Pub Date : 2024-12-01Epub Date: 2024-12-30DOI: 10.56179/001c.127693
Lucas S Medeiros, Sergio M Q Lima, Mario de Pinna, Igor C A Souto-Santos, Stacy Pirro, Waldir M Berbel-Filho
Listrura and Microcambeva are two genera of small, rare and elusive catfishes of the Trichomycteridae family, endemic to the Atlantic Forest coastal drainages in Brazil. Listrura comprises 13 species with slender bodies, absent pelvic fins, and a distinct caudal-fin and caudal-peduncle morphology, while Microcambeva includes eight species with translucent bodies, typically buried in sandy substrates with exposed nasal barbels. The two genera inhabit fragile environments that are undergoing accelerated degradation, with Listrura camposae and L. nematopteryx classified as "Critically Endangered" (CR), and L. picinguabae as "Near Threatened" (NT). Microcambeva species face similar threats, with M. bendego proposed as CR and M. draco as "Endangered" (EN). Over the past two decades, collection efforts and taxonomic descriptions have expanded the diversity of these two genera, with descriptions of 11 species of Listrura and seven of Microcambeva species in that period. To address gaps in genetic data for those taxa, we herein present draft version of whole-genome sequences for two Listrura species - L. nematopteryx and L. boticario - and five Microcambeva species - M. barbata, M. watu, M. jucuensis, M. bendego, and M. ribeirae. These genomic data are critical for future studies on the evolutionary history and systematics of these unique catfishes, contributing to foundational knowledge of their biodiversity.
Listrura和Microcambeva是毛滴虫科的两种小型，稀有和难以捉摸的鲶鱼，是巴西大西洋森林沿岸排水的特有物种。Listrura有13种，身体细长，没有腹鳍，尾鳍和尾柄形态明显；Microcambeva有8种，身体半透明，通常埋在沙质基质中，鼻刺暴露在外。这两个属栖息在正在加速退化的脆弱环境中，Listrura camposae和L. nematopteryx被列为“极度濒危”（CR）， L. picinguabae被列为“近危”（NT）。小cambeva物种面临着类似的威胁，其中M. bendego被列为CR， M. draco被列为“濒危”（EN）。在过去的20年里，收集工作和分类描述扩大了这两个属的多样性，在这一时期，Listrura和Microcambeva分别描述了11种和7种。为了解决这些分类群遗传数据的空白，我们在此提出了两个Listrura物种（L. nematopteryx和L. boticario）和五个Microcambeva物种（M. barbata， M. watu， M. juuensis， M. bendego和M. ribeirae）的全基因组序列草案。这些基因组数据对未来研究这些独特鲶鱼的进化历史和系统分类学具有重要意义，有助于了解其生物多样性的基础知识。
{"title":"Whole-Genome Sequencing of two <i>Listrura</i> and five <i>Microcambeva</i> Species (Trichomycteridae, Siluriformes), Rare and Threatened catfishes from the Atlantic Forest.","authors":"Lucas S Medeiros, Sergio M Q Lima, Mario de Pinna, Igor C A Souto-Santos, Stacy Pirro, Waldir M Berbel-Filho","doi":"10.56179/001c.127693","DOIUrl":"10.56179/001c.127693","url":null,"abstract":"<p><p><i>Listrura</i> and <i>Microcambeva</i> are two genera of small, rare and elusive catfishes of the Trichomycteridae family, endemic to the Atlantic Forest coastal drainages in Brazil. <i>Listrura</i> comprises 13 species with slender bodies, absent pelvic fins, and a distinct caudal-fin and caudal-peduncle morphology, while <i>Microcambeva</i> includes eight species with translucent bodies, typically buried in sandy substrates with exposed nasal barbels. The two genera inhabit fragile environments that are undergoing accelerated degradation, with <i>Listrura camposae</i> and <i>L. nematopteryx</i> classified as \"Critically Endangered\" (CR), and <i>L. picinguabae</i> as \"Near Threatened\" (NT). <i>Microcambeva</i> species face similar threats, with <i>M. bendego</i> proposed as CR and <i>M. draco</i> as \"Endangered\" (EN). Over the past two decades, collection efforts and taxonomic descriptions have expanded the diversity of these two genera, with descriptions of 11 species of <i>Listrura</i> and seven of <i>Microcambeva</i> species in that period. To address gaps in genetic data for those taxa, we herein present draft version of whole-genome sequences for two <i>Listrura</i> species - <i>L. nematopteryx</i> and <i>L. boticario</i> - and five <i>Microcambeva</i> species - <i>M. barbata</i>, <i>M. watu</i>, <i>M. jucuensis</i>, <i>M. bendego</i>, and <i>M. ribeirae</i>. These genomic data are critical for future studies on the evolutionary history and systematics of these unique catfishes, contributing to foundational knowledge of their biodiversity.</p>","PeriodicalId":72362,"journal":{"name":"Biodiversity genomes","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11801385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143366894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
T. J. Colston, Steven T. Cassidy, Kara J.M. Taylor, S. Pirro, Martha Haufiku, Tresia Kavili, Seth J. Eiseb, Carl N. Keiser
We present the complete genome sequences of Stegodyphus bicolor and Stegodyphus dumicola. Illumina sequencing was performed on genetic material from specimens collected in Namibia in March 2023. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via Genbank.
{"title":"The Complete Genome Sequences of two Species of Stegodyphus Spiders (Araneae: Eresidae)","authors":"T. J. Colston, Steven T. Cassidy, Kara J.M. Taylor, S. Pirro, Martha Haufiku, Tresia Kavili, Seth J. Eiseb, Carl N. Keiser","doi":"10.56179/001c.122353","DOIUrl":"https://doi.org/10.56179/001c.122353","url":null,"abstract":"We present the complete genome sequences of Stegodyphus bicolor and Stegodyphus dumicola. Illumina sequencing was performed on genetic material from specimens collected in Namibia in March 2023. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via Genbank.","PeriodicalId":72362,"journal":{"name":"Biodiversity genomes","volume":"54 46","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141929030","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
We present genome sequences of 29 species of ducks from 8 genera. Illumina sequencing was performed on tissue from wild-collected museum specimens. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via Genbank.
{"title":"The Complete Genome Sequences of 29 Species of Ducks (Anatidae, Anseriformes).","authors":"Emily Griffith, Stacy Pirro","doi":"10.56179/001c.122134","DOIUrl":"10.56179/001c.122134","url":null,"abstract":"<p><p>We present genome sequences of 29 species of ducks from 8 genera. Illumina sequencing was performed on tissue from wild-collected museum specimens. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via Genbank.</p>","PeriodicalId":72362,"journal":{"name":"Biodiversity genomes","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11309123/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141908431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Species in the genus Hypoplectrus are found primarily in coral reefs in the Caribbean Sea and the Gulf of Mexico, particularly around Florida and the Bahamas. They are a popular choice for hobbyist saltwater aquariums. Members of this genus are simultaneous hermaphrodites, as they have both male and female sexual organs at the same time as an adult. We present the genome sequences of 7 species of Hypoplectrus. Raw read data and assembled genomes are available in Genbank.
{"title":"The Complete Genome Sequences of 7 Hypoplectrus species (Serranidae, Perciformes)","authors":"Arturo Acero, S. Pirro, Ricardo Betancur","doi":"10.56179/001c.117765","DOIUrl":"https://doi.org/10.56179/001c.117765","url":null,"abstract":"Species in the genus Hypoplectrus are found primarily in coral reefs in the Caribbean Sea and the Gulf of Mexico, particularly around Florida and the Bahamas. They are a popular choice for hobbyist saltwater aquariums. Members of this genus are simultaneous hermaphrodites, as they have both male and female sexual organs at the same time as an adult. We present the genome sequences of 7 species of Hypoplectrus. Raw read data and assembled genomes are available in Genbank.","PeriodicalId":72362,"journal":{"name":"Biodiversity genomes","volume":"21 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141105252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abhimanyu Lele, Jacob R. Drucker, T. Hains, S. Pirro, John Bates, Elisa Bonaccorso
We present the complete genome sequences of 37 Ecuadorian bird species widespread throughout the tropical Andes.
我们展示了分布于热带安第斯山脉的 37 种厄瓜多尔鸟类的完整基因组序列。
{"title":"The Complete Genome Sequences of 37 Bird Species from the Ecuadorian Andes","authors":"Abhimanyu Lele, Jacob R. Drucker, T. Hains, S. Pirro, John Bates, Elisa Bonaccorso","doi":"10.56179/001c.117756","DOIUrl":"https://doi.org/10.56179/001c.117756","url":null,"abstract":"We present the complete genome sequences of 37 Ecuadorian bird species widespread throughout the tropical Andes.","PeriodicalId":72362,"journal":{"name":"Biodiversity genomes","volume":"17 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141104854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
We present the whole genome sequence of Ajuga reptans. Illumina paired-end reads were assembled by a de novo method followed by a finishing step. The raw and assembled data are publicly available via GenBank: Sequence Read Archive (SRR24502601) and assembled genome (JAUEKW000000000).
{"title":"The Complete Genome Sequence of Ajuga reptans (Lamiaceae, Lamiales), Bugleweed","authors":"Toby Pirro, S. Pirro","doi":"10.56179/001c.117758","DOIUrl":"https://doi.org/10.56179/001c.117758","url":null,"abstract":"We present the whole genome sequence of Ajuga reptans. Illumina paired-end reads were assembled by a de novo method followed by a finishing step. The raw and assembled data are publicly available via GenBank: Sequence Read Archive (SRR24502601) and assembled genome (JAUEKW000000000).","PeriodicalId":72362,"journal":{"name":"Biodiversity genomes","volume":"72 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141106040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Louise Bodt, T. Hains, Daryl Coldren, S. Pirro, John Bates, Shannon Hackett
We present complete genome sequences of 23 species of finches from 6 genera.
我们展示了 6 个属 23 种雀鸟的完整基因组序列。
{"title":"The Complete Genome Sequences of 23 Finch Species (Fringillidae, Passeriformes)","authors":"Louise Bodt, T. Hains, Daryl Coldren, S. Pirro, John Bates, Shannon Hackett","doi":"10.56179/001c.117726","DOIUrl":"https://doi.org/10.56179/001c.117726","url":null,"abstract":"We present complete genome sequences of 23 species of finches from 6 genera.","PeriodicalId":72362,"journal":{"name":"Biodiversity genomes","volume":"121 18","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141115645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Melissa M. Rincon Sandoval, S. Pirro, Ricardo Betancur
We present genome sequences of 63 species of catfish from the Ariidae family. Illumina sequencing was performed on tissue from wild-collected museum specimens. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via Genbank.
{"title":"The Draft Genome Sequences of 63 Species of Catfish (Ariidae, Siluriformes)","authors":"Melissa M. Rincon Sandoval, S. Pirro, Ricardo Betancur","doi":"10.56179/001c.117717","DOIUrl":"https://doi.org/10.56179/001c.117717","url":null,"abstract":"We present genome sequences of 63 species of catfish from the Ariidae family. Illumina sequencing was performed on tissue from wild-collected museum specimens. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via Genbank.","PeriodicalId":72362,"journal":{"name":"Biodiversity genomes","volume":"35 36","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141117468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
R. A. Pyron, S. Pirro, T. Hains, T. J. Colston, Edward A. Myers, Kyle A. O’Connell, David A. Beamer
We present partial genome sequences of 50 salamander species (Urodela) from 10 genera and 4 families. These span nearly the entire range of genome sizes in salamanders, from ~14–130GB, the latter of which is among the largest of all animal genomes. Only three salamander genomes were available to this point, from Ambystomatidae (one species) and Salamandridae (two species from two genera), to which we have added Amphiumidae (one species), Plethodontidae (45 species from 6 genera), Proteidae (one species), and Sirenidae (three species from two genera). These span ~140 million years of evolutionary divergence, leaving only Cryptobranchidae, Hynobiidae, and Rhyacotritonidae as salamander families without genome assemblies. These data should facilitate additional future work on speciation and genome evolution, both within Urodela and across Animalia.
{"title":"The Draft Genome Sequences of 50 Salamander species (Caudata, Amphibia)","authors":"R. A. Pyron, S. Pirro, T. Hains, T. J. Colston, Edward A. Myers, Kyle A. O’Connell, David A. Beamer","doi":"10.56179/001c.116891","DOIUrl":"https://doi.org/10.56179/001c.116891","url":null,"abstract":"We present partial genome sequences of 50 salamander species (Urodela) from 10 genera and 4 families. These span nearly the entire range of genome sizes in salamanders, from ~14–130GB, the latter of which is among the largest of all animal genomes. Only three salamander genomes were available to this point, from Ambystomatidae (one species) and Salamandridae (two species from two genera), to which we have added Amphiumidae (one species), Plethodontidae (45 species from 6 genera), Proteidae (one species), and Sirenidae (three species from two genera). These span ~140 million years of evolutionary divergence, leaving only Cryptobranchidae, Hynobiidae, and Rhyacotritonidae as salamander families without genome assemblies. These data should facilitate additional future work on speciation and genome evolution, both within Urodela and across Animalia.","PeriodicalId":72362,"journal":{"name":"Biodiversity genomes","volume":"28 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140665847","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
P. Bragança, John P. Sullivan, S. Pirro, Albert Chakona
We present the complete genome sequences of 12 species of Enteromius. Illumina sequencing was performed on genetic material from museum specimens. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via Genbank.
{"title":"The Complete Genome Sequences of 12 Species of Enteromius (Cyprinidae, Cypriniformes, Actinopteri)","authors":"P. Bragança, John P. Sullivan, S. Pirro, Albert Chakona","doi":"10.56179/001c.116676","DOIUrl":"https://doi.org/10.56179/001c.116676","url":null,"abstract":"We present the complete genome sequences of 12 species of Enteromius. Illumina sequencing was performed on genetic material from museum specimens. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via Genbank.","PeriodicalId":72362,"journal":{"name":"Biodiversity genomes","volume":" December","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140682640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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