 37.1 years; LQ = 5.71) and short-lived (Supplementary Table 1). Although MLKL was solely
Molossus molossus (MLS = 5.6 years; LQ = 0.99) [6] to seen under significant positive selection between M.
ascertain the molecular signatures associated with myotis and M. molossus, this gene also showed high
longevity in bats. Based on the genome-wide Ka/Ks ratios between all possible comparisons of bat
alignments of single-copy orthologous genes between species (Figure 1C and 1D).
these two species, we detected and further investigated
the genes that were fast-evolving and showed Transcriptomic profiles exhibit a substantial
significant positive selection. We also deep sequenced difference in long-lived and short-lived bats
blood transcriptomes from eight adult individuals for
each species, and explored the genes and pathways that To ascertain the differences on the transcriptional
were differentially expressed. To ascertain if long-lived level, we further sequenced and compared their blood
bats have evolved a transcriptomic signature of transcriptomes (n = 16) using Illumina RNA-Seq. Out
longevity, we further investigated the expression of of 12,467 orthologs, we excluded 1,832 genes that
‘pro’- and ‘anti’-longevity genes in the blood were not expressed in either M. molossus or M. myotis

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and retained 10,635 genes for downstream analyses. while 2,684 (25.24%) genes were down-regulated
The correlation analysis revealed a considerable (Figure 2B). Interestingly, there was no significant
difference in global transcriptomic profiles between M. difference in the distribution of Ka/Ks ratios between
molossus and M. myotis (Figure 2A, See Methods). differentially and non-differentially expressed genes
The samples showed statistically higher intraspecific (P = 0.162, Kolmogorov-Smirnov test). Next, we
Spearman’s correlation coefficients (ρ = 0.957) in tested if the Ka/Ks ratios of 10,635 orthologs had an
contrast to the interspecific counterparts (ρ = 0.766) (P association with their differential expression patterns
= 2.2×10-16, Wilcoxon signed-rank test). In addition, in M. molossus and M. myotis. We found that there
4,846 (45.57%) genes were differentially expressed was no significant association between the genes
(FDR < 0.05). 2,162 (20.33%) genes showed up- differentially expressed and their Ka/Ks ratios (P =
regulation in M. myotis compared to M. molossus 0.352, χ2 test, See Methods).

Figure 1. Analysis of Ka/Ks substitution rates of 12,467 single-copy genes between M. myotis and M. molossus. (A)
Distribution of Ka/Ks ratios of 12,467 single-copy genes. To better visualize the distribution, six genes with Ka/Ks > 1.5 were not included in
this plot. (B) Genes with Ka/Ks > 1. Three genes highlighted in red show significant positive selection (Ka/Ks > 1; FDR < 0.05 Fisher’s exact
test). (C) Significance (FDR) of Ka/Ks ratios of FATE1, CCDC175 and MLKL between 6 bat species through pairwise comparisons. The red values
indicate significant positive selection while the blue values indicate significant purifying selection. The black values indicate no selection. (D)
Ka/Ks ratios of FATE1, CCDC175 and MLKL between 6 bat species through pairwise comparisons. The red values indicate Ka/Ks ratios > 1
while the blue values indicate Ka/Ks ratios < 1.

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DNA repair and autophagy are enriched by the lived bats, we investigated the 20 GO terms that were
genes that have genetically higher expression in enriched by these 2,086 genes. We compared expression
long-lived bats levels of all the genes under each enriched GO term
between M. myotis and M. molossus using Wilcoxon
For each of 10,635 genes, we calculated the proportion of signed-rank test (paired mode, one-tailed test) (See
interspecific expression variation using a linear mixed Methods). Out of these 20 terms, the genes under 6 terms
model (See Methods). On average, 24.9% of gene had significantly higher expression in long-lived bats
expression variance was explained by ‘species’ while ‘sex’ than in short-lived bats (FDR < 0.05) (Figure 4A). These
only explained a small proportion of variation (Figure 3A). GO terms include DNA geometric change (GO:
To investigate the gene expression that genetically differed 0032392), RNA localization (GO:0006403), autophagy
in M. myotis and M. molossus, we focused on 2,086 genes (GO:0006914), nucleobase-containing compound
with at least 80% of their expression variance resulted catabolic process (GO:0034655), plasma membrane
from ‘species’ which represented interspecific variation bounded cell projection assembly (GO:0120031), and
(See Methods). As was expected, 2,083 of these genes organelle localization (GO:0051640) (Figure 4B). In
(99.86%) were also detected as differentially expressed contrast, none of these 20 GO terms exhibited
genes (DEGs) (Figure 3B). significantly higher expression in M. molossus than in M.
myotis, respectively (Wilcoxon signed-rank test, paired
In total, 1,060 genes had higher expression levels in M. mode, one-tailed, FDR < 0.05). The genes under each of
molossus while 1,026 genes in M. myotis. GO terms that these 20 enriched GO terms are available in
were enriched for the genes with higher expression in Supplementary Table 2.
short-lived bats include glycerolipid metabolic process,
G1/S transition of mitotic cell cycle and RNA 3’-end Long-lived bats have evolved a transcriptomic
processing (Figure 3C). In contrast, the genes that had signature of longevity
higher expression in long-lived bats were enriched in a
variety of biological processes such as RNA localization, To ascertain whether long-lived bats have naturally
viral life cycle and peptide biosynthetic process (Figure evolved a transcriptomic signature of longevity, we
3D). Interestingly, we observed that DNA repair and compiled a list of anti-longevity and pro-longevity
macroautophagy were also enriched for the genes that genes and compared their expression in the M. myotis
exhibited higher expression in long-lived bats (Figure 3D). and M. molossus blood transcriptomes. We observed
that there was no significant difference in the expression
Pathway analysis reveals up-regulated autophagy of the pro-longevity genes (n = 28) in long-lived and
pathways in long-lived bats short-lived bats (P = 0.381, Wilcoxon signed-rank test,
paired mode, one-tailed, Figure 5A), while the anti-
To identify the biological processes that were longevity genes (n=19) had significantly lower
differentially expressed between short-lived and long- expression in long-lived bats (P = 0.0364, Wilcoxon

Figure 2. Comparisons of M. myotis and M. molossus blood transcriptomes. (A) Spearman’s correlation coefficients between M.
myotis and M. molossus blood transcriptomes based on expression levels of 10,635 single-copy genes. We excluded 1,832 genes that were
neither expressed in M. myotis nor M. molossus. (B) Differential gene expression analysis between M. myotis and M. molossus blood
transcriptomes. Genes with FDR < 0.05 were considered differentially expressed genes (DEGs).

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signed-rank test, paired mode, one-tailed, Figure 5B). selection were detected in 3 genes (FATE1, MLKL
To assess its significance, we randomly subsampled 19 and CCDC175) between M. molossus and M. myotis,
genes out of 2,086 genes for 1,000 times, and performed two of which (FATE1 and CCDC175) were also
Wilcoxon signed-rank tests as stated above and under significant positive selection among other bat
analysed the distribution of the P-values. We noticed species (Supplementary Table 1). This suggests that
that P = 0.0364 fell outside the range of 95% highest FATE1 and CCDC175 evolved fast along all bat
density interval (lower: 0.0844, upper: 0.998), lineages examined and their positive selection might
suggesting that the significance of the test did not result not be associated with longevity. We noticed that
from random chance. MLKL was uniquely seen under significant positive
selection between M. molossus and M. myotis (Figure
DISCUSSION 1C). MLKL is a key signaling molecule in the
necroptosis pathway, a programmed cell death process
Identifying positive selection is a powerful approach [18], and deregulation of this gene has been reported to
to detect genomic adaptations that may contribute to promote necroptosis-induced inflammation in aged
species-specific phenotypes. In this study, we aimed to mice [19]. Interestingly, a recent study investigating
identify signatures of positive selection within a short- several long- and short-lived rodents revealed a
lived bat species (Molossus molossus) and a longer- different set of PSGs, which were enriched in cellular
lived bat species (Myotis myotis) to reveal genomic homeostasis and mTOR pathway [10]. The disparity of
adaptations that correlate with longevity. Similar to PSGs may result from different taxa and methods used
previous studies examining positive selection in bat in these two studies or suggest that the longevity
lineages [16, 17], the majority of genes investigated in mechanisms evolved in long-lived mammals are
this study were under purifying selection, which is not species-specific. In our study, we only examined two
surprising given the evolutionary constraint on protein- bat lineages that have extremely divergent lifespans. As
coding genes. However, signs of significant positive more and more high-quality bat genomes will become

Figure 3. Gene expression variation analysis. (A) Evaluation of gene expression variance using a linear mixed model. Residual variance
represents the contribution from uncharacterized variables. (B) Overlap of differentially expressed genes (blue) and the genes with at least
80% of expression variation resulted from ‘species’ (grey). (C) GO terms that were enriched by 1,060 genes that had higher expression in M.
molossus. (D) GO terms that were enriched by 1,026 genes that had higher expression in M. myotis.

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available [20], a more powerful and comprehensive Although we did not observe strong signals of positive
investigation, such as applying branch-site tests for selection on these protein-coding genes, we did notice a
positive selection to multiple long- and short-lived significant difference in their expression between M.
branches, is required. myotis and M. molossus. Interestingly, we showed that

Figure 4. Expression analysis of the 20 GO terms between M. myotis and M. molossus. (A) Differential expression analysis of GO
terms enriched by 2,086 genes that showed >80% interspecific expression variation. Differentially expressed GO terms were determined by
comparing gene expression under each GO term using Wilcoxon signed-rank test (paired mode; one-tailed test). GO terms with FDR < 0.05
were considered differentially expressed. (B) Distribution of gene expression under each of 6 differentially expressed GO terms between M.
myotis and M. molossus.

Figure 5. Expression analysis of anti- and pro-longevity genes between M. myotis and M. molossus. (A) Comparison of anti-
longevity gene expression (n = 19) between M. myotis and M. molossus using Wilcoxon signed-rank test (paired mode, one-tailed test). (B)
Comparison of pro-longevity gene expression (n = 28) between M. myotis and M. molossus using Wilcoxon signed-rank test (paired mode,
one-tailed test).

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differential or non-differential expression of these genes energy homeostasis [29, 30]. We found that UVRAG,
had no association with the selective pressures acting on which was identified as a tumor suppressor, was up-
them (P = 0.352, χ2 test). Only one of the three PSGs regulated 13.7-fold in long-lived M. myotis compared to
(FATE1) found in our study was differentially M. molossus. UVRAG induces autophagosome
expressed. Therefore, we hypothesize that differential formation and maturation, and its overexpression
gene expression is likely due to post-transcriptional promotes autophagy and suppress tumor cell growth
regulation of non-coding genes rather than natural [31]. Other autophagy-related genes (e.g. ATG3,
selection on these protein-coding genes [21]. ATG4A, ATG4C) also exhibited significantly higher
expression in M. myotis. Increased autophagy activity
Differential expression analysis measures the difference may allow long-lived M. myotis to better counteract the
in mean expression of genes between these two species age-related accumulation of damaged proteins and
but fails to uncover the intraspecific gene expression organelles, thus to improve the metabolic fitness of
variation [22]. Transcriptomes are subjected to change cells. Consistent with our finding, recent studies on
due to instant alterations of physiological status or rodents [32] and whales [11] show that autophagy is
environmental context. As the biometrics of M. myotis significantly enhanced in long-lived species relative to
and M. molossus individuals used in this study, such as their short-lived counterparts. These results imply that
age, disease status and environmental circumstances, enhanced DNA repair and autophagy activity may
are unknown, a large proportion of intraspecific represent a universal mechanism to achieve longevity in
transcriptional variation is expected. One purpose of long-lived species, independent of their phylogenetic
this study is to identify gene expression that genetically distance. Interesting, we also found that the genes
differs in these two species; hence we need to explore enriched in ‘Viral life cycle’ had significantly higher
the genes which have high interspecific but low expression in M. myotis (Figure 3D). This may be due
intraspecific expression variation. To resolve this, we to the possibility that the M. myotis individuals, sampled
employed a linear mixed model to quantify gene from the colonies in France, carried a higher viral load
expression variation (See Methods). We focused on or could represent naturally evolved anti-viral
2,086 genes with at least 80% of their overall mechanism in long-lived bats. This may result in
expression variance resulted from interspecific activation of the genes that control viral replication in
difference, and indeed, a huge overlap between these M. myotis. Coupled with some other enriched GO terms
genes and DEGs was revealed (Figure 3B). We (e.g. RNA localization, glycerolipid metabolic process
excluded 2,763 DEGs with large proportions of and mitotic cell cycle phase transition), its roles in the
intraspecific and other unknown variation from further aging process in bats will need further exploration.
analyses, as their differential expression might not
reflect genetic difference between these two species. Focusing on these 2,086 genes, we further explored the
biological processes and expression of all the genes that
Among these 2,086 genes, we noticed that the genes were enriched under each GO term (See Methods). We
having higher expression in long-lived M. myotis were found that, compared to M. molossus, the genes under 6
enriched in DNA repair and autophagy. For example, enriched GO categories had significantly higher
WRN and XPC were expressed 6.7-fold and 4.8-fold expression in M. myotis, respectively (Figure 4A and
higher in M. myotis compared to M. molossus, 4B, Wilcoxon signed-rank test, FDR-adjusted P < 0.05).
respectively. WRN has been shown to regulate the repair Apart from autophagy which has a crucial role in the
of DNA double strand breaks (DSBs) and may play a regulation of lifespan, the other 5 terms have not been
role in telomere maintenance [23], while XPC may act clearly linked with aging yet. These 5 differentially
as a general sensor of damaged DNA and involve in expressed GO categories may indicate the general
base excision repair (BER) [24]. Genomic stability is transcriptomic differences between these two species.
under constant challenge by intrinsic and extrinsic
agents [25]. In most mammals, the capability of Next, we investigated a list of pro-longevity and anti-
genomic maintenance attenuates with advancing age, longevity genes [33] to ascertain if long-lived bats have
leading to accumulation of DNA damage and thus, age- naturally evolved a transcriptomic profile of longevity.
related phenotypes [26, 27]. However, together with our These genes are mainly involved in DNA repair,
previous findings in long-lived M. myotis bats [14], immunity, and cell growth and proliferation, which
multiple lines of evidence have revealed up-regulation have been functionally validated to shorten or prolong
of genes directly involved in DNA damage signalling lifespan in mice via overexpression, knockdown or
and repair in a few long-lived mammals during aging, knockout experiments [33]. Our results suggest that,
such as human [28], naked mole-rat [28] and bowhead while the expression levels of the pro-longevity genes
whale [11]. In addition, autophagy is a critical recycling did not significantly differ between these two species,
pathway which maintains cellular metabolism and M. myotis are likely to achieve longevity by suppressing

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the expression of some anti-longevity genes. Most 12,467 single-copy orthologs between M. myotis and M.
remarkably, IGF1R and DGAT1 were down-regulated molossus. These alignments were obtained from the
23.7-fold and 23.2-fold in long-lived M. myotis Bat1K project [12, 20]. For each pair of orthologs, we
compared to short-lived M. molossus, respectively. calculated the ratio of nonsynonymous (Ka) and
IGF1R is an insulin receptor which exerts pleiotropic synonymous (Ks) substitution rates using
roles in glucose metabolism, cell growth development KaKs_Calculator (v2.0) [40] with the Model Averaging
and survival [34]. However, deregulation of IGF1R (MA) method. Model averaging weights each candidate
expression, commonly seen within individuals in their model (7 in total) and engages more than one model to
late-life stage, is associated with the occurrence and estimate average parameters across models. Fisher’s
development of diabetes, inflammation and cancer [34]. exact test was performed to determine the significance
It has been reported that igf1r-knockout mice live on of positive selection. The genes with Ka/Ks >1 and
average 26% longer than their wide-type littermates adjusted P-value (FDR) < 0.05 were considered
[35]. In addition, a previous study observed decreased significant positive selection. We further inspected and
expression of genes involved in insulin/IGF-1 signalling filtered the positively selected genes (PSGs) due to
pathways in the liver of naked mole-rat compared with short alignment (less than 100 bp) and low sequence
mice [36]. Likewise, the role of DGAT1 is diverse and coverage (less than 80%).
its overexpression promotes the development of insulin
resistance, obesity and fatty-acid induced inflammation To ascertain if the PSGs identified are unique to the M.
[37, 38]. Deficiency of DGAT1 protects against the myotis and M. molossus comparison, we included 4
metabolic consequences of aging and extends mean and other bat species, which are equivalent in genome
maximal lifespan in mice [39]. These candidates, completeness and annotation (Pipistrellus kuhlii,
together with their expression patterns in long-lived Phyllostomus discolor, Rhinolophus ferrumequinum and
bats, could present promising therapeutic targets to Rousettus aegyptiacus), and investigated Ka/Ks ratios of
delay aging in humans. However, how M. myotis bats genes via pairwise comparisons (n = 15). The
naturally regulate and control expression of these genes alignments of single-copy orthologs across these six
requires further investigation, particularly on non- species were obtained from the Bat1K project [12, 20].
coding regions that may underlie the regulatory The method for Ka/Ks calculation and the criteria for
mechanisms of their longevity adaptations [14]. defining PSGs were the same as stated above.

In summary, comparative genomic and transcriptomic Blood sample collection and RNA sequencing
analyses on M. molossus and M. myotis resulted in the
discovery of some genetic signatures that may underlie The sampling procedures were undertaken in accordance
the exceptional longevity in long-lived bats. We show with the ethical guidelines and permits issued by ‘Arrêté’
that, even though most of the genes are under purifying by the Préfet du Morbihan and the Ministerio de
selection, long-lived M. myotis bats exhibit a different Ambiente de Panamá. M. myotis and M. molossus
expression profile of enhanced DNA repair and autophagy individuals were captured in Brittany, France and
pathways, and diminished anti-longevity genes, which Gamboa, Panama, respectively. The blood sampling
likely contributes to their extraordinary long lifespan. In procedures were extensively described in [41]. Blood
the future, selection tests on multiple pairs of samples were collected in cryotubes (2 ml, Nalgene
phylogenetically matched long- and short-lived branches labware) and were immediately flash frozen in liquid
are required to address if long-lived bats exhibit nitrogen. All samples were further preserved at -150°C
convergent signatures of longevity or if each lineage has for long-term storage before total RNA extraction. Whole
evolved its own longevity adaptations. In addition, blood total RNA extraction was carried out following the
longitudinal studies of bats within different LQs will need manufacturer’s protocols (RNAzol@ BD kit, catalog no.
to be carried out to identify the age-associated genes and RB192, Molecular Research Centre, Inc) with
pathways that are differentiated between long- and short- modifications as reported in [41]. The samples with RIN
lived bats. As the PSGs and DEGs are suggested on the scores > 8.0 and total RNA > 2 μg satisfied the criteria
basis of in silico analyses, in vitro functional assays are for RNA-Seq. In this study, 16 qualified RNA samples (8
required to confirm their roles in bat longevity. each for M. myotis and M. molossus) were used for
Illumina RNA-Seq library preparation. Prior to
MATERIALS AND METHODS extraction, the RNA samples were purified by Turbo
DNA-freeTM kit (catalog number AM1907, Ambion) to
Genome-wide analysis of Ka/Ks substitution rates deplete residual DNA, and were further treated with
Globin-Zero Gold rRNA Removal kit (Epicentre
To assess the selective pressure acting on protein- Illumina) to remove abundant rRNA and globin
coding genes, we analysed genome-wide alignments of transcripts. RNA-Seq libraries were prepared using the

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Tru-Seq Stranded RNA Library Prep kit (Illumina), and M. molossus. Using Metascape [47], function
further barcoded and sequenced on an Illumina enrichment analyses were performed on the genes that
HiSeq2500 sequencer to generate 125-bp paired-end had higher expression levels in M. myotis and M.
reads. Sample details and statistics of the RNA-Seq molossus, respectively. The GO terms with FDR < 0.05
libraries are available in Supplementary Table 3. were considered significantly enriched.

Comparative transcriptomic analyses Differential expression of biological processes

between M. myotis and M. molossus
For each sample, raw reads were trimmed adaptors and
low-quality regions (< Q25) using Cutadapt (v.1.14) To identify the biological processes (GO terms) that
[42]. The filtered reads were subsequently quantified were differentially expressed between M. myotis and M.
against the reference genes using Salmon (v0.9) [43] molossus, we investigated gene expression at the GO
with the following parameters: -k 31, -ISF. -k indicates term level. To achieve this, we focused on the 2,086
the length of seed while -ISF indicates a library of genes that may truly represent the genetic difference
stranded-specific paired-end reads oriented towards between these two species, and performed a GO
each other. Here, we used 12,467 pairs of single-copy enrichment analysis using Metascape [47]. The GO
orthologs as references for expression analysis for terms with FDR < 0.05 were considered significantly
respective species. The genes which were not expressed enriched terms. Subsequently, we collected all the genes
in either M. molossus or M. myotis were excluded from under each enriched term in M. myotis and M. molossus,
downstream analysis. Based on gene expression, we and compared their expression levels using Wilcoxon
computed pairwise Spearman’s correlation coefficients signed-rank tests (paired mode, one-tailed test). The
across samples using the R package cor (v.3.6.0) [44]. significance of tests was adjusted by Benjamini-
Prior to analysis, raw expression counts were Hochberg FDR, and the GO terms with FDR < 0.05
normalized using TMM (Trimmed Mean of M-value) were considered differentially expressed between M.
method and further log2-transformed. Next, differential myotis and M. molossus.
gene expression analysis was performed using the R
package DESeq2 [45]. The genes with an FDR < 0.01 Expression of anti- and pro-longevity genes in M.
were considered differentially expressed genes (DEGs). myotis and M. molossus
In addition, we also investigated the distributions of the
Ka/Ks ratios of differentially and non-differentially To further investigate whether M. myotis harbored a
expressed genes using a Kolmogorov-Smirnov test. We transcriptomic signature of longevity relative to M.
further performed a χ2 test to ascertain if the PSGs molossus, we compiled a list of anti-longevity genes (n
between M. myotis and M. molossus correlated with the = 19) and pro-longevity genes (n = 28) from GenAge
DEGs identified (P-value < 0.05 was considered [33]. These genes have been validated to either shorten
significant). (anti-longevity) or extend (pro-longevity) lifespan in
mice via overexpression, knockdown or knockout. We
Gene expression variation analysis tested whether their expression significantly differed in
these two species using Wilcoxon signed-rank tests
Differential gene expression analysis measures the (paired mode; one-tailed test), respectively. Our result
difference in mean expression between two groups but showed that expression levels of the anti-longevity
does not quantify expression variation within each genes had significantly lower expression (P < 0.05) in
group. To detect gene expression which may truly long-lived M. myotis than short-lived M. molossus. To
represent genetic difference between M. myotis and M. evaluate the significance of this test, we randomly
molossus, we employed a linear mixed model (LMM) to subsampled 19 genes out of 2,086 genes and performed
identify genes with high interspecific but low Wilcoxon signed-rank tests as previously described.
intraspecific variation. Normalised gene expression This was repeated 1,000 times with the P-value of each
values were considered as dependent variables, whereas test collected and their distribution further analysed
‘species’ and ‘sex’ were considered as explanatory using the R package HDInterval. The list of anti- and
variables and were modelled as random effects. The pro-longevity genes investigated in this study and their
variance from uncharacterized sources was treated as expression levels in M. myotis and M. molossus blood
residual variance. The LMM was implemented using can be available in Supplementary Table 4.
the R package variancePartition [46]. We focused on
the genes for which at least 80% of their expression AUTHOR CONTRIBUTIONS
variation was explained by ‘species’. This resulted in
2,086 genes that were further categorized into two E.C.T. and Z.H. devised this study. E.C.T., C.V.W., and
groups depending on their expression in M. myotis and Z.H. collected Myotis myotis samples. D.D. collected

www.aging-us.com 15970 AGING

Molossus molossus samples. C.V.W., and Z.H. old, yet staying young: the role of telomeres in bats’
performed RNA extraction. Z.H. performed all the data exceptional longevity. Sci Adv. 2018; 4:eaao0926.
analysis and wrote the first draft. All the authors edited https://doi.org/10.1126/sciadv.aao0926
and approved the manuscript. PMID:29441358
6. Healy K, Guillerme T, Finlay S, Kane A, Kelly SB,
ACKNOWLEDGMENTS McClean D, Kelly DJ, Donohue I, Jackson AL, Cooper N.
Ecology and mode-of-life explain lifespan variation in
We thank Dr. Graham Hughes for the suggestions on birds and mammals. Proc Biol Sci. 2014; 281:20140298.
selection tests. We also thank the numerous volunteers https://doi.org/10.1098/rspb.2014.0298
and students from Bretagne Vivante and University PMID:24741018
College Dublin for their help in Myotis myotis sample
collection and the owners/authorities for allowing 7. Wilkinson GS, Adams DM. Recurrent evolution of
access to the sites. extreme longevity in bats. Biol Lett. 2019;
15:20180860.
CONFLICTS OF INTEREST https://doi.org/10.1098/rsbl.2018.0860
PMID:30966896
The authors declare that there are no conflicts of 8. Muntané G, Farré X, Rodríguez JA, Pegueroles C,
interest. Hughes DA, de Magalhães JP, Gabaldón T, Navarro A.
Biological processes modulating longevity across
FUNDING primates: a phylogenetic genome-phenome analysis.
Mol Biol Evol. 2018; 35:1990–2004.
This study was funded by a European Research Council https://doi.org/10.1093/molbev/msy105
Research Grant (No. ERC-2012-StG311000), a UCD PMID:29788292
Wellcome Institutional Strategic Support Fund,
9. Sahm A, Bens M, Henning Y, Vole C, Groth M, Schwab
financed jointly by University College Dublin and SFI-
M, Hoffmann S, Platzer M, Szafranski K, Dammann P.
HRB-Wellcome Biomedical Research Partnership (No.
Higher gene expression stability during aging in long-
204844/Z/16/Z), and an Irish Research Council
lived giant mole-rats than in short-lived rats. Aging
Consolidator Laureate Award to Emma. C. Teeling.
(Albany NY). 2018; 10:3938–56.
https://doi.org/10.18632/aging.101683
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SUPPLEMENTARY MATERIALS

Supplementary Tables

Supplementary Table 1. Positive selected genes (PSGs) identified among 6 bat species through pairwise comparisons.
Ensembl Transcript ID Gene Symbol Ka Ks Ka/Ks FDR
Molossus molossus versus Pipistrellus kuhlii
ENST00000537690 CCDC175 0.3273 0.2503 1.31 0.0036
Molossus molossus versus Phyllostomus discolor
ENST00000393316 BCL2L15 0.314 0.1867 1.682 0.0156
ENST00000618484 BPIFA1 0.5722 0.3442 1.662 0.0001
Molossus molossus versus Rhinolophus ferrumequinum
ENST00000378186 MS4A13 0.33 0.1873 1.762 0.0274
ENST00000380232 IFNB1 0.4029 0.259 1.556 0.0424
ENST00000368051 CD84 0.2354 0.1565 1.504 0.03
ENST00000537690 CCDC175 0.2651 0.2173 1.22 0.0436
Molossus molossus versus Rousettus aegyptiacus
ENST00000369102 C1orf54 0.2231 0.0985 2.264 0.0111
ENST00000537690 CCDC175 0.268 0.2173 1.233 0.0336

Ensembl Transcript ID Gene Symbol Ka Ks Ka/Ks FDR

Myotis myotis versus Phyllostomus discolor
NA
Myotis myotis versus Pipistrellus kuhlii
ENST00000391930 IL20 0.1981 0.0841 2.357 0.0061
ENST00000378186 MS4A13 0.1849 0.0831 2.226 0.0131
ENST00000546561 TSPAN8 0.2668 0.1396 1.911 0.0016
ENST00000389019 SLCO6A1 0.1507 0.0912 1.653 0.0159
ENST00000537690 CCDC175 0.1775 0.115 1.543 0.0013
ENST00000273352 ADGRG7 0.1874 0.1474 1.272 0.0477
Myotis myotis versus Rhinolophus ferrumequinum
ENST00000372670 WFDC6 0.2698 0.1064 2.535 0.0304
ENST00000370350 FATE1 0.3787 0.2216 1.79 0.0074
ENST00000537690 CCDC175 0.321 0.2407 1.334 0.0014
Myotis myotis versus Rousettus aegyptiacus
ENST00000445202 PATE3 0.2811 0.1345 2.091 0.0358
ENST00000381627 RLN2 0.3601 0.1987 1.812 0.0205
ENST00000370350 FATE1 0.3579 0.2039 1.755 0.0037
ENST00000537690 CCDC175 0.3025 0.2511 1.205 0.0439

Ensembl Transcript ID Gene Symbol Ka Ks Ka/Ks FDR

Phyllostomus discolor versus Pipistrellus kuhlii
ENST00000546561 TSPAN8 0.3542 0.2529 1.4 0.0373
Phyllostomus discolor versus Rhinolophus ferrumequinum
ENST00000296739 SPZ1 0.2467 0.1614 1.528 0.0072
Phyllostomus discolor versus Rousettus aegyptiacus
ENST00000371431 AKAP19 0.2644 0.1427 1.853 0.037
Pipistrellus kuhlii versus Rhinolophus ferrumequinum
ENST00000378186 MS4A13 0.3606 0.1745 2.066 0.0023
ENST00000370250 FATE1 0.419 0.2327 1.801 0.0053
ENST00000537690 CCDC175 0.3427 0.2656 1.29 0.0047
Pipistrellus kuhlii versus Rousettus aegyptiacus
NA
Rhinolophus ferrumequinum versus Rhinolophus ferrumequinum
ENST00000382208 DEFB135 0.3642 0.1551 2.349 0.0129
Genes that exhibited Ka/Ks > 1 and FDR < 0.05 (Fisher exact test) were considered positively selected genes.

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Please browse Full Text version to see the data of Supplementary Table 2.
Supplementary Table 2. Information of the 20 GO terms enriched by 2,084 genes that may represent the genetic
difference between M. myotis and M. molossus.

Supplementary Table 3. Information of M. myotis and M. molossus RNA-Seq samples.

Species Sample ID Age Sex Raw reads Clean reads
AHKX-1 Adult Female 32,087,001 29,122,203
AHKX-2 Adult Male 39,138,864 35,776,979
AHKX-3 Adult Female 34,994,963 32,206,385
AHKX-4 Adult Male 42,599,132 38,612,182
M. molossus
AHKX-5 Adult Female 44,567,553 40,710,399
AHKX-6 Adult Female 39,533,956 36,065,884
AHKX-7 Adult Male 41,315,334 38,443,201
AHKX-8 Adult Female 41,544,292 38,563,116
AJCC-7 Adult Female 69,608,563 63,479,697
AJCC-9 Adult Female 56,347,739 50,896,083
AJCC-11 Adult Female 57,600,266 54,034,263
AJCC-13 Adult Female 75,867,273 70,421,670
M. myotis
AJCC-17 Adult Female 61,537,380 55,193,047
AJCC-18 Adult Female 66,857,830 60,145,110
AJCC-22 Adult Female 60,840,476 55,478,542
AJCC-27 Adult Female 69,521,460 63,916,035

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Supplementary Table 4. The expression of anti- and pro-longevity genes in M. myotis and M. molossus.
TMM normalized expression of anti-longevity genes
Gene Description M.myotis M. molossus
INSR Insulin receptor 2792.163 5929.826
GSTA4 Glutathione S-transferase Alpha 4 89.007 1284.609
TERF2 Telomeric repeat binding factor 2 251.694 31.528
COQ7 Cozenzyme Q7, Hydroxylase 57.091 328.937
EIF5A2 Eukaryotic translation initiation factor 5A2 27.979 21.402
EEF1E1 Eukaryotic translation elongation factor 1 Epsilon 1 20.796 5.661
EPS8 Epidermal growth factor receptor pathway substrate 8 139.443 1.307
CDKN1A Cyclin dependent kinase inhibitor 1A 10.976 43.224
MTOR Mechanistic target of rapamycin kinase 279.099 285.992
BAX BCL2 associated X, apoptosis regulator 14.122 22.982
PARP1 Poly(ADP-ribose) polymerase 1 74.309 233.679
SHC1 SHC adaptor protein 1 25.109 57.983
KCNA3 Potassium voltage-gated channel subfamily A member 3 15.122 36.579
IGF1R Insulin like growth factor 1 receptor 22.789 540.124
MYC MYC proto-oncogene, BHLH transcription factor 12.103 8.237
ADCY5 Adenylate cyclase 5 19.26 0
DGAT1 Diacylglycerol O-acyltransferase 1 3.479 80.706
MIF Macrophage migration inhibitory factor 0 5.14
GHR Growth hormone receptor 3.1 0
TMM normalized expression of pro-longevity genes
Gene Description M. myotis M. molossus
RICTOR RPTOR independent companion of MTOR complex 2 12869.042 595.476
ARHGAP1 Rho GTPase activating protein 1 43.247 38.333
BUB1B BUB1 mitotic checkpoint serine/threonine kinase 7222.727 4630.683
PTEN Phosphatase and tensin homolog 1830.856 0
ZMPSTE24 Zinc metallopeptidase STE24 1628.613 393.672
UCP2 Uncoupling protien 2 577.02 2683.561
TPP2 Tripeptidyl peptidase 2 2404.549 955.757
PPM1D Protein Phosphatase, Mg2+/Mn2+ dependent 1D 1184.73 7689.797
CDK7 Cyclin dependent kinase 7 552.9 146.54
CISD2 CDGSH iron sulfur domain 2 150.344 216.23
SQSTM1 Sequestosome 1 456.844 361.879
PRDX1 Peroxiredoxin 1 184.507 58.715
SOD2 Superoxide dismutase 2 103.747 353.785
STUB1 STIP1 homology and U-box containing protein 1 166.509 44.34
GRN Granulin precursor 261.758 33.561
SIRT1 Sirtuin 1 372.305 509.23
GSK3A Glycogen synthase kinase 3 Alpha 148.867 300.306
ATM ATM serine/threonine kinase 1244.425 5006.536
CLOCK Clock circadian regulator 203.001 22.427
XRCC5 X-ray repair cross complementing 5 137.304 190.863
CAT Catalase 0 10.697
FOXM1 Forkhead box M1 107.912 225.901
RAE1 Ribonucleic acid export 1 36.031 293.434
MSRA Methionine sulfoxide reductase A 11.906 4.044
TOP3B DNA topoisomerase III Beta 50.827 61.747
ARNTL Aryl hydrocarbon receptor nuclear translocator like 28.035 13.074
NUDT1 Nudix hydrolase 1 0 57.421
SIRT6 Surtuin 6 0.381 5.36
Note: for each species, gene expression value is represented by the median of TMM normalized expression across all samples
(n=8)
Gene expression values were normalized using Trimmed Mean of M-value (TMM) method.

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