Reproductive ecology of female caecilian amphibians (genus Ichthyophis): a baseline study

The remarkable diversity of reproductive modes, including levels of parental care that are extensive relative to those of the other major amphibian groups, makes the limbless tropical caecilians ideally suited for evolutionary reproductive studies. Here we present key life history data for the oviparous caecilian Ichthyophis cf. kohtaoensis. We used non-invasive methods to analyse reproductive traits, seasonality of breeding and characteristics of oviposition sites in the field (Mekong valley, north-eastern Thailand). A correlation was established between reproductive activity and season, indicated by the age of egg clutches found in the field. Eggs at early developmental stages were found at the beginning of the rainy season, those with well-developed embryos at the peak of the monsoon. The body condition of females guarding younger clutches was superior to that of females with older clutches, indicative of a loss of energy reserves during the period of parental care. Maternal total length correlated positively with the number of eggs as well as with the total length of newly hatched larvae. The terrestrial oviposition sites of females were located close to temporary and permanent ponds, small brooks and rivers. It is hoped that the study will, in addition to contributing to our understanding of the evolution of caecilian reproduction, provide a basis for further comparisons of reproductive strategies among amphibians and other terrestrial tetrapods.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 207–217.     

Microanatomy of the digestive system of Supachai's caecilian,Ichthyophis supachaii Taylor, 1960 (Amphibia: Gymnophiona)

The gross anatomy and microanatomy of the digestive system of Ichthyophis supachaii were investigated. The microscopic structures of the digestive system are similar to those in other caecilians. Functional and developing teeth are present in adults. The tongue contains the genioglossus muscle. The digestive tract is elongated and consists of the mucosa, submucosa, muscularis and adventitia/serosa. The oesophagus contains longitudinal folds and lacks oesophageal glands. We report for the first time the caecilian gastric rugae and specific localization of oxynticopeptic cells in the anterior gastric region. The intestinal folds are exclusively present in the anterior intestinal region. The liver comprises 30–40 incomplete hepatic lobes, lying in an imbricate manner. Each lobe is enveloped by haematopoietic tissue that produces and delivers blood cells into sinusoids. Hepatic parenchyma is organized into anastomosing, two‐cell‐thick plates, having sinusoids at the basal domain and bile canaliculi at the apical domain of hepatocytes. Pigment cells are scattered inside sinusoids. The pancreas contains pancreatic acini interspersed with islets of Langerhans. The gallbladder proper is thin and continuous with the cystic duct wall. Neutral and carboxylated acid mucosubstances are secreted along the digestive tract, while sulphated mucosubstances are not produced by the stomach and anterior intestinal regions.     

Improved genome assembly provides new insights into genome evolution in a desert poplar (Populus euphratica)

Populus euphratica is well adapted to extreme desert environments and is an important model species for elucidating the mechanisms of abiotic stress resistance in trees. The current assembly of P. euphratica genome is highly fragmented with many gaps and errors, thereby impeding downstream applications. Here, we report an improved chromosome‐level reference genome of P. euphratica (v2.0) using single‐molecule sequencing and chromosome conformation capture (Hi‐C) technologies. Relative to the previous reference genome, our assembly represents a nearly 60‐fold improvement in contiguity, with a scaffold N50 size of 28.59 Mb. Using this genome, we have found that extensive expansion of Gypsy elements in P. euphratica led to its rapid increase in genome size compared to any other Salicaceae species studied to date, and potentially contributed to adaptive divergence driven by insertions near genes involved in stress tolerance. We also detected a wide range of unique structural rearrangements in P. euphratica, including 2,549 translocations, 454 inversions, 121 tandem and 14 segmental duplications. Several key genes likely to be involved in tolerance to abiotic stress were identified within these regions. This high‐quality genome represents a valuable resource for poplar breeding and genetic improvement in the future, as well as comparative genomic analysis with other Salicaceae species.     

A chromosome-level genome assembly of Ostrea denselamellosa provides initial insights into its evolution

The oyster Ostrea denselamellosa is a live-bearing species with a sharp decline in the natural population. Despite recent breakthroughs in long-read sequencing, high quality genomic data are very limited in O. denselamellosa. Here, we carried out the first whole genome sequencing at the chromosome-level in O. denselamellosa. Our studies yielded a 636 Mb assembly with scaffold N50 around 71.80 Mb. 608.3 Mb (95.6% of the assembly) were anchored to 10 chromosomes. A total of 26,412 protein-coding genes were predicted, of which 22,636 (85.7%) were functionally annotated. By comparative genomics, we found that long interspersed nuclear element (LINE) and short interspersed nuclear element (SINE) made up a larger proportion in O. denselamellosa genome than in other oysters'. Moreover, gene family analysis showed some initial insight into its evolution. This high-quality genome of O. denselamellosa provides a valuable genomic resource for studies of evolution, adaption and conservation in oysters.     

The Phylogeography and Population Demography of the Yunnan Caecilian (Ichthyophis bannanicus): Massive Rivers as Barriers to Gene Flow

Ichthyophis bannanicus is the only caecilian species in China. In this study, the phylogeography and population demography of I. bannanicus were explored, based on the mitochondrial DNA genes (cyt b and ND2) and 15 polymorphic microsatellite loci. Altogether 158 individuals were collected from five populations in Yunnan province, Guangxi province, Guangdong province, and Northern Vietnam. Phylogeographical and population structure analysis identified either two groups (Xishuangbanna, Northern Vietnam-Yulin-Yangchun-Deqing) or three groups (Xishuangbanna, Northern Vietnam-Yulin-Yangchun, and Deqing), indicating that the Red River and Pearl River systems may have acted as gene-flow barriers for I. bannanicus. Historical population expansion that happened 15–17 Ka ago was detected for mtDNA data and was possibly triggered by warmer weather after the Last Glacial Maximum. However, the Bayesian simulations of population history based on microsatellite data pinpointed population decline in all populations since 19,123 to 1,029 years ago, demonstrating a significant influence of anthropogenic habitat alteration on I. bannanicus.     

Histomorphological studies of the testis and male genital ducts of Supachai's caecilian,Ichthyophis supachaii Taylor, 1960 (Amphibia: Gymnophiona)

We investigated the structure of the male reproductive system in Ichthyophis supachaii. The testis comprises a series of mulberry‐like lobes, each of which contains testis lobules occupied by germ cysts. A single cyst consists of synchronously developing germ cells. Six spermatogenic cell types, viz. primary spermatogonia, secondary spermatogonia, primary spermatocytes, secondary spermatocytes, spermatids and spermatozoa, have been identified and described. Notably, the testis of I. supachaii encompasses specific organization patterns of spermatids and spermatozoa during spermiogenesis. Spermiating cysts rupture and release spermatozoa to the collecting ducts, which are subsequently transported to the sperm duct, Wolffian duct and cloaca. We report for the first time ciliated cells in the epithelium of the caecilian Wolffian duct. The cloaca is divided into the urodeum and phallodeum. The urodeum has ciliated and glandular epithelia at its dorsolateral and ventral regions, respectively, as the lining of its internal surface. The muscular phallodeum is lined by ciliated epithelium. Paired Mullerian ducts lie parallel to the intestine and join the cloaca. The posterior portion of the duct is modified as the Mullerian gland. The most posterior region is non‐glandular and lined by ciliated epithelium. Our findings contribute further to information on the reproductive biology of caecilians in Thailand.     

Microscopic structures of the ovary and female genital ducts of Supachai's caecilian,Ichthyophis supachaii Taylor, 1960 (Amphibia: Gymnophiona)

The structures of the female reproductive system (ovary, oviduct and cloaca) of Ichthyophis supachaii were investigated by dissection, histology and light microscopy. Paired, elongated, sac‐like ovaries are parallel to the gut and fat bodies. Follicle stages include germinal nests of oogonia and primary oocytes, early and late previtellogenic follicles, early and late vitellogenic follicles and atretic follicles. Germinal nests of oogonia comprise oogonia and prefollicular cells. Nests of primary oocytes contain clusters of synchronously developing primary oocytes enclosed by connective tissue. Primary oocytes are associated with follicular cells. Previtellogenic follicles initially form the vitelline envelope, theca cell layers and patches of ooplasmic glycoproteins. Vitellogenic follicles contain heterogeneously sized spherical yolk granules. Atresia is present in several stages of developing follicles. The oviduct is divided into the anterior, middle and posterior parts. All oviductal parts are lined by non‐ciliated epithelium. A small number of mucous cells are present in the middle part. The cloaca of female I. supachaii is divided into the anterior and posterior chambers. The anterior chamber is lined by glandular stratified columnar epithelium, while the posterior chamber has stratified cuboidal epithelium with less mucus production. Our results contribute to useful information on the reproductive biology of caecilians.     

Crustacean (malacostracan) Hox genes and the evolution of the arthropod trunk

Representatives of the Insecta and the Malacostraca (higher crustaceans) have highly derived body plans subdivided into several tagma, groups of segments united by a common function and/or morphology. The tagmatization of segments in the trunk, the part of the body between head and telson, in both lineages is thought to have evolved independently from ancestors with a distinct head but a homonomous, undifferentiated trunk. In the branchiopod crustacean, Artemia franciscana, the trunk Hox genes are expressed in broad overlapping domains suggesting a conserved ancestral state (Averof, M. and Akam, M. (1995) Nature 376, 420-423). In comparison, in insects, the Antennapedia-class genes of the homeotic clusters are more regionally deployed into distinct domains where they serve to control the morphology of the different trunk segments. Thus an originally Artemia-like pattern of homeotic gene expression has apparently been modified in the insect lineage associated with and perhaps facilitating the observed pattern of tagmatization. Since insects are the only arthropods with a derived trunk tagmosis tested to date, we examined the expression patterns of the Hox genes Antp, Ubx and abd-A in the malacostracan crustacean Porcellio scaber (Oniscidae, Isopoda). We found that, unlike the pattern seen in Artemia, these genes are expressed in well-defined discrete domains coinciding with tagmatic boundaries which are distinct from those of the insects. Our observations suggest that, during the independent tagmatization in insects and malacostracan crustaceans, the homologous 'trunk' genes evolved to perform different developmental functions. We also propose that, in each lineage, the changes in Hox gene expression pattern may have been important in trunk tagmatization.     

Chromosome-level assembly of the Hypophthalmichthys molitrix (Cypriniformes: Cyprinidae) genome provides insights into its ecological adaptation

Hypophthalmichthys molitrix (silver carp) is phytoplanktivorous and is an economically and ecologically important fish species. As a well-known invasive species, a number of factors associated with the ecological adaptations of this species are largely unknown. Here, we present a chromosomal-level assembly of the species based on the PacBio Sequel II platform and Hi-C scaffolding technology. Based on the high-quality genome sequences and previous genome sequencing projects, a number of genes that were probably subject to positive selection reside in the genome of H. molitrix, and the last common ancestors of H. molitrix and H. nobilis were identified. Some of these genes may partially explain the mechanisms of H. molitrix for surviving damage due to toxic algae. Demographic history estimation suggests that the effective population size (EPS) of the species may have constantly increased along with the uplift of the Qinghai-Tibet Plateau, started to decline when quaternary glaciation started, and further declined during the Younger Dryas Period. Moreover, the introgression from H. nobilis to H. molitrix in North America was corroborated based on the whole-genome sequencing data, and the proportion of introgressed regions was estimated to be approximately 5.8%. Based on the high-quality assembly, the possible mechanisms by which H. molitrix adapts to its endemic and invaded locations were profiled.     

Comparative morphology and evolution of the lungless caecilian Atretochoana eiselti (Taylor) (Amphibia: Gymnophiona: Typhlonectidae)

Atretochoana eiselti is a radically divergent aquatic caecilian until recendy known from only a single specimen from South America. In addition to its status as the largest lungless tetrapod known, and the only known lungless caecilian, this species has a suite of highly unusual morphological features that sets it apart from all other tetrapods, including sealed choanae (internal nostrils), complete loss of pulmonary arteries and veins, novel cranial architecture, and a novel stapedial muscle. The external, buccal, skeletal, muscular and cardiovascular anatomies of Atretochoana eiselti are described and compared to these features in other caecilians, particularly representatives of all typhlonectid genera which are its closest relatives. The comparative morphological data are used as a basis for interpretations of the ecology and evolution of Atretochoana eiselti. It is argued that lunglessness and the transition to cutaneous gas exchange is correlated with life in cold, montane, fast-flowing streams. Here, high oxygen concentrations and reduced metabolic rate serve to relax the physiological limitations on body size imposed by a reliance upon cutaneous gas-exchange, and lungs can produce disadvantageous buoyancy. Cranial evolution has increased the gape of Atretochoana eiselti relative to other caecilians, and seems likely to be associated with a shift in prey size and possibly type. Several modifications of the cranium appear to be associated with enhanced cranial kinesis in which a distinct cheek unit is highly mobile. The novel stapedial musculature is interpreted as contributing to this cranial kinesis. Respiratory and cranial evolution are argued to be correlated, with the ventilatory function of the buccopharyngeal pump constraining the evolution of the skull. The evolution of lunglessness removed this constraint facilitating repatterning of the skull.     

Dolphin genome provides evidence for adaptive evolution of nervous system genes and a molecular rate slowdown

Cetaceans (dolphins and whales) have undergone a radical transformation from the original mammalian bodyplan. In addition, some cetaceans have evolved large brains and complex cognitive capacities. We compared approximately 10 000 protein-coding genes culled from the bottlenose dolphin genome with nine other genomes to reveal molecular correlates of the remarkable phenotypic features of these aquatic mammals. Evolutionary analyses demonstrated that the overall synonymous substitution rate in dolphins has slowed compared with other studied mammals, and is within the range of primates and elephants. We also discovered 228 genes potentially under positive selection (dN/dS > 1) in the dolphin lineage. Twenty-seven of these genes are associated with the nervous system, including those related to human intellectual disabilities, synaptic plasticity and sleep. In addition, genes expressed in the mitochondrion have a significantly higher mean dN/dS ratio in the dolphin lineage than others examined, indicating evolution in energy metabolism. We encountered selection in other genes potentially related to cetacean adaptations such as glucose and lipid metabolism, dermal and lung development, and the cardiovascular system. This study underlines the parallel molecular trajectory of cetaceans with other mammalian groups possessing large brains.     

Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes

With about 24,000 extant species, teleosts are the largest group of vertebrates. They constitute more than 99% of the ray-finned fishes (Actinopterygii) that diverged from the lobe-finned fish lineage (Sarcopterygii) about 450 MYA. Although the role of genome duplication in the evolution of vertebrates is now established, its role in structuring the teleost genomes has been controversial. At least two hypotheses have been proposed: a whole-genome duplication in an ancient ray-finned fish and independent gene duplications in different lineages. These hypotheses are, however, based on small data sets and lack adequate statistical and phylogenetic support. In this study, we have made a systematic comparison of the draft genome sequences of Fugu and humans to identify paralogous chromosomal regions ("paralogons") in the Fugu that arose in the ray-finned fish lineage ("fish-specific"). We identified duplicate genes in the Fugu by phylogenetic analyses of the Fugu, human, and invertebrate sequences. Our analyses provide evidence for 425 fish-specific duplicate genes in the Fugu and show that at least 6.6% of the genome is represented by fish-specific paralogons. We estimated the ages of Fugu duplicate genes and paralogons using the molecular clock. Remarkably, the ages of duplicate genes and paralogons are clustered, with a peak around 350 MYA. These data strongly suggest a whole-genome duplication event early during the evolution of ray-finned fishes, probably before the origin of teleosts.     

薏苡黑粉菌基因组测序揭示其物种分类及适应性进化

以薏苡黑粉菌病瘿为研究对象,采用固体和液体培养方法对薏苡黑粉菌进行分离纯化培养和形态观察;利用Illumina、Pacbio测序和Hi-C辅助基因组组装技术对黑粉菌进行测序、组装和注释,分析其基因组结构和组成特征。通过与其他6个黑粉菌物种基因组进行比较基因组学研究,分析薏苡黑粉菌的基因家族进化和系统发育关系。在pH 7的固体PDA和液体PDB培养基中实现了薏苡黑粉菌的纯化培养,固体培养菌落表现为白色、表面隆起、具褶皱,较湿润且不透明的形态特征。Illumina、Pacbio和Hi-C组装结果显示,薏苡黑粉菌具有20对染色体(2n=40),基因组大小20.093 417 Mb,GC含量53.81%;共预测和注释到7 476个蛋白编码基因和164个非编码基因,占整个基因组长度的61.02%和0.285 3%;查找到3 674个散在重复序列和8 139个串联重复序列,分别占整个基因组长度的2.754 4%和1.605 4%。同源基因家族聚类显示,7个黑粉菌物种Ustilago coicis、U. bromivora、U. maydis、U. hordei、Sporisorium reilianum、S. scitamineum和S. graminicola的编码基因被聚类为6 999个基因家族,其中共有基因家族5 379个。薏苡黑粉菌包含5 339个单拷贝基因、105个多拷贝基因、89个特异基因、752个其他基因和188个未分类基因。基因家族进化和系统发育聚类表明,薏苡黑粉菌U. coicis在~60.9 MYA分化出来,与雀麦黑粉菌U. bromivova、大麦坚黑粉菌U. hordei聚为一支,表现为更近的亲缘关系;而玉米黑粉菌U. maydis在~66.6 MYA分化出来与3个孢堆黑粉菌物种S. scitamineum、S. graminicola和S. reilianum聚为一支。     

A comparative genetic linkage map of eggplant (Solanum melongena) and its implications for genome evolution in the solanaceae

A molecular genetic linkage map based on tomato cDNA, genomic DNA, and EST markers was constructed for eggplant, Solanum melongena. The map consists of 12 linkage groups, spans 1480 cM, and contains 233 markers. Comparison of the eggplant and tomato maps revealed conservation of large tracts of colinear markers, a common feature of genome evolution in the Solanaceae and other plant families. Overall, eggplant and tomato were differentiated by 28 rearrangements, which could be explained by 23 paracentric inversions and five translocations during evolution from the species' last common ancestor. No pericentric inversions were detected. Thus, it appears that paracentric inversion has been the primary mechanism for chromosome evolution in the Solanaceae. Comparison of relative distributions of the types of rearrangements that distinguish pairs of solanaceous species also indicates that the frequency of different chromosomal structural changes was not constant over evolutionary time. On the basis of the number of chromosomal disruptions and an approximate divergence time for Solanum, approximately 0.19 rearrangements per chromosome per million years occurred during the evolution of eggplant and tomato from their last ancestor. This result suggests that genomes in Solanaceae, or at least in Solanum, are evolving at a moderate pace compared to other plant species.     

A near-complete genome assembly of Brassica rapa provides new insights into the evolution of centromeres

Brassica rapa comprises many important cultivated vegetables and oil crops. However, Chiifu v3.0, the current B. rapa reference genome, still contains hundreds of gaps. Here, we presented a near-complete genome assembly of B. rapa Chiifu v4.0, which was 424.59 Mb with only two gaps, using Oxford Nanopore Technology (ONT) ultralong-read sequencing and Hi-C technologies. The new assembly contains 12 contigs, with a contig N50 of 38.26 Mb. Eight of the ten chromosomes were entirely reconstructed in a single contig from telomere to telomere. We found that the centromeres were mainly invaded by ALE and CRM long terminal repeats (LTRs). Moreover, there is a high divergence of centromere length and sequence among B. rapa genomes. We further found that centromeres are enriched for Copia invaded at 0.14 MYA on average, while pericentromeres are enriched for Gypsy LTRs invaded at 0.51 MYA on average. These results indicated the different invasion mechanisms of LTRs between the two structures. In addition, a novel repetitive sequence PCR630 was identified in the pericentromeres of B. rapa. Overall, the near-complete genome assembly, B. rapa Chiifu v4.0, offers valuable tools for genomic and genetic studies of Brassica species and provides new insights into the evolution of centromeres.