A chromosome-level genome of Antechinus flavipes provides a reference for an Australasian marsupial genus with suicidal reproduction

The 15 species of small carnivorous marsupials that comprise the genus Antechinus exhibit semelparity, a rare life-history strategy where death occurs after one breeding season. Antechinus males, but not females, age rapidly (demonstrate organismal senescence) during the breeding season and show promise as new animal models of ageing. Some antechinus species are also threatened or endangered. Here, we report chromosome-level genomes of the yellow-footed antechinus Antechinus flavipes. The genome assembly has a total length of 3.2 Gb with a contig N50 of 51.8 Mb and a scaffold N50 of 636.7 Mb. We anchored and oriented 99.7% of the assembly on seven pseudochromosomes and found that repetitive DNA sequences occupy 51.8% of the genome. Draft genome assemblies of three related species in the subfamily Phascogalinae, two additional antechinus species (A. argentus and A. arktos) and the iteroparous sister species Murexia melanurus were also generated. Preliminary demographic analysis supports the hypothesis that climate change during the Pleistocene isolated species in Phascogalinae and shaped their population size. A transcriptomic profile across the A. flavipes breeding season allowed us to identify genes associated with aspects of the male die-off. The chromosome-level A. flavipes genome provides a steppingstone to understanding an enigmatic life-history strategy and a resource to assist the conservation of antechinuses.

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Feeding ecology and life-history strategy of nesting males in a fish with long parental care, Lusitanian toadfish (Halobatrachus didactylus, Batrachoididae)

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315415001022 ◽

2015 ◽

pp. 1-9 ◽

Cited By ~ 2

Author(s):

P.M. Félix ◽

M.C.P. Amorim ◽

T.J. Pereira ◽

P.J. Fonseca ◽

C. Sousa-Santos ◽

...

Keyword(s):

Life History ◽

Parental Care ◽

Breeding Season ◽

Feeding Behaviour ◽

Life History Strategy ◽

Otter Trawl ◽

Artificial Nests ◽

Limited Mobility ◽

Egg Cannibalism ◽

Male Condition

The Lusitanian toadfish,Halobatrachus didactylus, like other batrachoidids, is a benthic fish species with nesting behaviour during the breeding season. During this prolonged period it engages in mating activities and remains in the nest providing parental care. It is not known whether males feed while providing parental care but it is likely that their limited mobility may restrict their diet and influence their fitness. As a consequence, egg cannibalism could occur as a life-history strategy. The aim of the present study is to ascertain the feeding behaviour of nesting males, in comparison to mature non-nesting males, and to identify potential life-history traits related to egg cannibalism. Nest-holders were sampled from artificial nests placed in an intertidal area of the Tagus estuary, only exposed during spring low tides. The diet of nest-holders was compared with that of non-nesting mature males from the same area, captured by otter trawl. The present study demonstrates that despite their constrained mobility nest-holders feed during the breeding season, although in a more opportunistic fashion than non-nesting males. Nest-holders showed a generalist feeding behaviour, with a more heterogeneous diet. Egg cannibalism was not related to male condition, paternity or brood size but showed a higher incidence early in the season when water temperatures were lower. The results suggest a possible seasonal trade-off strategy between care and energy recovery, triggered by environmental factors, where under unfavourable conditions to sustain viable eggs the male may recover energy by eating eggs, thus benefiting future reproductive success, later in the season.

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Chromosome-Level Genome Assemblies Expand Capabilities of Genomics for Conservation Biology

Genes ◽

10.3390/genes12091336 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1336

Author(s):

Azamat Totikov ◽

Andrey Tomarovsky ◽

Dmitry Prokopov ◽

Aliya Yakupova ◽

Tatiana Bulyonkova ◽

...

Keyword(s):

Genetic Diversity ◽

Conservation Biology ◽

Threatened Species ◽

Mammalian Species ◽

Draft Genome ◽

Chromosome Length ◽

Chromosome Conformation ◽

Genome Wide ◽

Genome Assemblies ◽

Chromosome Level

Genome assemblies are in the process of becoming an increasingly important tool for understanding genetic diversity in threatened species. Unfortunately, due to limited budgets typical for the area of conservation biology, genome assemblies of threatened species, when available, tend to be highly fragmented, represented by tens of thousands of scaffolds not assigned to chromosomal locations. The recent advent of high-throughput chromosome conformation capture (Hi-C) enables more contiguous assemblies containing scaffolds spanning the length of entire chromosomes for little additional cost. These inexpensive contiguous assemblies can be generated using Hi-C scaffolding of existing short-read draft assemblies, where N50 of the draft contigs is larger than 0.1% of the estimated genome size and can greatly improve analyses and facilitate visualization of genome-wide features including distribution of genetic diversity in markers along chromosomes or chromosome-length scaffolds. We compared distribution of genetic diversity along chromosomes of eight mammalian species, including six listed as threatened by IUCN, where both draft genome assemblies and newer chromosome-level assemblies were available. The chromosome-level assemblies showed marked improvement in localization and visualization of genetic diversity, especially where the distribution of low heterozygosity across the genomes of threatened species was not uniform.

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Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny

10.21203/rs.3.rs-796229/v1 ◽

2021 ◽

Author(s):

Ulrich Technau ◽

Sophia Robb ◽

Grigory Genikhovich ◽

Juan Montenegro ◽

Witney Fropf ◽

...

Keyword(s):

Gene Regulation ◽

Draft Genome ◽

Gene Clusters ◽

Sea Anemone ◽

Gene Repertoire ◽

Sea Anemones ◽

Animal Evolution ◽

Topologically Associated Domains ◽

Genome Assemblies ◽

Chromosome Level

Abstract Draft genome sequences of non-bilaterian species have provided important insights into the evolution of the metazoan gene repertoire. However, there is little information about the evolution of gene clusters, genome architectures and karyotypes during animal evolution. Here we report chromosome-level genome assemblies of two related anthozoan cnidarians, the sea anemones, Nematostella vectensis and Scolanthus callimorphus. We find a robust set of 15 chromosomes with a clear one-to-one correspondence of the chromosomes between the two species. We show that, in contrast to Bilateria, Hox and NK clusters of investigated cnidarians are disintegrated, indicating that microsynteny conservation is largely lost. In line with that, we find no evidence for topologically associated domains, suggesting fundamental difference in long-range gene regulation compared to vertebrates. However, both sea anemone genomes show remarkable chromosomal conservation with other cnidarians, several bilaterians and the sponge Ephydatia muelleri, allowing us to reconstruct the putative cnidarian and metazoan chromosomes, consisting of 19 and 16 ancestral linkage groups, respectively. These data suggest that large parts of the ancestral metazoan genome have been retained in chromosomes of some extant lineages, yet, higher order gene regulation may have evolved only after the cnidarian-bilaterian split.

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Chromosome-Level Genome Assemblies: Expanded Capabilities for Conservation Biology Research

Proceedings ◽

10.3390/iecge-07149 ◽

2020 ◽

Vol 76 (1) ◽

pp. 10

Author(s):

Azamat Totikov ◽

Andrey Tomarovsky ◽

Lorena Derezanin ◽

Olga Dudchenko ◽

Erez Lieberman-Aiden ◽

...

Keyword(s):

Genetic Diversity ◽

High Throughput ◽

Conservation Biology ◽

Threatened Species ◽

Draft Genome ◽

Chromosome Conformation ◽

Genome Wide ◽

Genome Assemblies ◽

Biology Research ◽

Chromosome Level

Genome assemblies are becoming increasingly important for understanding genetic diversity in threatened species. However, due to limited budgets in the area of conservation biology, genome assemblies, when available, tend to be highly fragmented with tens of thousands of scaffolds. The recent advent of high throughput chromosome conformation capture (Hi-C) makes it possible to generate more contiguous assemblies containing scaffolds that are length of entire chromosomes. Such assemblies greatly facilitate analyses and visualization of genome-wide features. We compared genetic diversity in seven threatened species that had both draft genome assemblies and newer chromosome-level assemblies available. Chromosome-level assemblies allowed better estimation of genetic diversity, localization, and, especially, visualization of low heterozygosity regions in the genomes.

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Life-history strategies of native and introduced fish species from a Mediterranean lake

Animal Biology ◽

10.1163/157075603769682576 ◽

2003 ◽

Vol 53 (1) ◽

pp. 47-57 ◽

Cited By ~ 6

Author(s):

◽

Keyword(s):

Life History ◽

Parental Care ◽

Introduced Species ◽

Breeding Season ◽

Fish Species ◽

Generation Time ◽

Life History Traits ◽

Life History Strategy ◽

Life History Strategies ◽

High Fecundity

AbstractSeven life-history traits were used to describe the life-history strategies of 12 native and introduced species from a permanent lake in Spain. Multivariate analysis identified a continuum of life-history patterns between two extremes: 1) species with one or few spawnings per year, short breeding season, long generation time, large size, high fecundity, and no parental care. This set of life-history traits corresponded to the periodic life-history strategy described by Winemiller (1989) and Winemiller and Rose (1992); and 2) species with multiple spawnings per year, prolonged breeding season, short generation time, small size, low fecundity, parental care, and small to medium size of eggs. This association of life-history traits corresponded to the opportunistic life-history strategy described by Winemiller (1989) and Winemiller and Rose (1992). It seems that there were no apparent differences in life-history strategies between native and introduced species in Lake Banyoles. Native and introduced species were found among periodic and opportunistic strategists. Observed differences in the success of native and introduced species with comparable life-history strategies seems to suggest that the success of fish species in Lake Banyoles could not be explained on the basis of life-history features. Nevertheless, it seems that successful invasive species in Lake Banyoles display a suite of traits such as high fecundity, late maturity, and large body size. These characteristics may perhaps be viewed as biological predictors of successful invaders but more information is needed about life-history features of successful introduced species from other ecosystems.

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New evidence for facultative male die-off in island populations of dibblers, Parantechinus apicalis

Australian Journal of Zoology ◽

10.1071/zo00025 ◽

2000 ◽

Vol 48 (5) ◽

pp. 501 ◽

Cited By ~ 16

Author(s):

Harriet R. Mills ◽

Roberta Bencini

Keyword(s):

Life History ◽

Breeding Season ◽

High Mortality ◽

Life History Strategy ◽

Island Population ◽

Island Populations ◽

In Captivity ◽

Second Year ◽

New Evidence

The post-mating mortality of males in dasyurid species is thought to be a specific life-history strategy, associated with a tightly synchronised breeding season, that may enhance survivorship of juveniles. Parantechinus apicalis has been reported to exhibit male die-off in island populations but not in mainland populations, and males originating from both island and mainland populations are known to survive post-mating in captivity. However, males in the island populations have been reported to sometimes survive to breed in a second year. This study monitored captive and island populations over a three-year period (April 1997 – May 2000) to examine the extent of male die-off. In captivity, males showed no evidence of post-mating mortality. Males on one island were also found to survive post-mating, while another island population appeared to have high mortality of males in three years, and a complete male die-off after the 1999 breeding season. We conclude that P. apicalis may warrant inclusion in a new category of life-history strategy for species exhibiting facultative male die-off.

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