Chromosome‐level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of nanopore sequencing,Bionano and Hi‐C technology

Onychostoma macrolepis is an emerging commercial cyprinid fish species. It is a model system for studies of sexual dimorphism and genome evolution. Here, we report the chromosome‐level assembly of the O.macrolepis genome obtained from the integration of nanopore long‐read sequencing with physical maps produced using Bionano and Hi‐C technology. A total of 87.9 Gb of nanopore sequence provided approximately 100‐fold coverage of the genome. The preliminary genome assembly was 883.2 Mb in size with a contig N50 size of 11.2 Mb. The 969 corrected contigs obtained from Bionano optical mapping were assembled into 853 scaffolds and produced an assembly of 886.5 Mb with a scaffold N50 of 16.5 Mb. Finally, using the Hi‐C data, 881.3 Mb (99.4% of genome) in 526 scaffolds were anchored and oriented in 25 chromosomes ranging in size from 25.27 to 56.49 Mb. In total, 24,770 protein‐coding genes were predicted in the genome, and ~96.85% of the genes were functionally annotated. The annotated assembly contains 93.3% complete genes from the BUSCO reference set. In addition, we identified 409 Mb (46.23% of the genome) of repetitive sequence, and 11,213 non‐coding RNAs, in the genome. Evolutionary analysis revealed that O. macrolepis diverged from common carp approximately 24.25 million years ago. The chromosomes of O. macrolepis showed an unambiguous correspondence to the chromosomes of zebrafish. The high‐quality genome assembled in this work provides a valuable genomic resource for further biological and evolutionary studies of O. macrolepis.     

Chromosome‐level genome assembly of the razor clam Sinonovacula constricta (Lamarck, 1818)

Bivalves, a highly diverse and the most evolutionarily successful class of invertebrates native to aquatic habitats, provide valuable molecular resources for understanding the evolutionary adaptation and aquatic ecology. Here, we reported a high‐quality chromosome‐level genome assembly of the razor clam Sinonovacula constricta using Pacific Bioscience single‐molecule real‐time sequencing, Illumina paired‐end sequencing, 10X Genomics linked‐reads and Hi‐C reads. The genome size was 1,220.85 Mb, containing scaffold N50 of 65.93 Mb and contig N50 of 976.94 Kb. A total of 899 complete (91.92%) and seven partial (0.72%) matches of the 978 metazoa Benchmarking Universal Single‐Copy Orthologs were determined in this genome assembly. And Hi‐C scaffolding of the genome resulted in 19 pseudochromosomes. A total of 28,594 protein‐coding genes were predicted in the S. constricta genome, of which 25,413 genes (88.88%) were functionally annotated. In addition, 39.79% of the assembled genome was composed of repetitive sequences, and 4,372 noncoding RNAs were identified. The enrichment analyses of the significantly expanded and contracted genes suggested an evolutionary adaptation of S. constricta to highly stressful living environments. In summary, the genomic resources generated in this work not only provide a valuable reference genome for investigating the molecular mechanisms of S. constricta biological functions and evolutionary adaptation, but also facilitate its genetic improvement and disease treatment. Meanwhile, the obtained genome greatly improves our understanding of the genetics of molluscs and their comparative evolution.     

Clean conversion of cellulose into fermentable glucose

We studied the process of conversion of microcrystalline-cellulose into fermentable glucose in the formic acid reaction system using cross polarization/magic angle spinning ¹³C-nuclear magnetic resonance, X-ray diffraction and Fourier transform infrared spectroscopy. The results indicated that formic acid as an active agent was able to effectively penetrate into the interior space of the cellulose molecules, thus collapsing the rigid crystalline structure and allowing hydrolysis to occur easily in the amorphous zone as well as in the crystalline zone. The microcrystalline-cellulose was hydrolyzed using formic acid and 4% hydrochloric acid under mild conditions. The effects of hydrochloric acid concentration, the ratio of solid to liquid, temperature (55–75 °C) and retention time (0–9 h), and the concentration of glucose were analyzed. The hydrolysis velocities of microcrystalline-cellulose were 6.14 × 10^− 3 h^− 1 at 55 °C, 2.94 × 10^− 2 h^− 1 at 65 °C, and 6.84 × 10^− 2 h^− 1 at 75 °C. The degradation velocities of glucose were 0.01 h^− 1 at 55 °C, 0.14 h^− 1 at 65 °C, 0.34 h^− 1 at 75 °C. The activation energy of microcrystalline-cellulose hydrolysis was 105.61 kJ/mol, and the activation energy of glucose degradation was 131.37 kJ/mol.     

Partial characterization of a malonyl-CoA-sensitive carnitine O-palmitoyltransferase I from Macrobrachium borellii (Crustacea: Palaemonidae)

The shuttle system that mediates the transport of fatty acids across the mitochondrial membrane in invertebrates has received little attention. Carnitine O-palmitoyltransferase I (EC 2.3.1.21; CPT I) is a key component of this system that in vertebrates controls long-chain fatty acid β-oxidation. To gain knowledge on the acyltransferases in aquatic arthropods, physical, kinetic, regulatory and immunological properties of CPT of the midgut gland mitochondria of Macrobrachium borellii were assayed. CPT I optimum conditions were 34 °C and pH = 8.0. Kinetic analysis revealed a Km for carnitine of 2180 ± 281 μM and a Km for palmitoyl-CoA of 98.9 ± 8.9 μM, while V_max were 56.5 ± 6.6 and 36.7 ± 4.8 nmol min^− 1 mg protein^− 1, respectively. A Hill coefficient, n ~ 1, indicate a Michaelis–Menten behavior. The CPT I activity was sensitive to regulation by malonyl-CoA, with an IC₅₀ of 25.2 μM. Electrophoretic and immunological analyses showed that a 66 kDa protein with an isoelectric point of 5.1 cross-reacted with both rat liver and muscle-liver anti CPT I polyclonal antibodies, suggesting antigenic similarity with the rat enzymes. Although CPT I displayed kinetic differences with insect and vertebrates, prawn showed a high capacity for energy generation through β-oxidation of long-chain fatty acids.     

A chromosome‐level genome assembly of the parasitoid wasp Pteromalus puparum

Parasitoid wasps represent a large proportion of hymenopteran species. They have complex evolutionary histories and are important biocontrol agents. To advance parasitoid research, a combination of Illumina short‐read, PacBio long‐read and Hi‐C scaffolding technologies was used to develop a high‐quality chromosome‐level genome assembly for Pteromalus puparum, which is an important pupal endoparasitoid of caterpillar pests. The chromosome‐level assembly has aided in studies of venom and detoxification genes. The assembled genome size is 338 Mb with a contig N50 of 38.7 kb and a scaffold N50 of 1.16 Mb. Hi‐C analysis assembled scaffolds onto five chromosomes and raised the scaffold N50 to 65.8 Mb, with more than 96% of assembled bases located on chromosomes. Gene annotation was assisted by RNA sequencing for the two sexes and four different life stages. Analysis detected 98% of the BUSCO (Benchmarking Universal Single‐Copy Orthologs) gene set, supporting a high‐quality assembly and annotation. In total, 40.1% (135.6 Mb) of the assembly is composed of repetitive sequences, and 14,946 protein‐coding genes were identified. Although venom genes play important roles in parasitoid biology, their spatial distribution on chromosomes was poorly understood. Mapping has revealed venom gene tandem arrays for serine proteases, pancreatic lipase‐related proteins and kynurenine–oxoglutarate transaminases, which have amplified in the P. puparum lineage after divergence from its common ancestor with Nasonia vitripennis. In addition, there is a large expansion of P450 genes in P. puparum. These examples illustrate how chromosome‐level genome assembly can provide a valuable resource for molecular, evolutionary and biocontrol studies of parasitoid wasps.     

Seasonal variation in thermal energetics of the Australian owlet-nightjar (Aegotheles cristatus)

Many birds living in regions with seasonal fluctuations in ambient temperatures (T_a) typically respond to cold by increasing insulation and adjusting metabolic rate. Seasonal variation in thermal physiology has not been studied for the Caprimulgiformes, an order of birds that generally have basal metabolic rates (BMR) lower than predicted for their body mass. We measured the metabolic rate and thermal conductance of Australian owlet-nightjars (Aegotheles cristatus) during summer and winter using open-flow respirometry. Within the thermoneutral zone (TNZ; 31.3 to 34.8 °C), there was no seasonal difference in BMR or thermal conductance (C), but body temperature was higher in summer- (38.2 ± 0.3 °C) than winter-acclimatized (37.1 ± 0.5 °C) birds. Below the TNZ, resting metabolic rate (RMR) increased linearly with decreasing T_a, and RMR and C were higher for summer- than winter-acclimatized birds. The mean mass-specific BMR of owlet-nightjars (1.27 mL O₂ g^− 1 h^− 1) was close to the allometrically predicted value for a 45 g Caprimulgiformes, but well below that predicted for birds overall. These results suggest that owlet-nightjars increase plumage insulation to cope with low winter T_a, which is reflected in the seasonal difference in RMR and C below the TNZ, rather than adjusting BMR.     

Chromosomal-level genome assembly of the semi-dwarf rice Taichung Native 1, an initiator of Green Revolution

Here we report the 409.5 Mb chromosome-level assembly of the first bred semi-dwarf rice, the Taichung Native 1 (TN1), which served as the template for the development of the Green Revolution (GR) cultivar IR8 “miracle rice”. We sequenced the TN1 genome utilizing multiple platforms and produced PacBio long reads, Illumina paired-end reads, Illumina mate-pair reads and 10x Genomics linked reads. We used a hybrid approach to assemble the 226× coverage of sequences by a combination of de novo and reference-guided approaches. The assembled TN1 genome has an N50 scaffold size of 33.1 Mb with the longest measuring 45.5 Mb. We annotated 37,526 genes, in which 24,102 (64.23%) were assigned Blast2GO annotations. The genome has 4672 or 95.4% complete BUSCOs and a repeat content of 51.52%. We developed our own method of creating a GR pangenome using the orthologous relationships of the proteins of TN1, IR8, MH63 and IR64, identifying 16,999 core orthologue groups of Green Revolution. From the pangenome, we identified a set of shared and unique gene ontology terms for the accessory clusters, characterizing TN1, IR8, MH63 and IR64. This TN1 genome assembly and GR pangenome will be a resource for new genomic discoveries about Green Revolution, and for improving the disease and insect resistances and the yield of rice.     

Hibernation and daily torpor in an armadillo, the pichi (Zaedyus pichiy)

Hibernation and daily torpor are physiological strategies to cope with energetic challenges that occur in many mammalian and avian taxa, but no reliable information exists about daily torpor or hibernation for any xenarthran. Our objective was to determine whether the pichi (Zaedyus pichiy), a small armadillo (Xenarthra, Dasypodidae) that inhabits arid and semi-arid habitats in central and southern Argentina and Chile, enters shallow daily torpor or prolonged deep hibernation during winter when environmental temperature and food availability are low. We studied body temperature changes during winter in semi-captive pichis by means of temperature dataloggers implanted subcutaneously. All individuals entered hibernation, characterized by torpor events of 75 ± 20 h during which the subcutaneous temperature (T_sc) decreased to 14.6 ± 2.1 °C. These events were interrupted by periods of euthermia of 44 ± 38 h with a T_sc of 29.1 ± 0.7 °C. After the hibernation season, daily torpor bouts of 4 to 6 h occurred irregularly, with T_sc dropping to as low as 24.5 °C. We conclude that the pichi is a true hibernator and can enter daily torpor outside of the hibernation season.     

Thermal sensitivity of uncoupling protein expression in polar and temperate fish

Uncoupling proteins (UCP), capable of increasing proton leakage across the inner mitochondrial membrane, may play a role in the temperature-dependent setting of energy turnover in animals (and their mitochondria). Therefore, the genes and expression of fish UCP were investigated in the Antarctic eelpout Pachycara brachycephalum and a temperate confamilial species, the common eelpout Zoarces viviparus. UCP full-length cDNA was amplified from liver and muscle using RT–PCR and rapid amplification of cDNA ends (RACE). The fish UCP mRNA consists of 1906 bp in P. brachycephalum and of 1876 bp in Z. viviparus. Both zoarcid sequences contain open reading frames of 939 bp, encoding 313 amino acids, with 98% and 99% identity, respectively. Protein sequences of zoarcid UCP are closest related to fish and mammalian UCP2. For analysis of temperature-dependent expression common eelpouts were cold-acclimated from 10 °C to 2 °C and Antarctic eelpouts were warm-acclimated from 0 °C to 5 °C. Identical cDNA probes for both species were developed to investigate fish UCP mRNA expression, and protein expression levels were detected by Western Blot in the enriched membrane fraction. During cold-acclimation in Z. viviparus, mRNA levels increased by a factor up to 2.0, protein levels increased up to 1.5, in line with mitochondrial proliferation during cold-acclimation. Despite decreased mitochondrial protein content, in Antarctic eelpout UCP levels rose upon warm acclimation by a factor up to 2.0 (mRNA) and 1.6 (protein), respectively. Besides the ongoing discussion of UCP function in vertebrates, the data are indicative of a significant role of fish UCP in thermal adaptation of fish mitochondria.     

De novo assembly of a wild pear (Pyrus betuleafolia) genome

China is the origin and evolutionary centre of Oriental pears. Pyrus betuleafolia is a wild species native to China and distributed in the northern region, and it is widely used as rootstock. Here, we report the de novo assembly of the genome of P. betuleafolia‐Shanxi Duli using an integrated strategy that combines PacBio sequencing, BioNano mapping and chromosome conformation capture (Hi‐C) sequencing. The genome assembly size was 532.7 Mb, with a contig N50 of 1.57 Mb. A total of 59 552 protein‐coding genes and 247.4 Mb of repetitive sequences were annotated for this genome. The expansion genes in P. betuleafolia were significantly enriched in secondary metabolism, which may account for the organism's considerable environmental adaptability. An alignment analysis of orthologous genes showed that fruit size, sugar metabolism and transport, and photosynthetic efficiency were positively selected in Oriental pear during domestication. A total of 573 nucleotide‐binding site (NBS)‐type resistance gene analogues (RGAs) were identified in the P. betuleafolia genome, 150 of which are TIR‐NBS‐LRR (TNL)‐type genes, which represented the greatest number of TNL‐type genes among the published Rosaceae genomes and explained the strong disease resistance of this wild species. The study of flavour metabolism‐related genes showed that the anthocyanidin reductase (ANR) metabolic pathway affected the astringency of pear fruit and that sorbitol transporter (SOT) transmembrane transport may be the main factor affecting the accumulation of soluble organic matter. This high‐quality P. betuleafolia genome provides a valuable resource for the utilization of wild pear in fundamental pear studies and breeding.     

Protocols for hyperlactatemia induction in the lactate minimum test adapted to swimming rats

The lactate minimum test (LACmin) has been considered an important indicator of endurance exercise capacity and a single session protocol can predict the maximal steady state lactate (MLSS). The objective of this study was to determine the best swimming protocol to induce hyperlactatemia in order to assure the LACmin in rats (Rattus norvegicus), standardized to four different protocols (P) of lactate elevation. The protocols were P1: 6 min of intermittent jumping exercise in water (load of 50% of the body weight — bw); P2: two 13% bw load swimming bouts until exhaustion (tlim); P3: one tlim 13% bw load swimming bout; and P4: two 13% bw load swimming bouts (1st 30 s, 2nd to tlim), separated by a 30 s interval. The incremental phase of LACmin beginning with initial loads of 4% bw, increased in 0.5% at each 5 min. Peak lactate concentration was collected after 5, 7 and 9 min (mmol L^− 1) and differed among the protocols P1 (15.2 ± 0.4, 14.9 ± 0.7, 14.8 ± 0.6) and P2 (14.0 ± 0.4, 14.9 ± 0.4, 15.5 ± 0.5) compared to P3 (5.1 ± 0.1, 5.6 ± 0.3, 5.6 ± 0.3) and P4 (4.7 ± 0.2, 6.8 ± 0.2, 7.1 ± 0.2). The LACmin determination success rates were 58%, 55%, 80% and 91% in P1, P2, P3 and P4 protocols, respectively. The MLSS did not differ from LACmin in any protocol. The LACmin obtained from P4 protocol showed better assurance for the MLSS identification in most of the tested rats.     

Molecular cold-adaptation of protein function and gene regulation: The case for comparative genomic analyses in marine ciliated protozoa

Euplotes focardii is a marine ciliated protozoan discovered in the Ross Sea near Terra Nova Bay, Antarctica. This organism is strictly psychrophilic, survives and reproduces optimally at 4–5 °C, and has a genome rich in A/T base pairs. Like other ciliated protozoans, Euplotes spp. are characterized by nuclear dimorphism: 1) the germline micronucleus contains the entire genome as large chromosomes; and 2) the somatic macronucleus ( 50 megabases, or 5% of the micronuclear genome) contains small linear DNA nanochromosomes [1–12 kilobases], each of which constitutes a single genetic unit. These characteristics make E. focardii an ideal model for genome-level analysis to understand the evolutionary mechanisms that determine the adaptation of organisms to cold environments. Here we describe two examples that are controlled by phylogenetically appropriate comparison with mesophilic and psychrotolerant Euplotes species: 1) the genes and encoded proteins of the E. focardii tubulin superfamily, including α-, β-, and γ-tubulins; and 2) the genes of the heat-shock protein (Hsp) 70 family. The tubulins provide particular insight into protein-level structural changes that are likely to facilitate microtubule nucleation and polymerization in an energy poor environment. By contrast, the hsp70 genes of E. focardii and of its psychrotolerant relative E. nobilii reveal adaptive alterations in the regulation of gene expression in the cold. The unique characteristics of the E. focardii genome and the results that we present here argue strongly for a concerted effort to characterize the relatively low complexity macronuclear genome of this psychrophilic organism.     

Growth and protein synthesis of barramundi, Lates calcarifer, fed lupin as a partial protein replacement

Protein synthesis is an essential growth process in all animals. Little information is available on post-prandial protein synthesis and even less where different protein sources are compared. Protein synthesis was measured at 4 and 24 h after feeding juvenile barramundi in order to determine the effect of using lupin as a partial protein replacement for fish meal on the post-prandial protein metabolism. Juvenile barramundi (4.3 ±0.6 g) were held in a recirculation system (27 °C, salinity 10‰ and 24 h light) for 15 days. Fish were fed one of two isonitrogenous isoenergetic diets (40% crude protein, 16% lipid and 18.5 GE MJ kg^− 1). One diet was formulated with 100% fish meal as the protein source while the other had 45% of the protein replaced with lupin ingredients (lupin kernel meal (Lupinus angustifolius) and lupin protein concentrate). All fish were fed a ration of 6%·d^− 1 and feed intake was not significantly different between the two diets. Specific growth rate (SGR) and growth efficiency (in relation to protein (PPV) and energy (PEV)) were 6.5 ± 0.14%·d^− 1, 43.8 ± 2.72% and 38.31 ± 1.56%, respectively, and were not significantly different between the two diets. There was no significant difference in protein synthesis between the two diets at 4 and 24 h after feeding, however protein synthesis was significantly higher 4 h after feeding than at 24 h (p = 0.02). Neither growth performance nor protein metabolism was altered by replacing 45% of the protein with lupin protein and indicated this to be a suitable protein source for barramundi feeds.     

Febrile response to infection in the American alligator (Alligator mississippiensis)

Temperature probes were inserted into the stomachs of juvenile American alligators (Alligator mississippiensis) maintained outdoors at ambient fluctuating temperatures. Internal body temperatures (T_b) were measured every 15 min for two days, and then the alligators were injected with bacterial lipopolysaccharide (LPS), pyrogen-free saline, or left untreated. Alligators injected intraperitoneally with LPS exhibited maximum T_bs 2.6 ± 1.1 °C and 3.5 ± 1.2 °C higher than untreated control animals on days one and two after treatment, respectively. T_bs for these animals fell to within control ranges by day three postinjection. Similarly, mean preferred body temperatures (MPBTs) were significantly higher for LPS-injected alligators on days one (4.2 ± 1.8 °C) and two (3.5 ± 1.6 °C) after treatment. Intraperitoneal injection of heat-killed Aeromonas hydrophila, a gram-negative bacterium known to infect crocodilians, resulted in a fever while injection of Staphylococcus aureus (gram positive) did not elicit a febrile response. Injection of LPS in alligators maintained indoors in a constant temperature environment resulted in no increase in internal T_b. These results indicate that alligators did not exhibit a febrile response in the absence of a thermal gradient, and suggest that febrile responses observed are probably behavioral in nature.     

A high‐quality genome of taro (Colocasia esculenta (L.) Schott), one of the world's oldest crops

Taro (Colocasia esculenta (L.), Schott), from the Araceae family, is one of the oldest crops with important edible, medicinal, nutritional and economic value. Taro is a highly polymorphic species including diverse genotypes adapted to a broad range of environments, but the taro genome has rarely been investigated. Here, a high‐quality chromosome‐level genome of C. esculenta was assembled using data sequenced by Illumina, PacBio and Nanopore platforms. The assembled genome size was 2,405 Mb with a contig N50 of 400.0 kb and a scaffold N50 of 159.4 Mb. In total, 2,311 Mb (96.09%) of the contig sequences was anchored onto 14 chromosomes to form pseudomolecules, and 2,126 Mb (88.43%) was annotated as repetitive sequences. Of the 28,695 predicted protein‐coding genes, 26,215 genes (91.4%) could be functionally annotated. On the basis of phylogenetic analysis using 769 genes, C. esculenta and Spirodela polyrhiza were placed on one branch of the tree that diverged approximately 73.23 million years ago. The synteny analyses showed that there have been two whole‐genome duplication events in C. esculenta separated by a relatively short gap. According to comparative genome analysis, a larger number (1,189) of distinct gene families and long terminal repeats were enriched in C. esculenta. Our high‐quality taro genome will provide valuable resources for further genetic, ecological and evolutionary analyses of taro or other species in the Araceae.     

Structural differences in the motor domain of temperature-associated myosin heavy chain isoforms from grass carp fast skeletal muscle

We determined coding sequences for three types of grass carp myosin subfragment-1 (S1) heavy chain by extending 5′-regions of the three known genes encoding light meromyosin isoforms (10 °C, intermediate and 30 °C types). The primary structures of these three S1 heavy chain isoforms showed 81.4%, 81.2%, and 97.8% identities between the 10 °C and intermediate types, between the 10 °C and 30 °C types, and between the intermediate and 30 °C types, respectively. Isoform-specific differences were clearly observed between the 10 °C type and the other two types in 97 amino acid residues. Furthermore, among these amino acid mutations, 51 mutations occurred at the conserved residue sites of S1 heavy chain from fish and homoiotherm. Additionally, the 10 °C type showed striking differences compared with the other two types in the two surface loops, loop 1 located near the ATP-binding pocket and loop 2, which is one of the actin-binding sites, suggesting that such structural differences possibly affect their motor functions. Interestingly, this 10 °C-type myosin heavy chain isolated from adult grass carp skeletal muscle was surprisingly similar to the embryonic fast-type myosin heavy chain from juvenile silver carp in the structure of S1 heavy chain, indicating that it may also function as embryonic fast-type myosin heavy chain in juvenile stage.     

Complete mitochondrial genome sequence of the Himalayan Griffon,Gyps himalayensis (Accipitriformes: Accipitridae): Sequence,structure, and phylogenetic analyses

This is the first study to describe the mitochondrial genome of the Himalayan Griffon, Gyps himalayensis, which is an Old World vulture belonging to the family Accipitridae and occurring along the Himalayas and the adjoining Tibetan Plateau. Its mitogenome is a closed circular molecule 17,381 bp in size containing 13 protein‐coding genes, 22 tRNA coding genes, two rRNA‐coding genes, a control region (CR), and an extra pseudo‐control region (CCR) that are conserved in most Accipitridae mitogenomes. The overall base composition of the G. himalayensis mitogenome is 24.55% A, 29.49% T, 31.59% C, and 14.37% G, which is typical for bird mitochondrial genomes. The alignment of the Accipitridae species control regions showed high levels of genetic variation and abundant AT content. At the 5′ end of the domain I region, a long continuous poly‐C sequence was found. Two tandem repeats were found in the pseudo‐control regions. Phylogenetic analysis with Bayesian inference and maximum likelihood based on 13 protein‐coding genes indicated that the relationships at the family level were (Falconidae + (Cathartidae + (Sagittariidae + (Accipitridae + Pandionidae))). In the Accipitridae clade, G. himalayensis is more closely related to Aegypius monachus than to Spilornis cheela. The complete mitogenome of G. himalayensis provides a potentially useful resource for further exploration of the taxonomic status and phylogenetic history of Gyps species.     

The complete mitochondrial genome of Accipiter virgatus and evolutionary history of the pseudo-control regions in Falconiformes

The complete mitochondrial genome sequence of Accipiter virgatus was determined. This mt-genome was 17,952 bp in length and consisted of 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes, one control region (CR) and one pseudo-control region (CCR). Phylogenetic analyses of 14,644 bp of mitochondrial DNA (12 protein-coding genes, 2 rRNAs and 22 tRNAs) revealed the phylogenetic position of Cathartidae (Cathartes aura) was more closer to Ciconiidae (storks) than Accipitridae. To investigate the divergence times of the CCRs in Falconiformes, detailed analyses of the noncoding regions (CR and CCR) were performed. We found the recently reported novel gene order in Falconiformes had multiple independent origins and hence cannot be used to infer phylogenetic lineages. Indeed, the molecular clock suggested the CCR in Falconidae emerged about 65.4 million years (Mya), while that in Pandionidae–Accipitridae clade emerged about 19.16 Mya. The intra-genomic homology between the noncoding regions was detected in Spilornis cheela, which supporting the duplication hypothesis. Furthermore, the structure of CCR should be featured by a region containing tandem repeats as two definitely separated clusters of tandem repeats were found. The findings presented here should be considered in future phylogenetic and evolutionary studies targeting the pseudo-control regions of all Falconiformes species.