BIO275 Orange County Community College Article Summary Red Panda VS Giant Panda summary on the article attached below. please use the rubric to write the p

BIO275 Orange County Community College Article Summary Red Panda VS Giant Panda summary on the article attached below. please use the rubric to write the paper properly and also no outside sources are allowed other than the article itself. please use citations from the article to provide evidence and prove the point and use in-text citations.Your papers should be 3 pages long, double-spaced, and use 12-point font (Times New Roman) and 1-in margins. There See the attached grading rubric. Comparative genomics reveals convergent evolution
between the bamboo-eating giant and red pandas
Yibo Hua,1, Qi Wua,1, Shuai Maa,b,1, Tianxiao Maa,b,1, Lei Shana, Xiao Wanga,b, Yonggang Niea, Zemin Ningc, Li Yana,
Yunfang Xiud, and Fuwen Weia,b,2
a
Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; bUniversity of
Chinese Academy of Sciences, Beijing 100049, China; cWellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United
Kingdom; and dStraits (Fuzhou) Giant Panda Research and Exchange Center, Fuzhou 350001, China
Edited by Steven M. Phelps, University of Texas at Austin, Austin, TX, and accepted by Editorial Board Member Joan E. Strassmann December 15, 2016
(received for review August 19, 2016)
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de novo genome phenotype convergence
positive selection pseudogenization
| amino acid convergence |
genetic base” (13), and Stephen J. Gould later featured the new
digit in the title of his popular 1980 book, “The Panda’s Thumb”
(14). In the red panda, the pseudothumb also facilitates arboreal
locomotion (15). Despite this widespread interest, its genetic basis
has remained elusive. These shared characteristics between giant
and red pandas represent a classic model of convergent evolution
under presumably the same environmental pressures.
In this study, we identified genomic signatures of convergent
evolution in both pandas by comparing two genome assemblies, a
de novo sequenced red panda genome and a much improved giant
panda genome assembly with added sequencing data. These findings yield rich insights into pseudothumb development and nutritional utilization of bamboo.
Results and Discussion
We sequenced the genome of a wild male red panda by using the
Illumina Hiseq 2000 platform with a whole-genome shotgun sequencing strategy (SI Appendix, SI Materials and Methods). A total
of 292 Gb of sequence data (121.7-fold genome coverage) was
generated (SI Appendix, Table S1). The genome size of the final
de novo assembly was 2.34 Gb, comparable to that of the ferret
(2.41 Gb) and dog (2.44 Gb), with contig N50 of 98.98 Kb and
S
imilar selective pressures can lead to the parallel evolution of
identical or similar traits in distantly related species, often
referred to as adaptive phenotypic convergence (1–3). A critical
mechanism underlying phenotypic convergence is genetic convergence, including the same metabolic and regulatory pathways,
protein-coding genes, or even identical amino acid substitutions in
the same gene (1–3). However, genome-wide surveys of convergent evolution are relatively rare (4–6), and more empirical genome-scale studies are needed to elucidate the genetic bases of
phenotypic convergence.
The giant panda (Ailuropoda melanoleuca) and red panda
(Ailurus fulgens), two endangered and sympatric species that diverged approximately 43 million years ago (Mya), have distinct
phylogenetic positions in the order Carnivora (7). The giant panda
belongs to the family Ursidae (8), whereas the red panda belongs to
the family Ailuridae within the superfamily Musteloidea (9).
Uniquely in the Carnivora, both pandas are specialized herbivores
with an almost exclusive bamboo diet (>90%), although they still
retain a typical Carnivore digestive tract. Bamboo is a low-nutrition,
high-fiber food with only 13.2% protein, 3.4% fat, and 3.3% soluble
carbohydrate (10). Therefore, efficient absorption of nutrients, especially essential amino acids, essential fatty acids, and vitamins,
from the specialized bamboo diet is vital to growth, development,
and reproduction in both species.
Remarkably, both pandas have evolved a pseudothumb, an enlarged radial sesamoid (Fig. 1) that significantly facilitates feeding
dexterity by grasping bamboo (11–14), a phenotype of long-standing
interest to evolutionary biologists. D. Dwight Davis, for example,
noted that in the giant panda, “the highly specialized and obviously
functional radial sesamoid has a specific, but probably very simple,
www.pnas.org/cgi/doi/10.1073/pnas.1613870114
Significance
The giant panda and red panda are obligate bamboo-feeders that
independently evolved from meat-eating ancestors and possess
adaptive pseudothumbs, making them ideal models for studying
convergent evolution. In this study, we identified genomic signatures of convergent evolution associated with bamboo eating.
Comparative genomic analyses revealed adaptively convergent
genes potentially involved with pseudothumb development and
essential bamboo nutrient utilization. We also found that the
umami taste receptor gene TAS1R1 has been pseudogenized in
both pandas. These findings provide insights into genetic mechanisms underlying phenotypic convergence and adaptation to a
specialized bamboo diet in both pandas and offer an example of
genome-scale analyses for detecting convergent evolution.
Author contributions: F.W. designed research; Y.H., Q.W., S.M., and T.M. performed research; Y.H., Q.W., S.M., T.M., L.S., X.W., Y.N., Z.N., L.Y., and Y.X. analyzed data; Y.H. and
F.W. wrote the paper; and Y.N. and Y.X. prepared the sample.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission. S.M.P. is a Guest Editor invited by the Editorial
Board.
Data deposition: Sequence data have been deposited in the Sequence Read Archive under
accession nos. SRP064935 and SRP064940. The red panda whole genome shotgun project
has been deposited at DDBJ/EMBL/GenBank under accession no. LNAC00000000. The
version described in this paper is version LNAC01000000. The giant panda whole genome
shotgun project has been deposited at DDBJ/EMBL/GenBank under accession no.
LNAT00000000. The version described in this paper is version LNAT01000000.
1
Y.H., Q.W., S.M., and T.M. contributed equally to this work.
2
To whom correspondence should be addressed. Email: weifw@ioz.ac.cn.
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.
1073/pnas.1613870114/-/DCSupplemental.
PNAS | January 31, 2017 | vol. 114 | no. 5 | 1081–1086
EVOLUTION
Phenotypic convergence between distantly related taxa often mirrors
adaptation to similar selective pressures and may be driven by genetic
convergence. The giant panda (Ailuropoda melanoleuca) and red
panda (Ailurus fulgens) belong to different families in the order Carnivora, but both have evolved a specialized bamboo diet and adaptive
pseudothumb, representing a classic model of convergent evolution.
However, the genetic bases of these morphological and physiological
convergences remain unknown. Through de novo sequencing the red
panda genome and improving the giant panda genome assembly
with added data, we identified genomic signatures of convergent
evolution. Limb development genes DYNC2H1 and PCNT have undergone adaptive convergence and may be important candidate genes
for pseudothumb development. As evolutionary responses to a bamboo diet, adaptive convergence has occurred in genes involved in the
digestion and utilization of bamboo nutrients such as essential amino
acids, fatty acids, and vitamins. Similarly, the umami taste receptor
gene TAS1R1 has been pseudogenized in both pandas. These findings
offer insights into genetic convergence mechanisms underlying phenotypic convergence and adaptation to a specialized bamboo diet.
Fig. 1. Genome-wide phylogenetic tree of giant and red pandas, and their convergent pseudothumbs. (A) Phylogenomic tree, divergence time (blue), and
expansion (purple, +) and contraction (red, ?) of gene family in red and giant pandas, and other six Eutherian species. Three divergence times (red node) were
used as the calibration points for estimating divergence time. The estimated divergence times were showed with 95% confidence intervals (in parentheses). The
posterior probabilities for each branch of the tree were showed. (B) Diagram of pseudothumb (pt) of red panda (Upper) and giant panda (Lower).
scaffold N50 of 2.98 Mb (SI Appendix, Figs. S1–S5 and Table S2).
Alignment of the genome scaffolds to BAC clone sequences indicated that scaffold coverage was in the range of 97.04?99.85%
without any scaffold inconsistencies (SI Appendix, Fig. S6 and
Table S3), Core Eukaryotic Genes Mapping Approach (CEGMA)
evaluation (16) found that 242 (97.58%) of 248 core eukaryotic
genes were complete (SI Appendix, Table S4), and Benchmarking
Universal Single-Copy Orthologs (BUSCO) assessment (17) on
genome assembly showed that 2,632 (87.07%) of 3,023 conserved
vertebrate genes were assembled to be complete (SI Appendix,
Table S5). A total of 21,940 protein-coding genes were annotated
by combining homology-based and ab initio gene prediction
methods, with 90.77% of gene models supported by RNA-seq
transcripts (SI Appendix, Fig. S7 and Table S6). BUSCO assessment on gene annotation showed that 2,533 (83.79%) of 3,023
conserved vertebrate genes were annotated to be complete (SI
Appendix, Table S5). Repeat elements occupied 41.23% of the red
panda genome, similar to that of the giant panda (41.29%) and
dog (41.95%) (SI Appendix, Fig. S8 and Tables S7–S11). To make
the assembly quality of the giant panda genome comparable to
that of the red panda genome, we reassembled the giant panda
genome by combination of ?82 × new sequencing data and published mate-pair reads (SI Appendix, Table S12) (18). The reassembled genome was significantly improved compared with the
reference (version ailMel1) (18), with contig N50 from 40 Kb to
126.71 Kb and scaffold N50 from 1.28 Mb to 9.9 Mb (SI Appendix,
Table S13). Furthermore, extra contig sequences of 136 Mb were
assembled, presumably from gap regions of the reference genome.
Totally, 23,371 protein-coding genes were annotated in the improved genome, where 88.79% of gene models were verified by
RNA-seq transcripts (SI Appendix, Fig. S7 and Table S14).
To reveal the genomic signatures of convergent evolution in
both pandas, we first constructed a genome-wide phylogenetic tree
combining the published genomes of the polar bear, ferret, dog,
tiger, human, and mouse (SI Appendix, Table S15). A total of
171,041 protein-coding genes from these eight species were used
for gene family analysis, and 14,534 gene families were identified
(SI Appendix, Fig. S9), including 2,855 single-copy true orthologous
genes across all eight species. After removing 326 genes with
convergent amino acid substitutions and excluding the third codon
positions of exons, the constructed genome-wide phylogenetic tree
confirmed recent molecular conclusions (7–9) that the giant panda
belongs to the family Ursidae together with the polar bear, whereas
the red panda and ferret belong to the superfamily Musteloidea
1082 | www.pnas.org/cgi/doi/10.1073/pnas.1613870114
(Fig. 1). Based on the 133 genes evolving under the strict molecular
clock, a divergence time of 47.5 Mya (95% confidence interval,
39.5?54.4 Mya) between giant and red pandas was derived by using
three calibration points (Fig. 1). This result was slightly higher than
previous molecular-based estimate of 43 Mya (7).
Based on homologous gene annotations by syntenic alignment
across the eight species (Fig. 1), 14,254 orthologous genes were
used for genomic convergence and positive selection analyses. First,
convergent amino acid substitutions between both pandas were
identified based on Zhang and Kumar’s method (19). Considering
noise resulting from chance amino acid substitutions (6, 20), we
performed a statistical test to compare the observed number of
convergent sites with random expectation under the JTT-fgene and
JTT-fsite amino acid substitution models, respectively (21), and
found that 1,066 and 645 genes with convergent amino acid substitutions contained significantly more sites than the random expectation (q < 0.05). Because the result under the JTT-fsite model has a relatively large bias when the number of species analyzed is small (eight species in our study), we used the result under the JTT-fgene model for the next analysis. Because of possible impact of gene tree discordance on the identification of amino acid convergence (3, 22), we further removed 15 genes whose gene trees supported the clustering of the giant and red panda lineages. Second, 434 positively selected genes were identified by a branch-site model in PAML (SI Appendix, Tables S16–S18) (23). Similar to the above, because gene tree discordance could also affect the identification of positive selection (24), we removed 18 genes whose positive selection signatures were lost under their respective gene trees. Finally, to obtain more conservative signatures of adaptive convergence, we focused on positively selected genes with nonrandom convergent amino acid substitutions (i.e., adaptively convergent genes) (5, 20). As a result, 70 adaptively convergent genes were identified (SI Appendix, Tables S19 and S20), and gene ontology and KEGG enrichment analyses discovered significant terms and pathways involved in limb development and nutrient utilization, including appendage and limb development (GO:0048736, P = 0.0321), cilium assembly (GO:0042384, P = 0.0376), protein digestion and absorption (ko04974, P = 0.0086), and retinol metabolism (ko00830, P = 0.0217) (SI Appendix, Tables S21 and S22). Among the 70 adaptively convergent genes, DYNC2H1 and PCNT are involved in limb development and their missense or null mutations result in a polydactyly phenotype and abnormal skeletogenesis in both mice and humans (25–28). These findings suggest that convergent amino acid substitutions in these genes may Hu et al. organelles of the Sonic Hedgehog (SHH) signaling pathway, and abnormal cilia would inhibit the functions of GLI3, a major downstream target of the SHH pathway (25). Dysfunction of GLI3 produces ectopic digits and polydactyly in mice (29). Therefore, structural or functional variation in cilia may well contribute to developmental novelty of bones and limbs through the SHH pathway and GLI3 blockade (25). Indeed, across 62 Eutherian species, the R3128K substitution occurs exclusively in giant and red pandas and is verified by more additional individuals (Fig. 2B and SI Appendix, Table S23–S25). Moreover, these mutations have not been reported in population-level SNP datasets or databases of polar Fig. 2. Adaptively convergent genes closely related with limb development. (A) Structural domains of DYNC2H1 protein and the locations of two convergent amino acid sites. The structural domain annotation derives from the SMART database. (B) Comparison of two convergent amino acid substitutions of DYNC2H1 gene among the genomes of 59 Eutherian species and the gene fragments of three other Eutherian species (Ursus thibetanus, Mephitis mephitis, and Procyon lotor). The first convergent site is R3128K and the amino acid K only occurs in giant and red pandas. The second convergent site is K3999R and the amino acid R only occurs in giant and red pandas, Weddell seal, and walrus. (C) Roles of DYNC2H1 and PCNT proteins in IFT and ciliogenesis. DYNC2H1 is a core component of cytoplasmic dynein 2 complex. Hu et al. PNAS | January 31, 2017 | vol. 114 | no. 5 | 1083 EVOLUTION introduce subtle changes in the functional spectrum of focal proteins and consequently contribute to pseudothumb development in both pandas. The DYNC2H1 protein is a core component of the dynein complex, the motor of retrograde intraflagellar transport (IFT) during ciliogenesis (25, 26). Two convergent substitutions of R3128K and K3999R were identified (Fig. 2 A and B and Table 1). In particular, the R3128K substitution is located in a stalk domain between AAA domains 4 and 5 implicated in microtubule binding (Fig. 2A) (28). It has been reported that amino acid changes in the stalk domain of DYNC2H1 affect retrograde IFT and produce abnormal primary cilia (26). Primary cilia are signal transduction Table 1. Positively selected genes with nonrandom convergent amino acid substitution between giant and red pandas, which are closely related with limb development and essential nutrient utilization Gene symbol DYNC2H1* PCNT PRSS1* PRSS36 CPB1* GIF* CYP4F2 CYP3A5* ADH1C* Full gene name P value FDR Cytoplasmic dynein 2, heavy chain 1 Pericentrin Protease, serine, 1 Protease, serine, 36 Carboxypeptidase B1 Gastric intrinsic factor Cytochrome P450, family 4, subfamily F, polypeptide 2 Cytochrome P450, family 3, subfamily A, polypeptide 5 Alcohol dehydrogenase 1C (class I), gamma Polypeptide 1.06e-04 3.18e-05 3.47e-04 7.73e-12 3.13e-06 2.42e-04 9.99e-06 2.58e-09 1.75e-04 0.0372 0.0097 0.0362 3.45e-09 4.73e-04 0.0363 0.0022 3.03e-06 0.02 Convergent amino acid substitution R3128K, K3999R S2327P, Q2458R D119N, I140V R57S V218F, T271I, M310L M212L, D406K, H407D M92F T363S, V393L, M395I, T400S V187I *The gene passed the nonrandom convergence test not only under the JTT-fgene substitution model but also under the JTT-fsite model. bears, dogs, humans, and mice (SI Appendix, Table S25), highlighting the uniqueness of these variations and their potential functional importance in pseudothumb development. Similarly, the centrosomal coiled-coil protein PCNT is also involved in primary cilia assembly by forming a complex with IFT proteins (e.g., IFT20, IFT57, IFT88) (Fig. 2C, Table 1, and SI Appendix, Fig. S10). PCNT modification could affect basal body localization of IFT proteins, thus inhibiting primary cilia assembly (30). We propose that convergent amino acid substitutions in the two genes may work synergistically for pseudothumb development in both pandas, although their effects on other aspects of skeletal development remain elusive. This inference warrants further experimental validation in the future. Bamboo is an almost exclusive source of essential amino acids, essential fatty acids, and vitamins for giant and red pandas. To meet this nutritional challenge, pandas need to improve efficiency of nutrient absorption and utilization and, therefore, signatures of adaptive convergence related to essential nutrient utilization might be observed. Three genes (PRSS1, PRSS36, and CPB1) involved in dietary protein digestion showed adaptive convergence (Table 1 and SI Appendix, Fig. S10). All of these proteins belong to serine proteases and are secreted by the pancreas into the small intestine. Interestingly, both PRSS1 and PRSS36 are endopeptidases for proteolytic cleavage of Lys or Arg residues from the carboxyl terminal, whereas CPB1 is an exopeptidase and acts on preferential release of Lys or Arg from C-terminal. Quantitative measurements indicate that bamboo has much lower Lys and Arg content than animal meats and plant leaves (SI Appendix, Table S26). Taken together, it seems that the adaptive convergence of these genes may in synergy result in elevated efficiency for releasing Lys and Arg from dietary proteins and amino acid recycling, thus offsetting the limited nutrient supply in bamboo. Whereas vitamins A and B12 and arachidonic acid are essential nutrients, they are either absent or their content in bamboo is much lower than in meat, nuts, or green plants (SI Appendix, Tables S27 and S28). Four genes (ADH1C, CYP3A5, CYP4F2, and GIF) involved in utilization of these nutrients were identified to be under adaptive convergence (Table 1 and SI Appendix, Fig. S10). ADH1C and CYP3A5 are involved in the regulation of vitamin A metabolism that is essential to dark vision maintenance. ADH1C catalyzes conversion between retinal and retinol, whereas CYP3A5 is involved in the degradation of retinoic acids to prevent detrimental accumulation of excessive vitamin A (31). Vitamin A is needed by the retina of the eye in the form of retinal, which combines with protein opsin to form rhodopsin, the light-absorbing molecule necessary for dark vision (32). The giant and red pandas are active both in the daytime and at night, with slightly lower activity rate at night (10, 33). Because vitamin A exists only in... Purchase answer to see full attachment