Browsing by Author "Gan, Han Ming"
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- Conbiomics: the missing approach for the conservation of freshwater bivalvesPublication . Froufe, Elsa; Fonseca, Miguel M.; Teixeira, Amílcar; Varandas, Simone; Gonçalves, Duarte V.; Hinzmann, Mariana; Arenas-Arenas, Francisco José; Gan, Han Ming; Breton, Sophie; Prié, Vincent; Zieritz, Alexandra; Bogan, Arthur E.; Razgour, Orly; Vikhrev, Ilya V.; Bolotov, Ivan N.; Pfeiffer, John; Lopes-Lima, ManuelThe decline of freshwater biodiversity hás reached alarming proportions. The extinction rate of freshwater biodiversity is predicted to be five times faster than ali other groups of species. The Unionidae, being the largest of the freshwater bivalve families, is among the most endangered group in the world. They are important providers of aquatic ecosystem services and are characterized by an unusual pattem of mtDNA inheritance. However, phylogeny, population genetic structure and species-level diversity remains unclear for much of the group. With an experienced and well-qualified team, the present proposal aims to define the most important freshwater mussel taxa and most criticai áreas for conservation, at European and Global leveis, to inform the most relevant policy niakers. This will be achieved by integrating a genomics approach with available distribution data, in order to determine and map global species richness, phylogenetic diversity, and weighted endemism. This complementary approach will not only help conserve this vulnerable group but will offer wider benefits to freshwater ecosystems whose billions of people depend globally. Additionally, as these animals have an extraordinary unusual pattern of mtDNA inheritance, they will be used as model-taxa to study the evolution of mtDNA and life in general.
- Conbiomics: the missing approach for the conservation of freshwater bivalvesPublication . Froufe, Elsa; Fonseca, Miguel M.; Teixeira, Amílcar; Varandas, Simone; Gonçalves, Duarte V.; Hinzmann, Mariana; Arenas-Arenas, Francisco José; Gan, Han Ming; Breton, Sophie; Prié, Vincent; Zieritz, Alexandra; Bogan, Arthur E.; Razgour, Orly; Vikhrev, Ilya; Bolotov, Ivan N.; Pfeiffer, John; Lopes-Lima, ManuelThe decline of freshwater biodiversity hás reached alarming proportions. The extinction rate of freshwater biodiversity is predicted to be five times faster than ali other groups of species. The Unionidae, being the largest of the freshwater bivalve families, is among the most endangered group in the world. They are important providers of aquatic ecosystem services and are characterized by an unusual pattem of mtDNA inheritance. However, phylogeny, population genetic structure and species-level diversity remains unclear for much of the group. With an experienced and well-qualified team, the present proposal aims to define the most important freshwater mussel taxa and most criticai áreas for conservation, at European and Global leveis, to inform the most relevant policy niakers. This will be achieved by integrating a genomics approach with available distribution data, in order to determine and map global species richness, phylogenetic diversity, and weighted endemism. This complementary approach will not only help conserve this vulnerable group but will offer wider benefits to freshwater ecosystems whose billions of people depend globally. Additionally, as these animals have an extraordinary unusual pattern of mtDNA inheritance, they will be used as model-taxa to study the evolution of mtDNA and life in general.
- The crown pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)Publication . Gomes-dos-Santos, André; Lopes-Lima, Manuel; Machado, André M.; Ramos, António Marcos; Usié, Ana; Bolotov, Ivan N.; Vikhrev, Ilya V.; Breton, Sophie; Castro, L. Filipe C.; Fonseca, Rute R. da; Geist, Juergen; Österling, Martin E.; Prié, Vincent; Teixeira, Amílcar; Gan, Han Ming; Simakov, Oleg; Froufe, ElsaSince historical times, the inherent human fascination with pearls turned the freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) into a highly valuable cultural and economic resource. Although pearl harvesting in M. margaritifera is nowadays residual, other human threats have aggravated the species conservation status, especially in Europe. This mussel presents a myriad of rare biological features, e.g. high longevity coupled with low senescence and Doubly Uniparental Inheritance of mitochondrial DNA, for which the underlying molecular mechanisms are poorly known. Here, the first draft genome assembly of M. margaritifera was produced using a combination of Illumina Paired-end and Mate-pair approaches. The genome assembly was 2.4 Gb long, possessing 105,185 scaffolds and a scaffold N50 length of 288,726 bp. The ab initio gene prediction allowed the identification of 35,119 protein-coding genes. This genome represents an essential resource for studying this species' unique biological and evolutionary features and ultimately will help to develop new tools to promote its conservation.
- Expansion and systematics redefinition of the most threatened freshwater mussel family, the MargaritiferidaePublication . Lopes-Lima, Manuel; Bolotov, Ivan N.; Do, Van Tu; Aldridge, David C.; Fonseca, Miguel M.; Gan, Han Ming; Gofarov, Mikhail Y.; Kondakov, Alexander V.; Prié, Vincent; Sousa, Ronaldo; Varandas, Simone; Vikhrev, Ilya V.; Teixeira, Amílcar; Wu, Rui Wen; Wu, Xiaoping; Zieritz, Alexandra; Froufe, Elsa; Bogan, Arthur E.Two Unionida (freshwater mussel) families are present in the Northern Hemisphere; the Margaritiferidae, representing the most threatened of unionid families, and the Unionidae, which include several genera of unresolved taxonomic placement. The recent reassignment of the poorly studied Lamprotula rochechouartii from the Unionidae to the Margaritiferidae motivated a new search for other potential species of margaritiferids from members of Gibbosula and Lamprotula. Based on molecular and morphological analyses conducted on newly collected specimens from Vietnam, we here assign Gibbosula crassa to the Margaritiferidae. Additionally, we reanalyzed all diagnostic characteristics of the Margaritiferidae and examined museum specimens of Lamprotula andGibbosula.As a result, two additional speciesarealsomovedtotheMargaritiferidae, i.e.Gibbosula confragosa and Gibbosula polysticta. We performed a robust five marker phylogeny with all available margaritiferid species and discuss the taxonomy within the family. The present phylogeny reveals the division of Margaritiferidae into four ancient clades with distinct morphological, biogeographical and ecological characteristics that justify the division of the Margaritiferidae into two subfamilies (Gibbosulinae and Margaritiferinae) and four genera (Gibbosula, Cumberlandia, Margaritifera, and Pseudunio). The systematics of the Margaritiferidae family is redefined as well as their distribution, potential origin and main biogeographic patterns.
- The first Margaritiferidae male (M-Type) mitogenome: Mitochondrial gene order as a potential character for determining higher-order phylogeny within Unionida (Bivalvia)Publication . Lopes-Lima, Manuel; Fonseca, Miguel M.; Aldridge, David C.; Bogan, Arthur E.; Gan, Han Ming; Ghamizi, Mohamed; Sousa, Ronaldo; Teixeira, Amílcar; Varandas, Simone; Zanatta, David T.; Zieritz, Alexandra; Froufe, Elsa
- The male and female complete mitochondrial genome sequences of the Endangered freshwater mussel Potomida littoralis (Cuvier, 1798) (Bivalvia: Unionidae)Publication . Froufe, Elsa; Gan, Han Ming; Lee, Yin Peng; Carneiro, João; Varandas, Simone; Teixeira, Amílcar; Zieritz, Alexandra; Sousa, Ronaldo; Lopes-Lima, ManuelFreshwater mussels of the family Unionidae exhibit a particular form of mitochondria inheritance called double uniparental inheritance (DUI), in which the mitochondria are inherited by both male and female parents. The (M)ale and (F)emale mitogenomes are highly divergent within species. In the present study, we determine and describe the complete M and F mitogenomes of the Endangered freshwater mussel Potomida littoralis (Cuvier, 1798). The complete M and F mitogenomes sequences are 16 451 bp and 15 787 bp in length, respectively. Both F and M have the same gene content: 13 protein-coding genes (PCGs), 22 transfer RNA (trn) and 2 ribosomal RNA (rrn) genes. Bayesian analyses based on the concatenated nucleotide sequences of 12 PCGs and 2 rrn genes of both genomes, including mitogenome sequences available from related species, were performed. Male and Female lineages are monophyletic within the family, but reveal distinct phylogenetic relationships.
- The male and female complete mitochondrial genomes of the threatened freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) (Bivalvia: Margaritiferidae)Publication . Gomes-dos-Santos, André; Froufe, Elsa; Amaro, Rafaela; Ondina, Paz; Breton, Sophie; Guerra, Davide; Aldridge, David C.; Bolotov, Ivan N.; Vikhrev, Ilya V.; Gan, Han Ming; Gonçalves, Duarte V.; Bogan, Arthur E.; Sousa, Ronaldo; Stewart, Donald; Teixeira, Amílcar; Varandas, Simone; Zanatta, David; Lopes-Lima, ManuelThe complete mitogenomes of one (M-)ale (North America), one Hermaphroditic (Europe), and two (F-)emale (North America and Europe) individuals of the freshwater pearl mussel Margaritifera margaritifera were sequenced. The M-type and F-type (Female and Hermaphroditic) mitogenomes have 17,421 and 16,122 nucleotides, respectively. All with the same content: 13 protein-coding genes, 22 transfer RNA, two ribosomal RNA genes, and one sex-related ORF. The M-type is highly divergent (37.6% uncorrected p-distance) from the F-type mitogenomes. North American and European F-type mitogenomes exhibit low genetic divergence (68 nt substitutions), and the Female and Hermaphroditic European mitogenomes are almost identical, and matching sex-related ORFs.
- Mesozoic mitogenome rearrangements and freshwater mussel (Bivalvia: Unionoidea) macroevolutionPublication . Froufe, Elsa; Bolotov, Ivan N.; Aldridge, David C.; Bogan, Arthur E.; Breton, Sophie; Gan, Han Ming; Kovitvadhi, Uthaiwan; Kovitvadhi, Satit; Riccardi, Nicoletta; Secci-Petretto, Giulia; Sousa, Ronaldo; Teixeira, Amílcar; Varandas, Simone; Zanatta, David; Zieritz, Alexandra; Fonseca, Miguel M.; Lopes-Lima, ManuelUsing a new fossil-calibrated mitogenome-based approach, we identified macroevolutionary shifts in mitochondrial gene order among the freshwater mussels (Unionoidea). We show that the early Mesozoic divergence of the two Unionoidea clades, Margaritiferidae and Unionidae, was accompanied by a synchronous split in the gene arrangement in the female mitogenome (i.e., gene orders MF1 and UF1). Our results suggest that this macroevolutionary jump was completed within a relatively short time interval (95% HPD 201–226 Ma) that coincided with the Triassic–Jurassic mass extinction. Both gene orders have persisted within these clades for ~200 Ma. The monophyly of the so-called “problematic” Gonideinae taxa was supported by all the inferred phylogenies in this study using, for the first time, the M- and F-type mitogenomes either singly or combined. Within Gonideinae, two additional splits in the gene order (UF1 to UF2, UF2 to UF3) occurred in the Mesozoic and have persisted for ~150 and ~100 Ma, respectively. Finally, the mitogenomic results suggest ancient connections between freshwater basins of East Asia and Europe near the Cretaceous–Paleogene boundary, probably via a continuous paleo-river system or along the Tethys coastal line, which are well supported by at least three independent but almost synchronous divergence events.
- Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- And M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)Publication . Zieritz, Alexandra; Froufe, Elsa; Bolotov, Ivan N.; Gonçalves, Duarte V.; Aldridge, David C.; Bogan, Arthur E.; Gan, Han Ming; Gomes-dos-Santos, André; Sousa, Ronaldo; Teixeira, Amílcar; Varandas, Simone; Zanatta, David; Lopes-Lima, ManuelThe Unionidae represent an excellent model taxon for unravelling the drivers of freshwater diversity, but, phylogeographic studies on Southeast Asian taxa are hampered by lack of a comprehensive phylogeny and mutation rates for this fauna. We present complete female- (F) and male-type (M) mitogenomes of four genera of the Southeast Asian clade Contradentini+Rectidentini. We calculate substitution rates for the mitogenome, the 13 protein-coding genes, the two ribosomal units and three commonly used fragments (co1, nd1 and 16S) of both F- and M-mtDNA, based on a fossil-calibrated, mitogenomic phylogeny of the Unionidae. Phylogenetic analyses, including an M+F concatenated dataset, consistently recovers a monophyletic Gonideinae. Subfamily-level topology is congruent with that of a previous nuclear genomic study and with patterns in mitochondrial gene order, suggesting Unionidae F-type 2 as a synapomorphy of the Gonideinae. Our phylogeny indicates that the clades Contradentini+Rectidentini and Lamprotulini+Pseudodontini+Gonideini split in the early Cretaceous (~125 Mya), and that the crown group of Contradentini+Rectidentini originated in the late Cretaceous (~79 Mya). Most gonideine tribes originated during the early Palaeogene. Substitution rates were comparable to those previously published for F-type co1 and 16S for certain Unionidae and Margaritiferidae species (pairs).