Philippa Kaur

Sequence analysisProtein sequence searches were conducted in the GenBank nr database with BLASTP42 using default parameters, including automatically adjusting parameters for short input sequences (Table S1). Conserved domain searches were run against the GenBank Conserved Domain Database (CDD)43. Sequence alignments were conducted in CLC Main Workbench 20.0.4 (Qiagen) with the fast alignment algorithm, gap open cost = 10, and gap extension cost = 1. Biochemical properties of the fish putative thiaminase I protein sequences were predicted with the Create Sequence Statistics function in CLC Main Workbench 20.0.4 (Qiagen, Hilden, Germany). The molecular weights were calculated from the sum of the amino acids in the sequence, and the isoelectric points (pIs) were calculated from the pKa values for the individual amino acids in the sequence.Bacteria culturePure cultures of P. thiaminolyticus strain 818822 were cultured at 37 °C in Terrific Broth (MO BIO Laboratories, Carlsbad, CA) in either a shaking incubator or in a beveled flask with a stir bar and were harvested after 48–80 h of culture. Upon harvest, cultures were processed immediately or frozen whole in 50 mL Falcon tubes at − 80 °C. Fresh or thawed cultures were spun at 14,000×g, and culture supernatant was concentrated using Amicon-ultra 10 kDa molecular weight cut-off (MWCO) filters (EMD Millipore, Billerica, MA).The zebrafish and alewife candidate thiaminase I genes were cloned and overexpressed in E. coli to determine whether they produced functional thiaminases. The recombinant thiaminase I gene from P. thiaminolyticus was overexpressed in E. coli as a positive control. Candidate and control genes were synthesized (Integrated DNA Technologies, Inc., Coralville, Iowa) and placed into the pET52b vector (EMD Millipore). Insert sequences are provided in Supplementary Figs. S10–S13. The empty pET52b vector was used as a negative control. The plasmid was transformed into E. coli (Rosetta 2(DE3)pLysS Singles Competent Cells, EMD Millipore) according to the manufacturer’s instructions, and expression of candidate genes was induced by the addition of IPTG. Cells were lysed in 1X BugBuster (Millipore) according to the manufacturer’s instructions in the presence of benzonase nuclease, and soluble and insoluble fractions were separated by centrifugation.Tissue collectionsAdult common carp were captured from Lake Erie using short-set gill nets. Adult alewife and quagga mussels (Dreissena bugensis) were collected from Sturgeon Bay, Lake Michigan using bottom trawls. Fish collections were completed during July 2007. Sex of sampled fish was not identified. Upon collection, unanesthetized animals were immediately euthanized by flash freezing between slabs of dry ice and stored at − 80 °C. Fish were harvested by the Great Lakes Science Center, U.S. Geological Survey (USGS). Laboratory use of frozen animal tissues and wild type and recombinant bacteria was in accordance with institutional guidelines and biosafety procedures at Oregon State University and USGS. Animal care and use procedures were approved by the Great Lakes Science Center, USGS. All USGS sampling and handling of fish during research are carried out in accordance with guidelines for the care and use of fishes by the American Fisheries Society44. All methods are reported in accordance with applicable ARRIVE guidelines (https://arriveguidelines.org). Zebrafish from OSU’s zebrafish facility were anesthetized and euthanized by overdose with waterborne 200 ppm ethyl 3-aminobenzoate methanesulfonate (MS-222, Sigma-Aldrich, St. Louis, MO) following protocols approved by the OSU Animal Institutional Care and Use Committee and were frozen at − 80 °C after euthanization. Gills, liver, spleen, and the intestinal tract were dissected, and gill tissue was homogenized separately from liver, spleen, and gut, which were homogenized together and designated “viscera.” Homogenization and protein preparation procedures were the same as that for alewife. Zebrafish from Columbia Environmental Research Center (CERC), USGS cultures were anesthetized and euthanized by overdose with 200 ppm ethyl 3-aminobenzoate methanesulfonate (MS-222, Sigma-Aldrich, St. Louis, MO) in water following protocols approved by CERC Institutional Animal Care and Use Committee (IACUC). Whole fish (0.2–0.6 g) were homogenized in 10 mL cold phosphate buffer, pH 6.5. Whole common carp and alewife were thawed until they could just be dissected. Preliminary trial extractions on alewife stomach and intestines, spleen, and gills revealed similar results and revealed that gills and spleen tissue produced the cleanest protein preparations. Therefore, subsequent extractions for common carp and alewife used gill tissue. Samples were pooled from 3 to 5 individual fish, haphazardly chosen from the sampled fish without exclusions. Quagga mussels were thawed just sufficiently to be husked from their shell and were used whole. Researchers were aware of the species and tissue designation of each sample throughout the experiments. Animal tissues were placed in ice-cold (4 °C) beakers containing cold extraction buffer (16 mM K3HPO4, 84 mM KH2PO4, 100 mM NaCl, pH 6.5 with 1 mM DTT, 2 mM EDTA, 3 mM Pepstatin, 1X Protease inhibitor cocktail (Sigma), and 1 mM AEBSF). All extractions were carried out at 4 °C in pre-chilled glassware. Samples were mechanically homogenized using a rotor–stator tissue grinder. Samples were stirred gently for several hours to overnight at 4 °C, centrifuged at 14,000×g to remove debris, and strained through cheesecloth to remove any insoluble lipids. Extracts were then subjected to 30–75% ammonium sulfate precipitation. Pellets from the precipitation were resuspended in buffer (83 mM KH2PO4, 17 mM K2HPO4, and 100 mM NaCl), centrifuged to remove any remaining debris, and stored in 30% glycerol at − 20 °C.Protein electrophoresisNative PAGE was run using either pre-cast TGX gels (BioRad, Hercules, California) of varying percentage (7.5% to 12% or 8–16% gradient gels) or on hand-cast gels (TGX FastCast, BioRad) made according to the manufacturer’s instructions.Blue-native PAGE was used to estimate the mass of thiaminases in their native conformation. Blue-native PAGE45 gels were run using the NativePage Novex Bis–Tris system (Life Technologies) or hand-cast equivalents46. Light blue cathode buffer was used to facilitate visualization of the activity stain.Standard denaturing SDS-PAGE was used to estimate the molecular mass of thiaminases after denaturation. Denaturing SDS-PAGE was run using one of three relatively equivalent methods: pre-cast TGX gels (BioRad) according to the manufacturer’s instructions, hand-cast Tris–HCl gels using standard Laemmli chemistry47 with an operating pH of approximately 9.5, or hand-cast Bis–Tris gels (MOPS buffer) with an operating pH of approximately 7. For all denaturing and non-denaturing SDS-PAGE applications, standard Laemmli sample buffer was used, and samples were heated to 75 °C for 15 min to facilitate denaturation followed by brief centrifugation to eliminate any precipitated debris.Non-denaturing PAGE was used as an alternative to denaturing PAGE for the common carp thiaminase that could not be renatured (i.e., activity could not be recovered) following a denaturing SDS-PAGE. Non-denaturing PAGE was conducted using any of the three aforementioned gel chemistries with SDS-containing running buffers including reductant (DTT), but samples were not heated prior to application to the gel. Samples for non-denaturing PAGE were allowed to incubate in sample buffer at room temperature for 30 min prior to gel loading. This preserves the charge-shift induced by SDS but does not result in protein denaturation, facilitating in-gel analysis of thiaminase I activity after separation.To visualize proteins following electrophoresis, gels were stained with Coomassie stain (CBR-250 at 1 g/L in methanol/acetic acid/water (4:5:1) and destained with methanol/acetic acid/water (1.7:1:11.5). Mini-gels were run on BioRad’s mini-protean gel rigs. Midi-gels (16 cm length) were run on Hoefer’s SE660, and large-format gels (32 cm length) were run on a BioRad’s Protean Slab Cell. Mini-gels were generally run at room temperature, and midi- and large-format gels were run at 4 °C. Blue-native PAGE was always run at 4 °C.Two-dimensional electrophoresis (2DE) separated proteins in the first dimension based on pI and in the second dimension based on mass (either native or denatured). 2DE was performed by combining in-gel IEF with either denaturing SDS-PAGE, non-denaturing SDS-PAGE, or native PAGE. IPG strips were incubated in TRIS-buffered equilibration solution48 either with 6 M urea, SDS, and iodacetamide (denaturing) or without urea, SDS, and iodacetamide (non-denaturing) for 20 min. Low melting point agarose was used to solidify IGP strips in place. Agarose was cooled to just above the gelling temperature, as hot agarose inactivated thiaminase I activity.Isoelectric focusingIsoelectric focusing (IEF) was conducted both in-gel and in-liquid. In-gel IEF was conducted in immobilized pH gradient (IPG) strips using a Multifor II (GE Healthcare Life Sciences). Prior to rehydration, all protein preparations were desalted in low-salt (~ 5 to 10 mM) sodium or potassium phosphate buffer (pH 6.5) using 10 kDA MWCO filters. All samples were applied using sample volumes and protein concentrations recommended by the manufacturer. For standard denaturing in-gel IEF, rehydration solution consisted of 8 M urea, 2% CHAPS, 2% IPG buffer of the appropriate pH-range, 1% bromophenol blue, and 18 mM DTT. The IEF was conducted at maximum of 2 mA total current and 5 W total power, with an EPS3500 XL power supply in gradient mode. Voltage gradients were based on standard protocols recommended by the manufacturer. In-gel IEF was also performed under native conditions to allow thiaminase I activity staining of IPG strips. Protocols were essentially the same as those for denaturing conditions, with the following exceptions: (1) urea was eliminated and the CHAPS concentration was reduced to 0.5% in the rehydration solution; (2) rehydration was conducted at 14 °C; and (3) the water in the cooling tray was cooled to 4 °C.In-liquid IEF was conducted using a Rotofor (BioRad) according to the manufacturer’s instructions. Non-denaturing in-liquid IEF was also conducted using a focusing solution including no urea, 2% pH 3–10 biolyte, 0.5% CHAPS, 20% glycerol, and 5 mM DTT. The addition of glycerol helped retain activity but also increased focusing times. The Rotofor was run at a constant 15 W with a maximum current of 20 mA and voltage set for a maximum of 2000 V. Samples containing 8 M urea were cooled to 14 °C during focusing to avoid urea precipitation, whereas samples lacking urea were cooled to 4 °C during focusing. Protein extracts in salt solutions greater than 10 mM were desalted directly in focusing solution using a 10 kDA MWCO filter. Focusing runs were allowed to proceed until the voltage stabilized and fractions were harvested with the needle array and vacuum pump. Ampholytes were removed by addition of NaCl to 1 M and then samples were desalted into phosphate buffer using a 10kD MWCO filter.Thiaminase I activity measurementsFor quantitative measurements of thiaminase I activity, we conducted a radiometric assay at CERC as previously described49. Zebrafish homogenates were diluted 1:8, 1:16, or 1:32 in cold phosphate buffer, pH 6.5. Two replicates per dilution were assayed. Activity was calculated from the greatest dilution that gave activity within the linear range of the assay and was reported as pmol thiamine consumed per g tissue (wet weight) per minute (pmol/g/min).Thiaminase I activity stainingAfter electrophoresis, gels were stained for thiaminase I activity using a previously described diazo-coupling reaction19,50. Briefly, gels were washed 3 times in water, twice in 25 mM sodium phosphate buffer with 1 mM DTT, and once in 25 mM sodium phosphate buffer without DTT. Gels were then incubated in 0.89 mM thiamine-HCl and co-substrate (1.45 mM pyridoxine, 24 mM nicotinic acid, or 20 mM pyridine) in 25 mM sodium phosphate buffer for 10 min. Gels were briefly rinsed in water and placed in a lidded container and incubated at 37 °C for 30 min to allow thiamine degradation by any thiaminases in the gel. The diazo stain19,50 was then applied to detect remaining thiamine in the gel for five minutes with gentle agitation. Stained gels were rinsed with water and photographed, and further stained with Coomassie to visualize proteins. More

Evapotranspiration measurements and above-ground biomassFigure 1 shows daily evapotranspiration (ET, mm day−1) of each CC tested before mowing (DOY, day of the year, 184) and at 2, 8, 17 and 25 days after mowing (DOY 190, 196, 205 and 213); bare soil was also included as a reference. Before mowing, ET rates showed significant differences between and within the three groups. CR plants had a mean ET of 8.1 mm day−1, which was lower, compared to the other two groups (10.6 and 18.6 mm day−1 for GR and LE, respectively) and the bare soil control (8.5 mm day−1). On DOY 184, values as high as 9.4 (Glechoma hederacea L., GH) and 9.8 mm day−1 (Trifolium subterraneum L. cv. Denmark, TS) were found (Fig. 1), while ranging around 7 mm day-1, Dichondra repens J.R.Forst. & G.Forst. (DR), Hieracium pilosella L. (HP), and Sagina subulata (Swartz) C. Presl (SS) ET were lower than soil evaporation itself.Figure 1Vertical bars represent the daily water use as referred to unit of soil (ET, mm day−1) for the bare soil (yellow) and all the cover crop species as divided into creeping plants (shades of blue), legumes (shades of green) and grasses (shades of orange). Evapotranspiration was measured though a gravimetric method before (i.e. − 4) and at 2, 8, 17 and 25 days after mowing. ET data are mean values ± SE (n = 4).Full size imageOn the same day, a large ET variation was recorded within the GR group as Festuca arundinacea Schreb. cv. Thor (FA) scored the highest daily ET values (13.4 mm day−1), whereas in Festuca ovina L. cv. Ridu (FO), water loss was reduced by 45% (7.5 mm day−1). Within the 15 CCs, LE registered the highest pre-mowing ET with Trifolium michelianum Savi cv. Bolta (TM) peaking at 22.6 mm day−1. However, within LE, Medicago polymorpha L. cv. Scimitar (MP) showed ET values as low as 12.1 mm day−1 (Fig. 1).Two days after mowing, all tested CCs recorded ET values lower than 9 mm day−1 (Fig. 1). Moreover, water use reduction among LE ranged between 56% (M. polymorpha, MP) and 73% (T. michelianum, TM), such that T. michelianum (TM, 6.1 mm day−1), Medicago truncatula Gaertn. cv. Paraggio (MT, 5.6 mm day−1) and M. polymorpha (MP, 5.2 mm day−1) registered ET values lower than the bare soil (7.0 mm day−1). Even though registering a consistent ET reduction after mowing, GR retained ET rates slightly higher than bare soil, except for F. ovina (FO), which recorded the lowest at 6.3 mm day−1. Subsequent samplings showed that most of the CCs had a progressive recovery in water use (Fig. 1) and data taken 17 days after mowing confirmed that Lotus corniculatus L. cv. Leo (LC) and all GR fetched pre-mowing ET rates. Medicago lupulina L. cv. Virgo (ML) registered a partial recovery with similar rates (about 13 mm day−1) at 17 and 25 days after the mowing event. F. ovina and all remaining LE stayed below 10 mm day−1 with ET values close to the control until the end of the trial. At 17 days from grass cutting, under a quite high exceeding-the-pot biomass, both G. hederacea (GH) and T. subterraneum (TS) reached ET values as high as 12.0 and 11.4 mm day−1, respectively. On the other hand, D. repens (DR), H. pilosella (HP), and S. subulata (SS) even though with slightly higher ET values than those registered at the beginning of the trial (DOY 184), remained close to the soil evaporation rates until DOY 213.Aboveground dry clipped biomass at the first mowing date (ADW_MW1, DOY 188) showed large differences among groups, as represented in Table 1. ADW_MW1 within LE was quite variable, as values ranged between 274.3 g m−2 (M. polymorpha, MP) and 750.0 g m−2 (T. michelianum, TM). With a mean value of 565.9 g m−2, LE aboveground biomass was 80% higher than the mean GR ADW_MW1 (110.2 g m-2). F. ovina (FO) scored the lowest value at 48.4 g m−2 among grasses, while within the creeping group, G. hederacea (GH) and T. subterraneum (TS) had biomass development outside the pot edges totalling 89.6 g m−2 and 23.2 g m−2, respectively.Table 1 Aboveground dry biomass clipped at the first mowing event (ADW _MW1), the corresponding leaf area surface index (LAI) and water use per leaf area unit (ETLEAF) of all cover crops tested.Full size tableLeaf area index (LAI, m2 m−2) at mowing showed the highest values in LE with LAI peaking at 12.4 (Table 1). Among GR, LAI did not show significant differences, being around 1.2. Concerning CR, LAI was assessed at 0.2 and 0.8 for T. subterraneum (TS) and G. hederacea (GH) respectively, while LAI estimated through photo analysis ranged between 1.3 (D. repens, DR) and 3.6 (T. subterraneum TS).Evapotranspiration per leaf area unit (ETLEAF) was notably higher in GR, ranging between 7.75 (F. ovina, FO) and 9.22 (Lolium perenne L. cv. Playfast, LP) mm m−2 day−1 (Table 1). In descending order, ETLEAF was the highest in D. repens (DR, 5.46 mm m−2 day−1). Similar ETLEAF was found when comparing some LE and CR species such as M. truncatula (MT, 3.40 mm m−2 day−1), M. lupulina (ML, 4.05 mm m−2 day−1), G. hederacea (GH, 3.68 mm m−2 day−1), H. pilosella (HP, 3.86 mm m-2 day-1) and T. subterraneum (TS, 2.74 mm m−2 day−1). T. michelianum (TM), with 1.81 mm m-2 day-1 scored the lowest ETLEAF of all species (Table 1).Plotting LAI versus the before-mowing ET yielded a significant quadratic relationship (R2  > 0.76) (Fig. 2a) which helped to distinguish two different data clouds. Till LAI values of about 6, the model was linear, having at its lower end all GR and CR species with the inclusion of M. polymorpha (MP) as a legume, while, at the other end, M. truncatula (MT), L. corniculatus (LC) and M. lupulina (ML) were grouped together. T. michelianum (TM) was isolated from all CCs at 22.56 mm day−1.Figure 2Panel (a): quadratic regression of leaf area index (LAI, m2 m−2) vs cover crop evapotranspiration per unit of soil (ET, mm day−1). Each data point is mean value ± SE (n = 4). The quadratic model equation is y = − 0.128×2 + 2.9968x + 5.4716, R2 = 0.76. Panel (b): the quadratic regression between LAI corresponding to the clipped biomass (m2 m−2) and cover crop ET reduction (%). Each data point is mean value ± SE (n = 4). Quadratic model equation is y = − 0.8985×2 + 16.503x + 5.1491, R2 = 0.94.Full size imageWhen regressing the fraction of ET reduction, compared to pre-mowing values vs LAI (Fig. 2b), the same quadratic model achieved a very close fit (R2 = 0.94, p  1 mm) root diameters as affected by soil cover.Full size tableThe highest values of diameter class length (DCL, mm cm−3) for very fine roots (DCL_VF,  1.0 mm) roots although, most notably, L. corniculatus roots showed the highest abundance for both DCL_M (23.08 cm cm−3) and DCL_C (0.54 cm cm−3).At the 10–20 cm soil depth, GR confirmed the highest values for both very fine and fine roots, with F. arundinacea reaching maximum DCL of 2.269 and 5.215 cm cm-3, respectively (Table 2). L. corniculatus largely outscored any other species for both medium and coarse root diameter (6.173 and 0.037 cm cm−3, respectively), with F. arundinacea ranking second (3.157 and 0.016 cm cm−3, respectively).The highest root dry weight (RDW, mg cm-3) within the topsoil layer was reached by L. corniculatus (8.7 mg cm−3) and F. arundinacea (7.6 mg cm-3). Notably, such values were significantly higher than those recorded on the remaining species, except for the F. arundinacea vs F. rubra commutata comparison (Table 2). At 10–20 depth, scant variation was recorded in RDW measured in grasses, whereas L. corniculatus held its supremacy within legumes (4.5 mg cm−3). Within the creeping type, D. repens (DR) and G. hederacea (GH) scored RDW values as high as those determined for grass species (namely F. arundinacea , P. pratensis and F. rubra commutata), whereas S. subulata (SS) essentially had no root development.Soil aggregates and mean weight diameter (MWD)Table 3 reports the proportional aggregate weight (g kg−1) for both 0–10 and 10–20 cm soil depths. Compared to bare soil, the largest increase in large macroaggregates (LM,  > 2000 µm) in the top 10 cm of soil was achieved by L. corniculatus with 461 g kg−1. L. corniculatus differed from the rest of the LE group, whose grand mean (90 g kg−1) was the lowest of the three tested groups. As a legume, T. subterraneum (TS, 122 g kg−1) recorded the lowest values compared to fellow CR species, ranging between 211 (D. repens, DR) and 316 g kg−1 (G. hederacea, GH). GR recorded LM values slightly lower than those of CR, with a mean value of 217 vs 224 g kg-1.Table 3 Proportional aggregate weight (g kg−1) of sand-free aggregate-size fractions acquired from wet sieving as affected by soil cover and mean weight diameter (MWD). Aggregate-size fraction divided as macroaggregates with large size ( > 2 mm, LM) and small size (2 mm—250 μm, sM), microaggregates (250 μm—53 μm, m), and silt and clay ( More

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Species distribution modeling, spatial climate segregation and niche widthTo explore the selective regimes of the four species on external environmental factors, we first constructed species distribution modeling (SDM). We obtained a dataset including 22 environmental factors represented by climate, relief, and vegetation variables from 620 localities for DS, 1028 localities for OS, 581 localities for MM and 332 localities for PR, covering most of the species’ distribution ranges (Supplementary Fig. 1). The distribution areas of the four species overlapped widely. The contributions of environmental factors to SDMs showed similarities among the four species. The summer NDVI made important contributions for DS (41.0), OS (44.8), MM (32.5) and PR (8.1), and sand cover contributed significantly to PR (72.7) and DS (16.0) (Fig. 1c). Then, we assessed which set of environmental variables was most closely associated with species distribution via principal component analysis. The bioclimatic space occupied by the four species revealed a large overlap (Fig. 1d), which was consistent with SDM (Supplementary Fig. 1). The distribution of OS was more closely associated with higher-precipitation areas, whereas MM seemed to prefer areas with higher temperatures. Finally, we evaluated the macrohabitat niche breadth of each species. The breadths of environmental space occupation were similar for DS (0.527), MM (0.571), and PR (0.548) and slightly higher for OS (0.622), which suggests that niche selection among the four species is partially overlapping. In total, the four species are mostly similar in the selection of external environmental factors.High-quality genomic landscapes of the four desert rodentsTo investigate the genetic mechanism for desert adaptation of the four sympatric desert rodents, we generated four high-quality de novo genomes (Supplementary Fig. 2). The DS was sequenced using a combined strategy and generated 377.67 Gb of data from Illumina reads, 261.01 Gb from PacBio long reads, 299.51 Gb from 10X Genomics reads, and 389.13 Gb from Hi-C reads (Supplementary Table 1). The final genome size was 2.81 Gb with contig N50 of 31.41 Mb and ~472X mean coverage (Table 1, Supplementary Fig. 3, and Supplementary Tables 2, 3). The contigs for DS were further assembled into pseudochromosomes with lengths on the order of full chromosomes and a scaffold N50 size of 147.24 Mb (Fig. 2a, b, Table 1, and Supplementary Fig. 4). The OS, MM and PR were sequenced using the same hybrid strategy and generated 162.58 Gb, 172.22 Gb, and 214.34 Gb Illumina reads and 183.09 Gb, 161.34 Gb, and 186.45 Gb Oxford Nanopore Technologies long reads, respectively (Supplementary Table 1). The final assembly of OS, MM and PR was 2.83 Gb, 2.43 Gb, and 2.16 Gb with contig N50 of 25.87 Mb, 24.08 Mb, and 42.68 Mb, respectively (Table 1, Supplementary Fig. 4, and Supplementary Tables 2, 3).Table 1 Genome assembly statistics of the four desert rodents.Full size tableFig. 2: High-quality assembly of Dipus sagitta genome and genomic elements of the four sequenced desert rodents.a Hi-C heat map of Dipus sagitta genome assembly. b CIRCOS plot showing the distribution of GC content, transposable elements (TE), and coding sequences (CDS) in the D. sagitta genome. c Orthologous coding sequences composition inferred for thirteen rodents’ genomes. Mcar Mus caroli, Mmus Mus musculus, Mpah Mus Pahari, Mmer Meriones meridianus, Mung Meriones unguiculatus, Cgri Cricetulus griseus, Prob Phodopus roborovskii, Sgal Spalax galili, Osib Orientallactaga sibirica, Dsag Dipus sagitta, Jjac Jaculus jaculus, Hgla Heterocephalus glaber, Cpor Cavia porcellus. d Proportion of transposable elements (TEs). The barplots show the proportions of different types of TEs in corresponding species on the phylogenetic tree.Full size imageAnalyses of the four draft genomes showed that 92.9–95.9% of mammalian BUSCOs were complete, and the GC content was 41.38–42.16% (Table 1 and Supplementary Table 3). Whole-genome annotation was performed via three complementary methods: ab initio prediction, homology-based prediction and RNA-seq based prediction. A total of 23,482, 22,859, 22,533, and 22,314 protein-coding genes were annotated for DS, OS, MM, and PR, respectively (Fig. 2c, Supplementary Fig. 5, Supplementary Table 4). Approximately 98.8–99.1% of genes were functionally annotated for the four species (Supplementary Table 4). Transposable elements (TEs) accounted for 31.38–53.02% of genome assemblies, which predominantly consisted of long-terminal repeats (LTRs), long interspersed nuclear elements (LINEs) and other unknown TEs (Fig. 2d). DS and OS displayed significant LTR expansion of 47.39% and 50.88% in four sequenced genomes, while MM showed an unexpectedly high LINE expansion of 28.99% and sharp LTR contraction to 9.38% (Supplementary Table 5).Phylogenetic relationship and evolutionary historyUsing 5,102 single-copy orthologous groups, we constructed a high-confidence phylogenetic tree using the maximum-likelihood algorithm, including time calibrations based on fossil records and previous studies (Figs. 1b, 2c)22. The phylogenetic tree strongly supported nodes uniting the subfamilies Murinae and Gerbillinae, which together represented the family Muridae (Supplementary Fig. 6). This group was sister to a clade containing cricetids. Spalacidae was recovered as the earliest divergent lineage from Muridae and Cricetidae in the superfamily Muroidea. The split of the most recent common ancestor of Dipodoidea and Muroidea dated to ~56.5 Mya (Fig. 1b, Supplementary Fig. 7). In the Miocene epoch (23 Mya–5.3 Mya), accelerated global geotectonic movement aggravated global climate drying and cooling23. Geological disruptions that modified landscapes and offered new habitats favored the early adaptive radiation of extant desert rodents. The ancestors of four sequenced species emerged separately during this period (Supplementary Note 1). Our phylogenetic tree is consistent with previous evolutionary research on rodents22 and supports the independent evolution of desert adaptations in Jerboas, Gerbils and Hamsters.Expanded and contracted gene familiesComparative genomic analysis revealed 23/32, 4/22, 39/73, and 22/83 gene families exhibiting significant expansion/contraction in the genomes of DS, OS, MM, and PR, respectively (Fig. 1b and Supplementary Fig. 8). Genes belonging to the expanded/contracted families were functionally enriched (Fisher Exact  More

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